## [Apbs-users] Comparison of CHARMM and APBS results

 [Apbs-users] Comparison of CHARMM and APBS results From: Sandeep Somani - 2005-07-04 13:20:19 ```Hi All I was trying to compare the results for a standard electrostatic solvation energy from CHARMM PB solver (PBEQ) and that from APBS. As a test case I used just a single amino-acid (ARG) protein with a net charge of +1(pqr listed below). These are the numbers i get for solvation energy (electrostatic energy in vacuum - solvent): APBS = 453.021 kJ/mol CHARMM = 193.320 kJ/mol quite a big discrepancy! I have been trying to tweak the parameters to ensure that the two calculations are set up identically. I ensured that the following parameters are same in both calculations: # charge, radius and positions of each atom (ofcourse!) # grid center = (0,0,0) # grid spacing = 0.4 Ang ( as a result box size in APBS is much bigger as i use a bigger mesh 97x97x97 points) # dielectric constants for the solvent (pdie=4,sdie=80) and vacuum (pdie=4,sdie=1) # ion conc = 0 # method = linearized PB # temperature = 298 APBS input file is also listed below. i guess that leaves boundary condition as the only major parameter to tweak. i used the common 'bcfl sdh' setting in APBS while CHARMM says: " BOUNDARY POTENTIAL CALCULATION METHOD The Debye-Huckel approximation for half number of boundary points along 1d-axis and potential of the rest will be interpolated from nearest grid points " are these two boundary condition methods equivalent ? any idea what could be the cause of the discrepancy ? though I would like to think that APBS numbers are more accurate :) regards sandeep *************************************************************** PQR: ==== ATOM 1 N ARG 1 2.963 -0.189 0.810 -0.3000 1.8500 ATOM 2 H ARG 1 3.686 0.542 0.656 0.3300 0.2245 ATOM 3 H2 ARG 1 3.686 0.542 0.656 0.3300 0.2245 ATOM 4 H3 ARG 1 3.686 0.542 0.656 0.3300 0.2245 ATOM 5 CA ARG 1 2.377 -0.565 -0.459 0.2100 2.2750 ATOM 6 HA ARG 1 2.797 -0.303 0.500 0.1000 1.3200 ATOM 7 CB ARG 1 0.882 -0.240 -0.372 -0.1800 2.1750 ATOM 8 HB1 ARG 1 0.427 -0.767 0.494 0.0900 1.3200 ATOM 9 HB2 ARG 1 0.427 -0.767 0.494 0.0900 1.3200 ATOM 10 CG ARG 1 0.283 -0.976 0.824 -0.1800 2.1750 ATOM 11 HG1 ARG 1 -0.805 -1.139 0.667 0.0900 1.3200 ATOM 12 HG2 ARG 1 -0.805 -1.139 0.667 0.0900 1.3200 ATOM 13 CD ARG 1 -1.220 -1.246 0.697 0.2000 2.1750 ATOM 14 HD1 ARG 1 -1.778 -0.287 0.645 0.0900 1.3200 ATOM 15 HD2 ARG 1 -1.778 -0.287 0.645 0.0900 1.3200 ATOM 16 NE ARG 1 -2.023 -0.027 0.622 -0.7000 1.8500 ATOM 17 HE ARG 1 -2.604 0.141 -0.174 0.4400 0.2245 ATOM 18 CZ ARG 1 -2.856 0.393 -0.333 0.6400 2.0000 ATOM 19 NH1 ARG 1 -2.929 -0.182 -1.542 -0.8000 1.8500 ATOM 20 HH11 ARG 1 -2.342 -0.962 -1.761 0.4600 0.2245 ATOM 21 HH12 ARG 1 -2.342 -0.962 -1.761 0.4600 0.2245 ATOM 22 NH2 ARG 1 -3.600 1.488 -0.130 -0.8000 1.8500 ATOM 23 HH21 ARG 1 -3.530 1.987 0.734 0.4600 0.2245 ATOM 24 HH22 ARG 1 -3.530 1.987 0.734 0.4600 0.2245 ATOM 25 C ARG 1 3.048 0.259 -1.551 0.3400 2.0000 ATOM 26 O ARG 1 3.941 1.080 -1.209 -0.6700 1.7000 ATOM 27 OXT ARG 1 3.941 1.080 -1.209 -0.6700 1.7000 APBS Input: =========== read mol pqr arg.pqr end elec mg-auto dime 97 97 97 cglen 38.8 38.8 38.8 # 12.8197 5.4961 4.3945 fglen 38.8 38.8 38.8 # 12.8197 5.4961 4.3945 cgcent 0 0 0 # mol 1 fgcent 0 0 0 # mol 1 mol 1 lpbe bcfl sdh ion 1 0.00 2.0 ion -1 0.000 2.0 pdie 4.0 sdie 80.00 srfm smol chgm spl2 srad 1.4 swin 0.3 temp 298.00 gamma 0.105 calcenergy total calcforce no write pot dx pot write smol dx acc end elec mg-auto dime 97 97 97 cglen 38.8 38.8 38.8 # 12.8197 5.4961 4.3945 fglen 38.8 38.8 38.8 # 12.8197 5.4961 4.3945 cgcent 0 0 0 # mol 1 fgcent 0 0 0 # mol 1 mol 1 lpbe bcfl sdh ion 1 0.000 2.0 ion -1 0.000 2.0 pdie 4.0 sdie 1.00 srfm smol chgm spl2 srad 1.4 swin 0.3 temp 298.00 gamma 0.105 calcenergy total calcforce no end print energy 2 - 1 end quit APBS log ======== Parsing input file arg.in... Parsed input file. Got PQR paths for 1 molecules Reading PQR-format atom data from arg.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 27 atoms Centered at (1.705e-01, 3.705e-01, -4.685e-01) Net charge 1.00e-00 e Preparing to run 4 PBE calculations. ---------------------------------------- CALCULATION #1: MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 153.010 MB total, 153.010 MB high water Using cubic spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.404 x 0.404 x 0.404 Grid lengths: 38.800 x 38.800 x 38.800 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.000 K Surface tension: 0.105 kJ/mol/A^2 Electrostatic energies will be calculated Solving PDE (see io.mc* for details)... Total electrostatic energy = 2.706605597683E+03 kJ/mol ---------------------------------------- CALCULATION #2: MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 152.988 MB total, 155.266 MB high water Using cubic spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.404 x 0.404 x 0.404 Grid lengths: 38.800 x 38.800 x 38.800 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.000 K Surface tension: 0.105 kJ/mol/A^2 Electrostatic energies will be calculated Potential to be written to pot.dx Molecular solvent accessibility to be written to acc.dx Solving PDE (see io.mc* for details)... Total electrostatic energy = 2.706605597683E+03 kJ/mol Writing potential to pot.dx Writing molecular accessibility to acc.dx ---------------------------------------- CALCULATION #3: MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 153.010 MB total, 155.266 MB high water Using cubic spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.404 x 0.404 x 0.404 Grid lengths: 38.800 x 38.800 x 38.800 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 4.000 Solvent dielectric: 1.000 Using "molecular" surface definition; harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.000 K Surface tension: 0.105 kJ/mol/A^2 Electrostatic energies will be calculated Solving PDE (see io.mc* for details)... Total electrostatic energy = 3.159627129610E+03 kJ/mol ---------------------------------------- CALCULATION #4: MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 152.988 MB total, 155.266 MB high water Using cubic spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.404 x 0.404 x 0.404 Grid lengths: 38.800 x 38.800 x 38.800 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 4.000 Solvent dielectric: 1.000 Using "molecular" surface definition; harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.000 K Surface tension: 0.105 kJ/mol/A^2 Electrostatic energies will be calculated Solving PDE (see io.mc* for details)... Total electrostatic energy = 3.159627129610E+03 kJ/mol ---------------------------------------- PRINT STATEMENTS print energy 2 - 1 end Local net energy (PE 0) = 4.530215319263E+02 kJ/mol Global net energy = 4.530215319263E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.000 MB total, 155.266 MB high water Thanks for using APBS! ```

 [Apbs-users] apbs-pymol plugin From: Joel Tyndall - 2005-06-16 23:07:25 Attachments: pymol-generated.pqr     pymol-generated.in ```Hi folks, I finally got around to installing apbs. I've tried to run it thru the pymol plugin and I get an error. It seems to run ok but then can't read in the map file (see below). any help would be welcome J set grid coarsedim is [111.56420230865479, 104.21170161962509, 79.228497600555414] finedim is [85.626001358032227, 81.301000952720642, 66.604998588562012] center is [13.830000877380371, 30.882500469684601, 25.5194993019104] finegridpoints is [193, 193, 161] radiobutton said to generate it Use PyMOL generated PQR and PyMOL generated Hydrogens and termini so i am returning pymol-generated.pqr radiobutton said to generate it Use PyMOL generated PQR and PyMOL generated Hydrogens and termini so i am returning pymol-generated.pqr WARNING: 124 atoms did not have formal charges assigned WARNING: 264 atoms did not have properties assigned ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 0.3.2 ....... information about PMG and FEtk may be found at ;. ---------------------------------------------------------------------- This executable compiled on Nov 10 2004 at 11:39:22 Parsing input file pymol-generated.in... parsePBE: Warning -- parsed deprecated "bcfl 1" statement parsePBE: Please use "bcfl sdh" instead. NOsh: Warning -- parsed deprecated statment "chgm 1". NOsh: Please use "chgm spl2" instead! parsePBE: Warning -- parsed deprecated "srfm 1" statement. parsePBE: Please use "srfm smol" instead. parsePBE: Warning -- parsed deprecated "calcenergy 0" statement. parsePBE: Please use "calcenergy no" instead. parsePBE: Warning -- parsed deprecated "calcforce 0" statement. parsePBE: Please use "calcforce no" instead. Parsed input file. Got PQR paths for 1 molecules Reading PQR-format atom data from pymol-generated.pqr. Valist_readPDB: Unable to parse resSeq token (A) as int! Valist_readPDB: Error while parsing residue name! Valist_readPQR: Error parsing ATOM field! Error while reading molecule from pymol-generated.pqr Error reading molecules! ObjectMapLoadDXFile-Error: Unable to open file! -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New Zealand Pukenga Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 913 Otepoti Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 ```
 [Apbs-users] apbs-pymol plugin From: Joel Tyndall - 2005-06-20 05:29:04 ```Hi folks, I finally got around to installing apbs. I've tried to run it thru the pymol plugin and I get an error. It seems to run ok but then can't read in the map file (see below). The .pqr and .in files are written. Any help would be welcome J set grid coarsedim is [111.56420230865479, 104.21170161962509, 79.228497600555414] finedim is [85.626001358032227, 81.301000952720642, 66.604998588562012] center is [13.830000877380371, 30.882500469684601, 25.5194993019104] finegridpoints is [193, 193, 161] radiobutton said to generate it Use PyMOL generated PQR and PyMOL generated Hydrogens and termini so i am returning pymol-generated.pqr radiobutton said to generate it Use PyMOL generated PQR and PyMOL generated Hydrogens and termini so i am returning pymol-generated.pqr WARNING: 124 atoms did not have formal charges assigned WARNING: 264 atoms did not have properties assigned ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 0.3.2 ....... information about PMG and FEtk may be found at ;. ---------------------------------------------------------------------- This executable compiled on Nov 10 2004 at 11:39:22 Parsing input file pymol-generated.in... parsePBE: Warning -- parsed deprecated "bcfl 1" statement parsePBE: Please use "bcfl sdh" instead. NOsh: Warning -- parsed deprecated statment "chgm 1". NOsh: Please use "chgm spl2" instead! parsePBE: Warning -- parsed deprecated "srfm 1" statement. parsePBE: Please use "srfm smol" instead. parsePBE: Warning -- parsed deprecated "calcenergy 0" statement. parsePBE: Please use "calcenergy no" instead. parsePBE: Warning -- parsed deprecated "calcforce 0" statement. parsePBE: Please use "calcforce no" instead. Parsed input file. Got PQR paths for 1 molecules Reading PQR-format atom data from pymol-generated.pqr. Valist_readPDB: Unable to parse resSeq token (A) as int! Valist_readPDB: Error while parsing residue name! Valist_readPQR: Error parsing ATOM field! Error while reading molecule from pymol-generated.pqr Error reading molecules! ObjectMapLoadDXFile-Error: Unable to open file! -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New Zealand Pukenga Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 913 Otepoti Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 ```
 [Apbs-users] Explicit waters in APBS From: Sandeep Somani - 2005-06-29 04:01:27 ```Hi I have a pdb file of a protein with water molecules buried deep inside a cavity inaccesible to the bulk solvent. I want to calculate the electrostatics with explicit buried waters. But when trying to generate a pqr file using the pdb2pqr program (in tools), the buried waters are ignored. I am using TIP3P waters and charmm force field. any help ? Thanks and Regards Sandeep ```
 [Apbs-users] Comparison of CHARMM and APBS results From: Sandeep Somani - 2005-07-04 13:20:19 ```Hi All I was trying to compare the results for a standard electrostatic solvation energy from CHARMM PB solver (PBEQ) and that from APBS. As a test case I used just a single amino-acid (ARG) protein with a net charge of +1(pqr listed below). These are the numbers i get for solvation energy (electrostatic energy in vacuum - solvent): APBS = 453.021 kJ/mol CHARMM = 193.320 kJ/mol quite a big discrepancy! I have been trying to tweak the parameters to ensure that the two calculations are set up identically. I ensured that the following parameters are same in both calculations: # charge, radius and positions of each atom (ofcourse!) # grid center = (0,0,0) # grid spacing = 0.4 Ang ( as a result box size in APBS is much bigger as i use a bigger mesh 97x97x97 points) # dielectric constants for the solvent (pdie=4,sdie=80) and vacuum (pdie=4,sdie=1) # ion conc = 0 # method = linearized PB # temperature = 298 APBS input file is also listed below. i guess that leaves boundary condition as the only major parameter to tweak. i used the common 'bcfl sdh' setting in APBS while CHARMM says: " BOUNDARY POTENTIAL CALCULATION METHOD The Debye-Huckel approximation for half number of boundary points along 1d-axis and potential of the rest will be interpolated from nearest grid points " are these two boundary condition methods equivalent ? any idea what could be the cause of the discrepancy ? though I would like to think that APBS numbers are more accurate :) regards sandeep *************************************************************** PQR: ==== ATOM 1 N ARG 1 2.963 -0.189 0.810 -0.3000 1.8500 ATOM 2 H ARG 1 3.686 0.542 0.656 0.3300 0.2245 ATOM 3 H2 ARG 1 3.686 0.542 0.656 0.3300 0.2245 ATOM 4 H3 ARG 1 3.686 0.542 0.656 0.3300 0.2245 ATOM 5 CA ARG 1 2.377 -0.565 -0.459 0.2100 2.2750 ATOM 6 HA ARG 1 2.797 -0.303 0.500 0.1000 1.3200 ATOM 7 CB ARG 1 0.882 -0.240 -0.372 -0.1800 2.1750 ATOM 8 HB1 ARG 1 0.427 -0.767 0.494 0.0900 1.3200 ATOM 9 HB2 ARG 1 0.427 -0.767 0.494 0.0900 1.3200 ATOM 10 CG ARG 1 0.283 -0.976 0.824 -0.1800 2.1750 ATOM 11 HG1 ARG 1 -0.805 -1.139 0.667 0.0900 1.3200 ATOM 12 HG2 ARG 1 -0.805 -1.139 0.667 0.0900 1.3200 ATOM 13 CD ARG 1 -1.220 -1.246 0.697 0.2000 2.1750 ATOM 14 HD1 ARG 1 -1.778 -0.287 0.645 0.0900 1.3200 ATOM 15 HD2 ARG 1 -1.778 -0.287 0.645 0.0900 1.3200 ATOM 16 NE ARG 1 -2.023 -0.027 0.622 -0.7000 1.8500 ATOM 17 HE ARG 1 -2.604 0.141 -0.174 0.4400 0.2245 ATOM 18 CZ ARG 1 -2.856 0.393 -0.333 0.6400 2.0000 ATOM 19 NH1 ARG 1 -2.929 -0.182 -1.542 -0.8000 1.8500 ATOM 20 HH11 ARG 1 -2.342 -0.962 -1.761 0.4600 0.2245 ATOM 21 HH12 ARG 1 -2.342 -0.962 -1.761 0.4600 0.2245 ATOM 22 NH2 ARG 1 -3.600 1.488 -0.130 -0.8000 1.8500 ATOM 23 HH21 ARG 1 -3.530 1.987 0.734 0.4600 0.2245 ATOM 24 HH22 ARG 1 -3.530 1.987 0.734 0.4600 0.2245 ATOM 25 C ARG 1 3.048 0.259 -1.551 0.3400 2.0000 ATOM 26 O ARG 1 3.941 1.080 -1.209 -0.6700 1.7000 ATOM 27 OXT ARG 1 3.941 1.080 -1.209 -0.6700 1.7000 APBS Input: =========== read mol pqr arg.pqr end elec mg-auto dime 97 97 97 cglen 38.8 38.8 38.8 # 12.8197 5.4961 4.3945 fglen 38.8 38.8 38.8 # 12.8197 5.4961 4.3945 cgcent 0 0 0 # mol 1 fgcent 0 0 0 # mol 1 mol 1 lpbe bcfl sdh ion 1 0.00 2.0 ion -1 0.000 2.0 pdie 4.0 sdie 80.00 srfm smol chgm spl2 srad 1.4 swin 0.3 temp 298.00 gamma 0.105 calcenergy total calcforce no write pot dx pot write smol dx acc end elec mg-auto dime 97 97 97 cglen 38.8 38.8 38.8 # 12.8197 5.4961 4.3945 fglen 38.8 38.8 38.8 # 12.8197 5.4961 4.3945 cgcent 0 0 0 # mol 1 fgcent 0 0 0 # mol 1 mol 1 lpbe bcfl sdh ion 1 0.000 2.0 ion -1 0.000 2.0 pdie 4.0 sdie 1.00 srfm smol chgm spl2 srad 1.4 swin 0.3 temp 298.00 gamma 0.105 calcenergy total calcforce no end print energy 2 - 1 end quit APBS log ======== Parsing input file arg.in... Parsed input file. Got PQR paths for 1 molecules Reading PQR-format atom data from arg.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 27 atoms Centered at (1.705e-01, 3.705e-01, -4.685e-01) Net charge 1.00e-00 e Preparing to run 4 PBE calculations. ---------------------------------------- CALCULATION #1: MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 153.010 MB total, 153.010 MB high water Using cubic spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.404 x 0.404 x 0.404 Grid lengths: 38.800 x 38.800 x 38.800 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.000 K Surface tension: 0.105 kJ/mol/A^2 Electrostatic energies will be calculated Solving PDE (see io.mc* for details)... Total electrostatic energy = 2.706605597683E+03 kJ/mol ---------------------------------------- CALCULATION #2: MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 152.988 MB total, 155.266 MB high water Using cubic spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.404 x 0.404 x 0.404 Grid lengths: 38.800 x 38.800 x 38.800 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.000 K Surface tension: 0.105 kJ/mol/A^2 Electrostatic energies will be calculated Potential to be written to pot.dx Molecular solvent accessibility to be written to acc.dx Solving PDE (see io.mc* for details)... Total electrostatic energy = 2.706605597683E+03 kJ/mol Writing potential to pot.dx Writing molecular accessibility to acc.dx ---------------------------------------- CALCULATION #3: MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 153.010 MB total, 155.266 MB high water Using cubic spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.404 x 0.404 x 0.404 Grid lengths: 38.800 x 38.800 x 38.800 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 4.000 Solvent dielectric: 1.000 Using "molecular" surface definition; harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.000 K Surface tension: 0.105 kJ/mol/A^2 Electrostatic energies will be calculated Solving PDE (see io.mc* for details)... Total electrostatic energy = 3.159627129610E+03 kJ/mol ---------------------------------------- CALCULATION #4: MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 152.988 MB total, 155.266 MB high water Using cubic spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.404 x 0.404 x 0.404 Grid lengths: 38.800 x 38.800 x 38.800 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 4.000 Solvent dielectric: 1.000 Using "molecular" surface definition; harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.000 K Surface tension: 0.105 kJ/mol/A^2 Electrostatic energies will be calculated Solving PDE (see io.mc* for details)... Total electrostatic energy = 3.159627129610E+03 kJ/mol ---------------------------------------- PRINT STATEMENTS print energy 2 - 1 end Local net energy (PE 0) = 4.530215319263E+02 kJ/mol Global net energy = 4.530215319263E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.000 MB total, 155.266 MB high water Thanks for using APBS! ```
 Re: [Apbs-users] Comparison of CHARMM and APBS results From: Nathan Baker - 2005-07-05 13:39:53 ```That is a surprisingly large difference. Are you sure you are using the same surface definition for both programs? Thanks, Nathan --- Sandeep Somani wrote: > Hi All > > I was trying to compare the results for a standard electrostatic > solvation energy from CHARMM PB solver (PBEQ) and that from APBS. > > As a test case I used just a single amino-acid (ARG) protein with a net > charge of +1(pqr listed below). > These are the numbers i get for solvation energy (electrostatic energy > in vacuum - solvent): > > APBS = 453.021 kJ/mol > CHARMM = 193.320 kJ/mol > > quite a big discrepancy! > I have been trying to tweak the parameters to ensure that the two > calculations are set up identically. > > I ensured that the following parameters are same in both calculations: > > # charge, radius and positions of each atom (ofcourse!) > # grid center = (0,0,0) > # grid spacing = 0.4 Ang ( as a result box size in APBS is much bigger > as i use a bigger mesh 97x97x97 points) > # dielectric constants for the solvent (pdie=4,sdie=80) and vacuum > (pdie=4,sdie=1) > # ion conc = 0 > # method = linearized PB > # temperature = 298 > > APBS input file is also listed below. > > i guess that leaves boundary condition as the only major parameter to > tweak. > i used the common 'bcfl sdh' setting in APBS while CHARMM says: > > " > BOUNDARY POTENTIAL CALCULATION METHOD > The Debye-Huckel approximation for half number of boundary points > along 1d-axis and potential of the rest will be interpolated from > nearest grid points > " > > are these two boundary condition methods equivalent ? > > any idea what could be the cause of the discrepancy ? > > though I would like to think that APBS numbers are more accurate :) > > regards > sandeep > > *************************************************************** > > PQR: > ==== > > ATOM 1 N ARG 1 2.963 -0.189 0.810 -0.3000 1.8500 > ATOM 2 H ARG 1 3.686 0.542 0.656 0.3300 0.2245 > ATOM 3 H2 ARG 1 3.686 0.542 0.656 0.3300 0.2245 > ATOM 4 H3 ARG 1 3.686 0.542 0.656 0.3300 0.2245 > ATOM 5 CA ARG 1 2.377 -0.565 -0.459 0.2100 2.2750 > ATOM 6 HA ARG 1 2.797 -0.303 0.500 0.1000 1.3200 > ATOM 7 CB ARG 1 0.882 -0.240 -0.372 -0.1800 2.1750 > ATOM 8 HB1 ARG 1 0.427 -0.767 0.494 0.0900 1.3200 > ATOM 9 HB2 ARG 1 0.427 -0.767 0.494 0.0900 1.3200 > ATOM 10 CG ARG 1 0.283 -0.976 0.824 -0.1800 2.1750 > ATOM 11 HG1 ARG 1 -0.805 -1.139 0.667 0.0900 1.3200 > ATOM 12 HG2 ARG 1 -0.805 -1.139 0.667 0.0900 1.3200 > ATOM 13 CD ARG 1 -1.220 -1.246 0.697 0.2000 2.1750 > ATOM 14 HD1 ARG 1 -1.778 -0.287 0.645 0.0900 1.3200 > ATOM 15 HD2 ARG 1 -1.778 -0.287 0.645 0.0900 1.3200 > ATOM 16 NE ARG 1 -2.023 -0.027 0.622 -0.7000 1.8500 > ATOM 17 HE ARG 1 -2.604 0.141 -0.174 0.4400 0.2245 > ATOM 18 CZ ARG 1 -2.856 0.393 -0.333 0.6400 2.0000 > ATOM 19 NH1 ARG 1 -2.929 -0.182 -1.542 -0.8000 1.8500 > ATOM 20 HH11 ARG 1 -2.342 -0.962 -1.761 0.4600 0.2245 > ATOM 21 HH12 ARG 1 -2.342 -0.962 -1.761 0.4600 0.2245 > ATOM 22 NH2 ARG 1 -3.600 1.488 -0.130 -0.8000 1.8500 > ATOM 23 HH21 ARG 1 -3.530 1.987 0.734 0.4600 0.2245 > ATOM 24 HH22 ARG 1 -3.530 1.987 0.734 0.4600 0.2245 > ATOM 25 C ARG 1 3.048 0.259 -1.551 0.3400 2.0000 > ATOM 26 O ARG 1 3.941 1.080 -1.209 -0.6700 1.7000 > ATOM 27 OXT ARG 1 3.941 1.080 -1.209 -0.6700 1.7000 > > APBS Input: > =========== > > read > mol pqr arg.pqr > end > elec > mg-auto > dime 97 97 97 > cglen 38.8 38.8 38.8 # 12.8197 5.4961 4.3945 > fglen 38.8 38.8 38.8 # 12.8197 5.4961 4.3945 > cgcent 0 0 0 # mol 1 > fgcent 0 0 0 # mol 1 > mol 1 > lpbe > bcfl sdh > ion 1 0.00 2.0 > ion -1 0.000 2.0 > pdie 4.0 > sdie 80.00 > srfm smol > chgm spl2 > srad 1.4 > swin 0.3 > temp 298.00 > gamma 0.105 > calcenergy total > calcforce no > write pot dx pot > write smol dx acc > end > elec > mg-auto > dime 97 97 97 > cglen 38.8 38.8 38.8 # 12.8197 5.4961 4.3945 > fglen 38.8 38.8 38.8 # 12.8197 5.4961 4.3945 > cgcent 0 0 0 # mol 1 > fgcent 0 0 0 # mol 1 > mol 1 > lpbe > bcfl sdh > ion 1 0.000 2.0 > ion -1 0.000 2.0 > pdie 4.0 > sdie 1.00 > srfm smol > chgm spl2 > srad 1.4 > swin 0.3 > temp 298.00 > gamma 0.105 > calcenergy total > calcforce no > end > > print energy 2 - 1 end > > quit > > APBS log > ======== > > Parsing input file arg.in... > Parsed input file. > Got PQR paths for 1 molecules > Reading PQR-format atom data from arg.pqr. > asc_getToken: Error occurred (bailing out). > Vio_scanf: Format problem with input. > 27 atoms > Centered at (1.705e-01, 3.705e-01, -4.685e-01) > Net charge 1.00e-00 e > Preparing to run 4 PBE calculations. > ---------------------------------------- > CALCULATION #1: MULTIGRID > Setting up problem... > Vpbe_ctor: Using max ion radius (2 A) for exclusion function > Debye length: 0 A > Current memory usage: 153.010 MB total, 153.010 MB high water > Using cubic spline charge discretization. > Grid dimensions: 97 x 97 x 97 > Grid spacings: 0.404 x 0.404 x 0.404 > Grid lengths: 38.800 x 38.800 x 38.800 > Grid center: (0.000, 0.000, 0.000) > Multigrid levels: 4 > Molecule ID: 1 > Linearized traditional PBE > Single Debye-Huckel sphere boundary conditions > 2 ion species (0.000 M ionic strength): > 2.000 A-radius, 1.000 e-charge, 0.000 M concentration > 2.000 A-radius, -1.000 e-charge, 0.000 M concentration > Solute dielectric: 4.000 > Solvent dielectric: 80.000 > Using "molecular" surface definition; harmonic average smoothing > Solvent probe radius: 1.400 A > Temperature: 298.000 K > Surface tension: 0.105 kJ/mol/A^2 > Electrostatic energies will be calculated > Solving PDE (see io.mc* for details)... > Total electrostatic energy = 2.706605597683E+03 kJ/mol > ---------------------------------------- > CALCULATION #2: MULTIGRID > Setting up problem... > Vpbe_ctor: Using max ion radius (2 A) for exclusion function > Debye length: 0 A > Current memory usage: 152.988 MB total, 155.266 MB high water > Using cubic spline charge discretization. > Grid dimensions: 97 x 97 x 97 > Grid spacings: 0.404 x 0.404 x 0.404 > Grid lengths: 38.800 x 38.800 x 38.800 > Grid center: (0.000, 0.000, 0.000) > Multigrid levels: 4 > Molecule ID: 1 > Linearized traditional PBE > Boundary conditions from focusing > 2 ion species (0.000 M ionic strength): > 2.000 A-radius, 1.000 e-charge, 0.000 M concentration > 2.000 A-radius, -1.000 e-charge, 0.000 M concentration > Solute dielectric: 4.000 > Solvent dielectric: 80.000 > Using "molecular" surface definition; harmonic average smoothing > Solvent probe radius: 1.400 A > Temperature: 298.000 K > Surface tension: 0.105 kJ/mol/A^2 > Electrostatic energies will be calculated > Potential to be written to pot.dx > Molecular solvent accessibility to be written to acc.dx > Solving PDE (see io.mc* for details)... > Total electrostatic energy = 2.706605597683E+03 kJ/mol > Writing potential to pot.dx > Writing molecular accessibility to acc.dx > ---------------------------------------- > CALCULATION #3: MULTIGRID > Setting up problem... > Vpbe_ctor: Using max ion radius (2 A) for exclusion function > Debye length: 0 A > Current memory usage: 153.010 MB total, 155.266 MB high water > Using cubic spline charge discretization. > Grid dimensions: 97 x 97 x 97 > Grid spacings: 0.404 x 0.404 x 0.404 > Grid lengths: 38.800 x 38.800 x 38.800 > Grid center: (0.000, 0.000, 0.000) > Multigrid levels: 4 > Molecule ID: 1 > Linearized traditional PBE > Single Debye-Huckel sphere boundary conditions > 2 ion species (0.000 M ionic strength): > 2.000 A-radius, 1.000 e-charge, 0.000 M concentration > 2.000 A-radius, -1.000 e-charge, 0.000 M concentration > Solute dielectric: 4.000 > Solvent dielectric: 1.000 > Using "molecular" surface definition; harmonic average smoothing > Solvent probe radius: 1.400 A > Temperature: 298.000 K > Surface tension: 0.105 kJ/mol/A^2 > Electrostatic energies will be calculated > Solving PDE (see io.mc* for details)... > Total electrostatic energy = 3.159627129610E+03 kJ/mol > ---------------------------------------- > CALCULATION #4: MULTIGRID > Setting up problem... > Vpbe_ctor: Using max ion radius (2 A) for exclusion function > Debye length: 0 A > Current memory usage: 152.988 MB total, 155.266 MB high water > Using cubic spline charge discretization. > Grid dimensions: 97 x 97 x 97 > Grid spacings: 0.404 x 0.404 x 0.404 > Grid lengths: 38.800 x 38.800 x 38.800 > Grid center: (0.000, 0.000, 0.000) > Multigrid levels: 4 > Molecule ID: 1 > Linearized traditional PBE > Boundary conditions from focusing > 2 ion species (0.000 M ionic strength): > 2.000 A-radius, 1.000 e-charge, 0.000 M concentration > 2.000 A-radius, -1.000 e-charge, 0.000 M concentration > Solute dielectric: 4.000 > Solvent dielectric: 1.000 > Using "molecular" surface definition; harmonic average smoothing > Solvent probe radius: 1.400 A > Temperature: 298.000 K > Surface tension: 0.105 kJ/mol/A^2 > Electrostatic energies will be calculated > Solving PDE (see io.mc* for details)... > Total electrostatic energy = 3.159627129610E+03 kJ/mol > ---------------------------------------- > PRINT STATEMENTS > print energy 2 - 1 end > Local net energy (PE 0) = 4.530215319263E+02 kJ/mol > Global net energy = 4.530215319263E+02 kJ/mol > ---------------------------------------- > CLEANING UP AND SHUTTING DOWN... > Destroying force arrays. > No energy arrays to destroy. > Destroying multigrid structures. > Destroying 1 molecules > Final memory usage: 0.000 MB total, 155.266 MB high water > > > Thanks for using APBS! > > > > > > > > > _______________________________________________ > apbs-users mailing list > apbs-users@... > http://cholla.wustl.edu/mailman/listinfo/apbs-users > > -- Assistant Professor, Dept. of Biochemistry and Molecular Biophysics Washington University in St. Louis http://cholla.wustl.edu ```
 RE: [Apbs-users] Comparison of CHARMM and APBS results From: Sandeep Somani - 2005-07-06 07:36:45 ```Dear Dr Nathan Surface definition used in APBS is : " Using "molecular" surface definition; harmonic average smoothing " while in CHARMM the default option is used: " the vdW surface is used for the dielectric boundary " Other difference is that for CHARMM is used Successive OverRelaxation for solving the linearized PB eqn as against Multi-Grid method of APBS. I have tried all the Boundary Conditions options in APBS without any success. So now I am totally clueless! With Regards Sandeep **************************************CHARMM LOG************************************* CHARMM> pbeq Calculations with the Poisson-Boltzmann Equation PBEQ> scalar wmain = radius PBEQ> PBEQ> solve dcel @dcel nclx @xcel ncly @ycel nclz @zcel maxit 1000 - PBEQ> epsw 80.0 epsp 4.0 temp 298 watr 1.4 intbp Parameter: DCEL -> "0.40" Parameter: XCEL -> "46" Parameter: YCEL -> "36" Parameter: ZCEL -> "35" Calculation with 27 atoms LINEARIZED PBEQ SOLVER: Successive OverRelaxation (SOR) method ITERATION PARAMETERs Maximum # iterations (MAXITS) = 1000 Tolerance of convergence (DEPS) =.200E-05 Mixing factor (LAMBDA,DOME) = 1.000 CHARGE DISTRIBUTION METHOD: the trilinear interpolation BOUNDARY POTENTIAL CALCULATION METHOD The Debye-Huckel approximation for half number of boundary points along 1d-axis and potential of the rest will be interpolated from nearest grid points PHYSICAL PARAMETERs Solvent probe radius (WATR) = 1.400 [Angs] Ion exclusion radius (Stern layer) = 0.000 [Angs] Solvent dielectric constant (EPSW) = 80.000 Protein dielectric constant (EPSP) = 4.000 Salt concentration (CONC) = 0.000 [moles]/[liter] Temperature (TEMP) = 298.000 [K] Debye-Huckel factor (KAPPA2) = 0.000 [1/Angs**2] NUMBER OF GRID POINTS: 47 37 35 Box in X from -9.200 to 9.200 Box in Y from -7.200 to 7.200 Box in Z from -6.800 to 6.800 Constructing all space-dependent functions Begin iterative solution Number of iterations: 154 The atomic contributions have been stored in WMAIN Electrostatic energy [KCAL/MOL] = 1022.14660 PBEQ> set ener80 = ?enpb RDCMND substituted energy or value "?ENPB" to "1022.15" Parameter: ENER80 <- "1022.15" PBEQ> PBEQ> solve dcel @dcel nclx @xcel ncly @ycel nclz @zcel maxit 1000 - PBEQ> epsw 1.0 epsp 4.0 temp 298 watr 1.4 intbp Parameter: DCEL -> "0.40" Parameter: XCEL -> "46" Parameter: YCEL -> "36" Parameter: ZCEL -> "35" Calculation with 27 atoms LINEARIZED PBEQ SOLVER: Successive OverRelaxation (SOR) method ITERATION PARAMETERs Maximum # iterations (MAXITS) = 1000 Tolerance of convergence (DEPS) =.200E-05 Mixing factor (LAMBDA,DOME) = 1.000 CHARGE DISTRIBUTION METHOD: the trilinear interpolation BOUNDARY POTENTIAL CALCULATION METHOD The Debye-Huckel approximation for half number of boundary points along 1d-axis and potential of the rest will be interpolated from nearest grid points PHYSICAL PARAMETERs Solvent probe radius (WATR) = 1.400 [Angs] Ion exclusion radius (Stern layer) = 0.000 [Angs] Solvent dielectric constant (EPSW) = 1.000 Protein dielectric constant (EPSP) = 4.000 Salt concentration (CONC) = 0.000 [moles]/[liter] Temperature (TEMP) = 298.000 [K] Debye-Huckel factor (KAPPA2) = 0.000 [1/Angs**2] NUMBER OF GRID POINTS: 47 37 35 Box in X from -9.200 to 9.200 Box in Y from -7.200 to 7.200 Box in Z from -6.800 to 6.800 Constructing all space-dependent functions Begin iterative solution Number of iterations: 426 The atomic contributions have been stored in WMAIN Electrostatic energy [KCAL/MOL] = 1068.39943 PBEQ> set ener1 = ?enpb RDCMND substituted energy or value "?ENPB" to "1068.4" Parameter: ENER1 <- "1068.4" PBEQ> PBEQ> calc dgpb = @dgpb + (@ener80 - @ener1) Parameter: DGPB -> "0" Parameter: ENER80 -> "1022.15" Parameter: ENER1 -> "1068.4" Evaluating: 0+(1022.15-1068.4) Parameter: DGPB <- "-46.25" **************************************END OF CHARMM LOG************************************* > -----Original Message----- > From: Nathan Baker [mailto:sobolevnrm@...] > Sent: Tuesday, July 05, 2005 7:40 PM > To: Sandeep Somani; apbs-users@... > Subject: Re: [Apbs-users] Comparison of CHARMM and APBS results > > > That is a surprisingly large difference. Are you sure you > are using the same surface definition for both programs? > > Thanks, > > Nathan > > --- Sandeep Somani wrote: > > > Hi All > > > > I was trying to compare the results for a standard electrostatic > > solvation energy from CHARMM PB solver (PBEQ) and that from APBS. > > > > As a test case I used just a single amino-acid (ARG) protein with a > > net charge of +1(pqr listed below). These are the numbers i get for > > solvation energy (electrostatic energy in vacuum - solvent): > > > > APBS = 453.021 kJ/mol > > CHARMM = 193.320 kJ/mol > > > > quite a big discrepancy! > > I have been trying to tweak the parameters to ensure that the two > > calculations are set up identically. > > > > I ensured that the following parameters are same in both > calculations: > > > > # charge, radius and positions of each atom (ofcourse!) > > # grid center = (0,0,0) > > # grid spacing = 0.4 Ang ( as a result box size in APBS is > much bigger > > as i use a bigger mesh 97x97x97 points) > > # dielectric constants for the solvent (pdie=4,sdie=80) and vacuum > > (pdie=4,sdie=1) > > # ion conc = 0 > > # method = linearized PB > > # temperature = 298 > > > > APBS input file is also listed below. > > > > i guess that leaves boundary condition as the only major > parameter to > > tweak. i used the common 'bcfl sdh' setting in APBS while > CHARMM says: > > > > " > > BOUNDARY POTENTIAL CALCULATION METHOD > > The Debye-Huckel approximation for half number of boundary points > > along 1d-axis and potential of the rest will be interpolated from > > nearest grid points > > " > > > > are these two boundary condition methods equivalent ? > > > > any idea what could be the cause of the discrepancy ? > > > > though I would like to think that APBS numbers are more accurate :) > > > > regards > > sandeep > > > > *************************************************************** > > > > PQR: > > ==== > > > > ATOM 1 N ARG 1 2.963 -0.189 0.810 > -0.3000 1.8500 > > ATOM 2 H ARG 1 3.686 0.542 0.656 > 0.3300 0.2245 > > ATOM 3 H2 ARG 1 3.686 0.542 0.656 > 0.3300 0.2245 > > ATOM 4 H3 ARG 1 3.686 0.542 0.656 > 0.3300 0.2245 > > ATOM 5 CA ARG 1 2.377 -0.565 -0.459 > 0.2100 2.2750 > > ATOM 6 HA ARG 1 2.797 -0.303 0.500 > 0.1000 1.3200 > > ATOM 7 CB ARG 1 0.882 -0.240 -0.372 > -0.1800 2.1750 > > ATOM 8 HB1 ARG 1 0.427 -0.767 0.494 > 0.0900 1.3200 > > ATOM 9 HB2 ARG 1 0.427 -0.767 0.494 > 0.0900 1.3200 > > ATOM 10 CG ARG 1 0.283 -0.976 0.824 > -0.1800 2.1750 > > ATOM 11 HG1 ARG 1 -0.805 -1.139 0.667 > 0.0900 1.3200 > > ATOM 12 HG2 ARG 1 -0.805 -1.139 0.667 > 0.0900 1.3200 > > ATOM 13 CD ARG 1 -1.220 -1.246 0.697 > 0.2000 2.1750 > > ATOM 14 HD1 ARG 1 -1.778 -0.287 0.645 > 0.0900 1.3200 > > ATOM 15 HD2 ARG 1 -1.778 -0.287 0.645 > 0.0900 1.3200 > > ATOM 16 NE ARG 1 -2.023 -0.027 0.622 > -0.7000 1.8500 > > ATOM 17 HE ARG 1 -2.604 0.141 -0.174 > 0.4400 0.2245 > > ATOM 18 CZ ARG 1 -2.856 0.393 -0.333 > 0.6400 2.0000 > > ATOM 19 NH1 ARG 1 -2.929 -0.182 -1.542 > -0.8000 1.8500 > > ATOM 20 HH11 ARG 1 -2.342 -0.962 -1.761 > 0.4600 0.2245 > > ATOM 21 HH12 ARG 1 -2.342 -0.962 -1.761 > 0.4600 0.2245 > > ATOM 22 NH2 ARG 1 -3.600 1.488 -0.130 > -0.8000 1.8500 > > ATOM 23 HH21 ARG 1 -3.530 1.987 0.734 > 0.4600 0.2245 > > ATOM 24 HH22 ARG 1 -3.530 1.987 0.734 > 0.4600 0.2245 > > ATOM 25 C ARG 1 3.048 0.259 -1.551 > 0.3400 2.0000 > > ATOM 26 O ARG 1 3.941 1.080 -1.209 > -0.6700 1.7000 > > ATOM 27 OXT ARG 1 3.941 1.080 -1.209 > -0.6700 1.7000 > > > > APBS Input: > > =========== > > > > read > > mol pqr arg.pqr > > end > > elec > > mg-auto > > dime 97 97 97 > > cglen 38.8 38.8 38.8 # 12.8197 5.4961 4.3945 > > fglen 38.8 38.8 38.8 # 12.8197 5.4961 4.3945 > > cgcent 0 0 0 # mol 1 > > fgcent 0 0 0 # mol 1 > > mol 1 > > lpbe > > bcfl sdh > > ion 1 0.00 2.0 > > ion -1 0.000 2.0 > > pdie 4.0 > > sdie 80.00 > > srfm smol > > chgm spl2 > > srad 1.4 > > swin 0.3 > > temp 298.00 > > gamma 0.105 > > calcenergy total > > calcforce no > > write pot dx pot > > write smol dx acc > > end > > elec > > mg-auto > > dime 97 97 97 > > cglen 38.8 38.8 38.8 # 12.8197 5.4961 4.3945 > > fglen 38.8 38.8 38.8 # 12.8197 5.4961 4.3945 > > cgcent 0 0 0 # mol 1 > > fgcent 0 0 0 # mol 1 > > mol 1 > > lpbe > > bcfl sdh > > ion 1 0.000 2.0 > > ion -1 0.000 2.0 > > pdie 4.0 > > sdie 1.00 > > srfm smol > > chgm spl2 > > srad 1.4 > > swin 0.3 > > temp 298.00 > > gamma 0.105 > > calcenergy total > > calcforce no > > end > > > > print energy 2 - 1 end > > > > quit > > > > APBS log > > ======== > > > > Parsing input file arg.in... > > Parsed input file. > > Got PQR paths for 1 molecules > > Reading PQR-format atom data from arg.pqr. > > asc_getToken: Error occurred (bailing out). > > Vio_scanf: Format problem with input. > > 27 atoms > > Centered at (1.705e-01, 3.705e-01, -4.685e-01) > > Net charge 1.00e-00 e > > Preparing to run 4 PBE calculations. > > ---------------------------------------- > > CALCULATION #1: MULTIGRID > > Setting up problem... > > Vpbe_ctor: Using max ion radius (2 A) for exclusion function > > Debye length: 0 A > > Current memory usage: 153.010 MB total, 153.010 MB high water > > Using cubic spline charge discretization. > > Grid dimensions: 97 x 97 x 97 > > Grid spacings: 0.404 x 0.404 x 0.404 > > Grid lengths: 38.800 x 38.800 x 38.800 > > Grid center: (0.000, 0.000, 0.000) > > Multigrid levels: 4 > > Molecule ID: 1 > > Linearized traditional PBE > > Single Debye-Huckel sphere boundary conditions > > 2 ion species (0.000 M ionic strength): > > 2.000 A-radius, 1.000 e-charge, 0.000 M concentration > > 2.000 A-radius, -1.000 e-charge, 0.000 M concentration > > Solute dielectric: 4.000 > > Solvent dielectric: 80.000 > > Using "molecular" surface definition; harmonic average smoothing > > Solvent probe radius: 1.400 A > > Temperature: 298.000 K > > Surface tension: 0.105 kJ/mol/A^2 > > Electrostatic energies will be calculated > > Solving PDE (see io.mc* for details)... > > Total electrostatic energy = 2.706605597683E+03 kJ/mol > > ---------------------------------------- > > CALCULATION #2: MULTIGRID > > Setting up problem... > > Vpbe_ctor: Using max ion radius (2 A) for exclusion function > > Debye length: 0 A > > Current memory usage: 152.988 MB total, 155.266 MB high water > > Using cubic spline charge discretization. > > Grid dimensions: 97 x 97 x 97 > > Grid spacings: 0.404 x 0.404 x 0.404 > > Grid lengths: 38.800 x 38.800 x 38.800 > > Grid center: (0.000, 0.000, 0.000) > > Multigrid levels: 4 > > Molecule ID: 1 > > Linearized traditional PBE > > Boundary conditions from focusing > > 2 ion species (0.000 M ionic strength): > > 2.000 A-radius, 1.000 e-charge, 0.000 M concentration > > 2.000 A-radius, -1.000 e-charge, 0.000 M concentration > > Solute dielectric: 4.000 > > Solvent dielectric: 80.000 > > Using "molecular" surface definition; harmonic average smoothing > > Solvent probe radius: 1.400 A > > Temperature: 298.000 K > > Surface tension: 0.105 kJ/mol/A^2 > > Electrostatic energies will be calculated > > Potential to be written to pot.dx > > Molecular solvent accessibility to be written to acc.dx > > Solving PDE (see io.mc* for details)... > > Total electrostatic energy = 2.706605597683E+03 kJ/mol > > Writing potential to pot.dx > > Writing molecular accessibility to acc.dx > > ---------------------------------------- > > CALCULATION #3: MULTIGRID > > Setting up problem... > > Vpbe_ctor: Using max ion radius (2 A) for exclusion function > > Debye length: 0 A > > Current memory usage: 153.010 MB total, 155.266 MB high water > > Using cubic spline charge discretization. > > Grid dimensions: 97 x 97 x 97 > > Grid spacings: 0.404 x 0.404 x 0.404 > > Grid lengths: 38.800 x 38.800 x 38.800 > > Grid center: (0.000, 0.000, 0.000) > > Multigrid levels: 4 > > Molecule ID: 1 > > Linearized traditional PBE > > Single Debye-Huckel sphere boundary conditions > > 2 ion species (0.000 M ionic strength): > > 2.000 A-radius, 1.000 e-charge, 0.000 M concentration > > 2.000 A-radius, -1.000 e-charge, 0.000 M concentration > > Solute dielectric: 4.000 > > Solvent dielectric: 1.000 > > Using "molecular" surface definition; harmonic average smoothing > > Solvent probe radius: 1.400 A > > Temperature: 298.000 K > > Surface tension: 0.105 kJ/mol/A^2 > > Electrostatic energies will be calculated > > Solving PDE (see io.mc* for details)... > > Total electrostatic energy = 3.159627129610E+03 kJ/mol > > ---------------------------------------- > > CALCULATION #4: MULTIGRID > > Setting up problem... > > Vpbe_ctor: Using max ion radius (2 A) for exclusion function > > Debye length: 0 A > > Current memory usage: 152.988 MB total, 155.266 MB high water > > Using cubic spline charge discretization. > > Grid dimensions: 97 x 97 x 97 > > Grid spacings: 0.404 x 0.404 x 0.404 > > Grid lengths: 38.800 x 38.800 x 38.800 > > Grid center: (0.000, 0.000, 0.000) > > Multigrid levels: 4 > > Molecule ID: 1 > > Linearized traditional PBE > > Boundary conditions from focusing > > 2 ion species (0.000 M ionic strength): > > 2.000 A-radius, 1.000 e-charge, 0.000 M concentration > > 2.000 A-radius, -1.000 e-charge, 0.000 M concentration > > Solute dielectric: 4.000 > > Solvent dielectric: 1.000 > > Using "molecular" surface definition; harmonic average smoothing > > Solvent probe radius: 1.400 A > > Temperature: 298.000 K > > Surface tension: 0.105 kJ/mol/A^2 > > Electrostatic energies will be calculated > > Solving PDE (see io.mc* for details)... > > Total electrostatic energy = 3.159627129610E+03 kJ/mol > > ---------------------------------------- > > PRINT STATEMENTS > > print energy 2 - 1 end > > Local net energy (PE 0) = 4.530215319263E+02 kJ/mol > > Global net energy = 4.530215319263E+02 kJ/mol > > ---------------------------------------- > > CLEANING UP AND SHUTTING DOWN... > > Destroying force arrays. > > No energy arrays to destroy. > > Destroying multigrid structures. > > Destroying 1 molecules > > Final memory usage: 0.000 MB total, 155.266 MB high water > > > > > > Thanks for using APBS! > > > > > > > > > > > > > > > > > > _______________________________________________ > > apbs-users mailing list > > apbs-users@... > > http://cholla.wustl.edu/mailman/listinfo/apbs-users > > > > > > > -- > Assistant Professor, Dept. of Biochemistry and Molecular > Biophysics Washington University in St. Louis http://cholla.wustl.edu > ```
 RE: [Apbs-users] Comparison of CHARMM and APBS results From: Nathan Baker - 2005-07-06 13:52:47 ```Differences in surface definitions can lead to large differences in energies. To use the VdW surface with APBS, simply choose "surf mol" and "srad 0.0". However, you'll want to check that CHARMM is not using any spline-based smoothing of the VdW surface. Thanks, Nathan --- Sandeep Somani wrote: > Dear Dr Nathan > > Surface definition used in APBS is : > " > Using "molecular" surface definition; harmonic average > smoothing > " > > while in CHARMM the default option is used: > " > the vdW surface is used for the dielectric boundary > " > > Other difference is that for CHARMM is used Successive OverRelaxation > for solving the linearized PB eqn as against Multi-Grid method > of APBS. > > I have tried all the Boundary Conditions options in APBS without any > success. > > So now I am totally clueless! > > With Regards > Sandeep > > > > > > **************************************CHARMM > LOG************************************* > > CHARMM> pbeq > > Calculations with the Poisson-Boltzmann Equation > > > PBEQ> scalar wmain = radius > > PBEQ> > > PBEQ> solve dcel @dcel nclx @xcel ncly @ycel nclz @zcel maxit 1000 > - > PBEQ> epsw 80.0 epsp 4.0 temp 298 watr 1.4 intbp > Parameter: DCEL -> "0.40" > Parameter: XCEL -> "46" > Parameter: YCEL -> "36" > Parameter: ZCEL -> "35" > > Calculation with 27 atoms > > LINEARIZED PBEQ SOLVER: Successive OverRelaxation (SOR) method > > ITERATION PARAMETERs > Maximum # iterations (MAXITS) = 1000 > Tolerance of convergence (DEPS) =.200E-05 > Mixing factor (LAMBDA,DOME) = 1.000 > > CHARGE DISTRIBUTION METHOD: the trilinear interpolation > > BOUNDARY POTENTIAL CALCULATION METHOD > The Debye-Huckel approximation for half number of boundary points > along 1d-axis and > potential of the rest will be interpolated from nearest grid points > > PHYSICAL PARAMETERs > Solvent probe radius (WATR) = 1.400 [Angs] > Ion exclusion radius (Stern layer) = 0.000 [Angs] > Solvent dielectric constant (EPSW) = 80.000 > Protein dielectric constant (EPSP) = 4.000 > Salt concentration (CONC) = 0.000 [moles]/[liter] > Temperature (TEMP) = 298.000 [K] > Debye-Huckel factor (KAPPA2) = 0.000 [1/Angs**2] > > NUMBER OF GRID POINTS: 47 37 35 > Box in X from -9.200 to 9.200 > Box in Y from -7.200 to 7.200 > Box in Z from -6.800 to 6.800 > > Constructing all space-dependent functions > > Begin iterative solution > Number of iterations: 154 > The atomic contributions have been stored in WMAIN > Electrostatic energy [KCAL/MOL] = 1022.14660 > > PBEQ> set ener80 = ?enpb > RDCMND substituted energy or value "?ENPB" to "1022.15" > Parameter: ENER80 <- "1022.15" > > PBEQ> > > PBEQ> solve dcel @dcel nclx @xcel ncly @ycel nclz @zcel maxit 1000 > - > PBEQ> epsw 1.0 epsp 4.0 temp 298 watr 1.4 intbp > Parameter: DCEL -> "0.40" > Parameter: XCEL -> "46" > Parameter: YCEL -> "36" > Parameter: ZCEL -> "35" > > Calculation with 27 atoms > > LINEARIZED PBEQ SOLVER: Successive OverRelaxation (SOR) method > > ITERATION PARAMETERs > Maximum # iterations (MAXITS) = 1000 > Tolerance of convergence (DEPS) =.200E-05 > Mixing factor (LAMBDA,DOME) = 1.000 > > CHARGE DISTRIBUTION METHOD: the trilinear interpolation > > BOUNDARY POTENTIAL CALCULATION METHOD > The Debye-Huckel approximation for half number of boundary points > along 1d-axis and > potential of the rest will be interpolated from nearest grid points > > PHYSICAL PARAMETERs > Solvent probe radius (WATR) = 1.400 [Angs] > Ion exclusion radius (Stern layer) = 0.000 [Angs] > Solvent dielectric constant (EPSW) = 1.000 > Protein dielectric constant (EPSP) = 4.000 > Salt concentration (CONC) = 0.000 [moles]/[liter] > Temperature (TEMP) = 298.000 [K] > Debye-Huckel factor (KAPPA2) = 0.000 [1/Angs**2] > > NUMBER OF GRID POINTS: 47 37 35 > Box in X from -9.200 to 9.200 > Box in Y from -7.200 to 7.200 > Box in Z from -6.800 to 6.800 > > Constructing all space-dependent functions > > Begin iterative solution > Number of iterations: 426 > The atomic contributions have been stored in WMAIN > Electrostatic energy [KCAL/MOL] = 1068.39943 > > PBEQ> set ener1 = ?enpb > RDCMND substituted energy or value "?ENPB" to "1068.4" > Parameter: ENER1 <- "1068.4" > > PBEQ> > > PBEQ> calc dgpb = @dgpb + (@ener80 - @ener1) > > Parameter: DGPB -> "0" > Parameter: ENER80 -> "1022.15" > Parameter: ENER1 -> "1068.4" > Evaluating: 0+(1022.15-1068.4) > Parameter: DGPB <- "-46.25" > > **************************************END OF CHARMM > LOG************************************* > > > > > -----Original Message----- > > From: Nathan Baker [mailto:sobolevnrm@...] > > Sent: Tuesday, July 05, 2005 7:40 PM > > To: Sandeep Somani; apbs-users@... > > Subject: Re: [Apbs-users] Comparison of CHARMM and APBS results > > > > > > That is a surprisingly large difference. Are you sure you > > are using the same surface definition for both programs? > > > > Thanks, > > > > Nathan > > > > --- Sandeep Somani wrote: > > > > > Hi All > > > > > > I was trying to compare the results for a standard electrostatic > > > solvation energy from CHARMM PB solver (PBEQ) and that from APBS. > > > > > > As a test case I used just a single amino-acid (ARG) protein with a > > > net charge of +1(pqr listed below). These are the numbers i get for > > > solvation energy (electrostatic energy in vacuum - solvent): > > > > > > APBS = 453.021 kJ/mol > > > CHARMM = 193.320 kJ/mol > > > > > > quite a big discrepancy! > > > I have been trying to tweak the parameters to ensure that the two > > > calculations are set up identically. > > > > > > I ensured that the following parameters are same in both > > calculations: > > > > > > # charge, radius and positions of each atom (ofcourse!) > > > # grid center = (0,0,0) > > > # grid spacing = 0.4 Ang ( as a result box size in APBS is > > much bigger > > > as i use a bigger mesh 97x97x97 points) > > > # dielectric constants for the solvent (pdie=4,sdie=80) and vacuum > > > (pdie=4,sdie=1) > > > # ion conc = 0 > > > # method = linearized PB > > > # temperature = 298 > > > > > > APBS input file is also listed below. > > > > > > i guess that leaves boundary condition as the only major > > parameter to > > > tweak. i used the common 'bcfl sdh' setting in APBS while > > CHARMM says: > > > > > > " > > > BOUNDARY POTENTIAL CALCULATION METHOD > > > The Debye-Huckel approximation for half number of boundary points > > > along 1d-axis and potential of the rest will be interpolated from > > > nearest grid points > > > " > > > > > > are these two boundary condition methods equivalent ? > > > > > > any idea what could be the cause of the discrepancy ? > > > > > > though I would like to think that APBS numbers are more accurate :) > > > > > > regards > > > sandeep > > > > > > *************************************************************** > > > > > > PQR: > > > ==== > > > > > > ATOM 1 N ARG 1 2.963 -0.189 0.810 > > -0.3000 1.8500 > > > ATOM 2 H ARG 1 3.686 0.542 0.656 > > 0.3300 0.2245 > > > ATOM 3 H2 ARG 1 3.686 0.542 0.656 > > 0.3300 0.2245 > > > ATOM 4 H3 ARG 1 3.686 0.542 0.656 > > 0.3300 0.2245 > > > ATOM 5 CA ARG 1 2.377 -0.565 -0.459 > > 0.2100 2.2750 > > > ATOM 6 HA ARG 1 2.797 -0.303 0.500 > > 0.1000 1.3200 > > > ATOM 7 CB ARG 1 0.882 -0.240 -0.372 > > -0.1800 2.1750 > > > ATOM 8 HB1 ARG 1 0.427 -0.767 0.494 > > 0.0900 1.3200 > > > ATOM 9 HB2 ARG 1 0.427 -0.767 0.494 > > 0.0900 1.3200 > > > ATOM 10 CG ARG 1 0.283 -0.976 0.824 > > -0.1800 2.1750 > > > ATOM 11 HG1 ARG 1 -0.805 -1.139 0.667 > > 0.0900 1.3200 > > > ATOM 12 HG2 ARG 1 -0.805 -1.139 0.667 > > 0.0900 1.3200 > > > ATOM 13 CD ARG 1 -1.220 -1.246 0.697 > > 0.2000 2.1750 > > > ATOM 14 HD1 ARG 1 -1.778 -0.287 0.645 > > 0.0900 1.3200 > > > ATOM 15 HD2 ARG 1 -1.778 -0.287 0.645 > > 0.0900 1.3200 > > > ATOM 16 NE ARG 1 -2.023 -0.027 0.622 > > -0.7000 1.8500 > > > ATOM 17 HE ARG 1 -2.604 0.141 -0.174 > > 0.4400 0.2245 > > > ATOM 18 CZ ARG 1 -2.856 0.393 -0.333 > > 0.6400 2.0000 > > > ATOM 19 NH1 ARG 1 -2.929 -0.182 -1.542 > > -0.8000 1.8500 > > > ATOM 20 HH11 ARG 1 -2.342 -0.962 -1.761 > > 0.4600 0.2245 > > > ATOM 21 HH12 ARG 1 -2.342 -0.962 -1.761 > > 0.4600 0.2245 > > > ATOM 22 NH2 ARG 1 -3.600 1.488 -0.130 > > -0.8000 1.8500 > > > ATOM 23 HH21 ARG 1 -3.530 1.987 0.734 > > 0.4600 0.2245 > > > ATOM 24 HH22 ARG 1 -3.530 1.987 0.734 > > 0.4600 0.2245 > > > ATOM 25 C ARG 1 3.048 0.259 -1.551 > > 0.3400 2.0000 > > > ATOM 26 O ARG 1 3.941 1.080 -1.209 > > -0.6700 1.7000 > > > ATOM 27 OXT ARG 1 3.941 1.080 -1.209 > > -0.6700 1.7000 > > > > > > APBS Input: > > > =========== > > > > > > read > > > mol pqr arg.pqr > > > end > > > elec > > > mg-auto > > > dime 97 97 97 > > > cglen 38.8 38.8 38.8 # 12.8197 5.4961 4.3945 > > > fglen 38.8 38.8 38.8 # 12.8197 5.4961 4.3945 > > > cgcent 0 0 0 # mol 1 > > > fgcent 0 0 0 # mol 1 > > > mol 1 > > > lpbe > > > bcfl sdh > > > ion 1 0.00 2.0 > > > ion -1 0.000 2.0 > > > pdie 4.0 > > > sdie 80.00 > > > srfm smol > > > chgm spl2 > > > srad 1.4 > > > swin 0.3 > > > temp 298.00 > > > gamma 0.105 > > > calcenergy total > > > calcforce no > > > write pot dx pot > > > write smol dx acc > > > end > > > elec > > > mg-auto > > > dime 97 97 97 > > > cglen 38.8 38.8 38.8 # 12.8197 5.4961 4.3945 > > > fglen 38.8 38.8 38.8 # 12.8197 5.4961 4.3945 > > > cgcent 0 0 0 # mol 1 > > > fgcent 0 0 0 # mol 1 > > > mol 1 > > > lpbe > > > bcfl sdh > > > ion 1 0.000 2.0 > > > ion -1 0.000 2.0 > > > pdie 4.0 > > > sdie 1.00 > > > srfm smol > > > chgm spl2 > > > srad 1.4 > > > swin 0.3 > > > temp 298.00 > > > gamma 0.105 > > > calcenergy total > > > calcforce no > > > end > > > > > > print energy 2 - 1 end > > > > > > quit > > > > > > APBS log > > > ======== > > > > > > Parsing input file arg.in... > > > Parsed input file. > > > Got PQR paths for 1 molecules > > > Reading PQR-format atom data from arg.pqr. > > > asc_getToken: Error occurred (bailing out). > > > Vio_scanf: Format problem with input. > > > 27 atoms > > > Centered at (1.705e-01, 3.705e-01, -4.685e-01) > > > Net charge 1.00e-00 e > > > Preparing to run 4 PBE calculations. > > > ---------------------------------------- > > > CALCULATION #1: MULTIGRID > > > Setting up problem... > > > Vpbe_ctor: Using max ion radius (2 A) for exclusion function > > > Debye length: 0 A > > > Current memory usage: 153.010 MB total, 153.010 MB high water > > > Using cubic spline charge discretization. > > > Grid dimensions: 97 x 97 x 97 > > > Grid spacings: 0.404 x 0.404 x 0.404 > > > Grid lengths: 38.800 x 38.800 x 38.800 > > > Grid center: (0.000, 0.000, 0.000) > > > Multigrid levels: 4 > > > Molecule ID: 1 > > > Linearized traditional PBE > > > Single Debye-Huckel sphere boundary conditions > > > 2 ion species (0.000 M ionic strength): > > > 2.000 A-radius, 1.000 e-charge, 0.000 M concentration > > > 2.000 A-radius, -1.000 e-charge, 0.000 M concentration > > > Solute dielectric: 4.000 > > > Solvent dielectric: 80.000 > > > Using "molecular" surface definition; harmonic average smoothing > > > Solvent probe radius: 1.400 A > > > Temperature: 298.000 K > > > Surface tension: 0.105 kJ/mol/A^2 > > > Electrostatic energies will be calculated > > > Solving PDE (see io.mc* for details)... > > > Total electrostatic energy = 2.706605597683E+03 kJ/mol > > > ---------------------------------------- > > > CALCULATION #2: MULTIGRID > > > Setting up problem... > > > Vpbe_ctor: Using max ion radius (2 A) for exclusion function > > > Debye length: 0 A > > > Current memory usage: 152.988 MB total, 155.266 MB high water > > > Using cubic spline charge discretization. > > > Grid dimensions: 97 x 97 x 97 > > > Grid spacings: 0.404 x 0.404 x 0.404 > > > Grid lengths: 38.800 x 38.800 x 38.800 > > > Grid center: (0.000, 0.000, 0.000) > > > Multigrid levels: 4 > > > Molecule ID: 1 > > > Linearized traditional PBE > > > Boundary conditions from focusing > > > 2 ion species (0.000 M ionic strength): > > > 2.000 A-radius, 1.000 e-charge, 0.000 M concentration > > > 2.000 A-radius, -1.000 e-charge, 0.000 M concentration > > > Solute dielectric: 4.000 > > > Solvent dielectric: 80.000 > > > Using "molecular" surface definition; harmonic average smoothing > > > Solvent probe radius: 1.400 A > > > Temperature: 298.000 K > > > Surface tension: 0.105 kJ/mol/A^2 > > > Electrostatic energies will be calculated > > > Potential to be written to pot.dx > > > Molecular solvent accessibility to be written to acc.dx > > > Solving PDE (see io.mc* for details)... > > > Total electrostatic energy = 2.706605597683E+03 kJ/mol > > > Writing potential to pot.dx > > > Writing molecular accessibility to acc.dx > > > ---------------------------------------- > > > CALCULATION #3: MULTIGRID > > > Setting up problem... > > > Vpbe_ctor: Using max ion radius (2 A) for exclusion function > > > Debye length: 0 A > > > Current memory usage: 153.010 MB total, 155.266 MB high water > > > Using cubic spline charge discretization. > > > Grid dimensions: 97 x 97 x 97 > > > Grid spacings: 0.404 x 0.404 x 0.404 > > > Grid lengths: 38.800 x 38.800 x 38.800 > > > Grid center: (0.000, 0.000, 0.000) > > > Multigrid levels: 4 > > > Molecule ID: 1 > > > Linearized traditional PBE > > > Single Debye-Huckel sphere boundary conditions > > > 2 ion species (0.000 M ionic strength): > > > 2.000 A-radius, 1.000 e-charge, 0.000 M concentration > > > 2.000 A-radius, -1.000 e-charge, 0.000 M concentration > > > Solute dielectric: 4.000 > > > Solvent dielectric: 1.000 > > > Using "molecular" surface definition; harmonic average smoothing > > > Solvent probe radius: 1.400 A > > > Temperature: 298.000 K > > > Surface tension: 0.105 kJ/mol/A^2 > > > Electrostatic energies will be calculated > > > Solving PDE (see io.mc* for details)... > > > Total electrostatic energy = 3.159627129610E+03 kJ/mol > > > ---------------------------------------- > > > CALCULATION #4: MULTIGRID > > > Setting up problem... > > > Vpbe_ctor: Using max ion radius (2 A) for exclusion function > > > Debye length: 0 A > > > Current memory usage: 152.988 MB total, 155.266 MB high water > > > Using cubic spline charge discretization. > > > Grid dimensions: 97 x 97 x 97 > > > Grid spacings: 0.404 x 0.404 x 0.404 > > > Grid lengths: 38.800 x 38.800 x 38.800 > > > Grid center: (0.000, 0.000, 0.000) > > > Multigrid levels: 4 > > > Molecule ID: 1 > > > Linearized traditional PBE > > > Boundary conditions from focusing > > > 2 ion species (0.000 M ionic strength): > > > 2.000 A-radius, 1.000 e-charge, 0.000 M concentration > > > 2.000 A-radius, -1.000 e-charge, 0.000 M concentration > > > Solute dielectric: 4.000 > > > Solvent dielectric: 1.000 > > > Using "molecular" surface definition; harmonic average smoothing > > > Solvent probe radius: 1.400 A > > > Temperature: 298.000 K > > > Surface tension: 0.105 kJ/mol/A^2 > > > Electrostatic energies will be calculated > > > Solving PDE (see io.mc* for details)... > > > Total electrostatic energy = 3.159627129610E+03 kJ/mol > > > ---------------------------------------- > > > PRINT STATEMENTS > > > print energy 2 - 1 end > > > Local net energy (PE 0) = 4.530215319263E+02 kJ/mol > > > Global net energy = 4.530215319263E+02 kJ/mol > > > ---------------------------------------- > > > CLEANING UP AND SHUTTING DOWN... > > > Destroying force arrays. > > > No energy arrays to destroy. > > > Destroying multigrid structures. > > > Destroying 1 molecules > > > Final memory usage: 0.000 MB total, 155.266 MB high water > > > > > > > > > Thanks for using APBS! > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > apbs-users mailing list > > > apbs-users@... > > > http://cholla.wustl.edu/mailman/listinfo/apbs-users > > > > > > > > > > > > -- > > Assistant Professor, Dept. of Biochemistry and Molecular > > Biophysics Washington University in St. Louis http://cholla.wustl.edu > > > > > _______________________________________________ > apbs-users mailing list > apbs-users@... > http://cholla.wustl.edu/mailman/listinfo/apbs-users > > -- Assistant Professor, Dept. of Biochemistry and Molecular Biophysics Washington University in St. Louis http://cholla.wustl.edu ```
 Re: [Apbs-users] apbs-pymol plugin From: Nathan Baker - 2005-06-20 14:21:58 ```Hi Joel -- This is a problem with chain IDs; they need to be removed from the PQR file prior to input to APBS. Thanks, Nathan --- Joel Tyndall wrote: > Hi folks, > > I finally got around to installing apbs. I've tried to run it thru the > pymol plugin and I get an error. It seems to run ok but then can't read > in the map file (see below). any help would be welcome > > J > > set grid > > coarsedim is [111.56420230865479, 104.21170161962509, 79.228497600555414] > finedim is [85.626001358032227, 81.301000952720642, 66.604998588562012] > center is [13.830000877380371, 30.882500469684601, 25.5194993019104] > finegridpoints is [193, 193, 161] > radiobutton said to generate it Use PyMOL generated PQR and PyMOL > generated Hydrogens and termini so i am returning pymol-generated.pqr > radiobutton said to generate it Use PyMOL generated PQR and PyMOL > generated Hydrogens and termini so i am returning pymol-generated.pqr > WARNING: 124 atoms did not have formal charges assigned > WARNING: 264 atoms did not have properties assigned > > ---------------------------------------------------------------------- > APBS -- Adaptive Poisson-Boltzmann Solver > Version 0.3.2 > > ....... > > information about PMG and FEtk may be found at ;. > ---------------------------------------------------------------------- > > > This executable compiled on Nov 10 2004 at 11:39:22 > > Parsing input file pymol-generated.in... > parsePBE: Warning -- parsed deprecated "bcfl 1" statement > parsePBE: Please use "bcfl sdh" instead. > NOsh: Warning -- parsed deprecated statment "chgm 1". > NOsh: Please use "chgm spl2" instead! > parsePBE: Warning -- parsed deprecated "srfm 1" statement. > parsePBE: Please use "srfm smol" instead. > parsePBE: Warning -- parsed deprecated "calcenergy 0" statement. > parsePBE: Please use "calcenergy no" instead. > parsePBE: Warning -- parsed deprecated "calcforce 0" statement. > parsePBE: Please use "calcforce no" instead. > Parsed input file. > Got PQR paths for 1 molecules > Reading PQR-format atom data from pymol-generated.pqr. > Valist_readPDB: Unable to parse resSeq token (A) as int! > Valist_readPDB: Error while parsing residue name! > Valist_readPQR: Error parsing ATOM field! > Error while reading molecule from pymol-generated.pqr > Error reading molecules! > ObjectMapLoadDXFile-Error: Unable to open file! > > -- > Joel Tyndall, PhD > > Lecturer > National School of Pharmacy > University of Otago > PO Box 913 Dunedin > New Zealand > > Pukenga > Te Kura Taiwhanga Putaiao > Te Whare Wananga o Otago > Pouaka Poutapeta 913 Otepoti > Aotearoa > > Ph / Waea +64 3 4797293 > Fax / Waeawhakaahua +64 3 4797034 > > > > ATOM 1 C ACE A 23 24.288 17.826 14.313 0.000 0.000 > ATOM 2 O ACE A 23 24.917 18.906 14.298 0.000 0.000 > ATOM 3 C ACE A 23 22.864 17.702 13.793 0.000 0.000 > ATOM 4 H ACE A 23 22.472 16.715 14.037 0.000 0.000 > ATOM 5 H ACE A 23 22.858 17.839 12.712 0.000 0.000 > ATOM 6 H ACE A 23 22.240 18.465 14.258 0.000 0.000 > ATOM 7 N GLY A 24 24.767 16.666 14.754 -0.416 1.824 > ATOM 8 CA GLY A 24 26.114 16.416 15.194 -0.025 1.908 > ATOM 9 C GLY A 24 26.119 16.275 16.728 0.597 1.908 > ATOM 10 O GLY A 24 26.108 15.189 17.316 -0.568 1.661 > ATOM 11 HA3 GLY A 24 26.756 17.246 14.900 0.070 1.387 > ATOM 12 H GLY A 24 24.125 15.887 14.783 0.272 0.600 > ATOM 13 HA GLY A 24 26.488 15.499 14.738 0.070 1.387 > ATOM 14 N SER A 25 26.082 17.456 17.330 -0.416 1.824 > ATOM 15 CA SER A 25 26.050 17.650 18.768 -0.025 1.908 > ATOM 16 C SER A 25 25.103 18.838 19.026 0.597 1.908 > ATOM 17 O SER A 25 24.852 19.618 18.088 -0.568 1.661 > ATOM 18 CB SER A 25 27.481 18.052 19.186 0.212 1.908 > ATOM 19 OG SER A 25 27.632 19.358 18.606 -0.655 1.721 > ATOM 20 HG SER A 25 27.486 20.027 19.279 0.428 0.000 > ATOM 21 H SER A 25 26.076 18.280 16.746 0.272 0.600 > ATOM 22 HA SER A 25 25.720 16.765 19.313 0.084 1.387 > ATOM 23 HB2 SER A 25 28.217 17.356 18.784 0.035 1.387 > ATOM 24 HB3 SER A 25 27.632 18.041 20.265 0.035 1.387 > ATOM 25 N ILE A 26 24.639 18.867 20.260 -0.416 1.824 > ATOM 26 CA ILE A 26 23.549 19.815 20.576 -0.060 1.908 > ATOM 27 C ILE A 26 24.058 21.261 20.462 0.597 1.908 > ATOM 28 O ILE A 26 23.209 22.114 20.153 -0.568 1.661 > ATOM 29 CB ILE A 26 22.962 19.478 21.981 0.130 1.908 > ATOM 30 CG1 ILE A 26 21.788 20.471 22.340 -0.043 1.908 > ATOM 31 CG2 ILE A 26 23.978 19.371 23.126 -0.320 1.908 > ATOM 32 CD1 ILE A 26 20.527 20.085 21.481 -0.066 1.908 > ATOM 33 HD13 ILE A 26 20.179 19.093 21.771 0.019 1.487 > ATOM 34 H ILE A 26 25.018 18.258 20.971 0.272 0.600 > ATOM 35 HA ILE A 26 22.737 19.717 19.856 0.087 1.387 > ATOM 36 HB ILE A 26 22.576 18.463 21.886 0.019 1.487 > ATOM 37 HG12 ILE A 26 22.089 21.494 22.114 0.024 1.487 > ATOM 38 HG23 ILE A 26 24.295 18.334 23.235 0.088 1.487 > ATOM 39 HD12 ILE A 26 20.793 20.083 20.424 0.019 1.487 > ATOM 40 HG13 ILE A 26 21.552 20.401 23.402 0.024 1.487 > ATOM 41 HG22 ILE A 26 23.518 19.710 24.054 0.088 1.487 > ATOM 42 HD11 ILE A 26 19.734 20.812 21.654 0.019 1.487 > ATOM 43 HG21 ILE A 26 24.844 19.994 22.902 0.088 1.487 > ATOM 44 N GLY A 27 25.346 21.441 20.740 -0.416 1.824 > ATOM 45 CA GLY A 27 25.967 22.810 20.689 -0.025 1.908 > ATOM 46 C GLY A 27 25.881 23.325 19.252 0.597 1.908 > ATOM 47 O GLY A 27 25.258 24.368 18.941 -0.568 1.661 > ATOM 48 HA3 GLY A 27 27.010 22.754 20.999 0.070 1.387 > ATOM 49 H GLY A 27 25.916 20.646 20.989 0.272 0.600 > ATOM 50 HA GLY A 27 25.439 23.486 21.361 0.070 1.387 > ATOM 51 N ALA A 28 26.464 22.566 18.365 -0.416 1.824 > ATOM 52 CA ALA A 28 26.464 22.821 16.913 0.034 1.908 > ATOM 53 C ALA A 28 25.054 22.924 16.353 0.597 1.908 > ATOM 54 O ALA A 28 24.728 23.841 15.561 -0.568 1.661 > ATOM 55 CB ALA A 28 27.204 21.691 16.230 -0.183 1.908 > ATOM 56 HB3 ALA A 28 27.330 21.925 15.173 0.060 1.487 > ATOM 57 H ALA A 28 26.950 21.745 18.697 0.272 0.600 > ATOM 58 HA ALA A 28 26.955 23.776 16.728 0.082 1.387 > ATOM 59 HB2 ALA A 28 26.634 20.768 16.333 0.060 1.487 > ATOM 60 HB1 ALA A 28 28.183 21.566 16.693 0.060 1.487 > ATOM 61 N ALA A 29 24.207 21.956 16.745 -0.416 1.824 > ATOM 62 CA ALA A 29 22.835 21.972 16.180 0.034 1.908 > ATOM 63 C ALA A 29 22.040 23.179 16.660 0.597 1.908 > ATOM 64 O ALA A 29 21.285 23.769 15.836 -0.568 1.661 > ATOM 65 CB ALA A 29 22.109 20.655 16.465 -0.183 1.908 > ATOM 66 HB3 ALA A 29 21.958 20.548 17.539 0.060 1.487 > ATOM 67 H ALA A 29 24.494 21.243 17.401 0.272 0.600 > ATOM 68 HA ALA A 29 22.923 22.068 15.098 0.082 1.387 > ATOM 69 HB2 ALA A 29 22.708 19.822 16.097 0.060 1.487 > ATOM 70 HB1 ALA A 29 21.142 20.657 15.961 0.060 1.487 > ATOM 71 N SER A 30 22.130 23.529 17.952 -0.416 1.824 > ATOM 72 CA SER A 30 21.294 24.711 18.383 -0.025 1.908 > ATOM 73 C SER A 30 21.772 26.016 17.762 0.597 1.908 > ATOM 74 O SER A 30 21.040 26.949 17.447 -0.568 1.661 > ATOM 75 CB SER A 30 21.212 24.798 19.907 0.212 1.908 > ATOM 76 OG SER A 30 22.528 25.088 20.378 -0.655 1.721 > ATOM 77 HG SER A 30 22.868 24.333 20.864 0.428 0.000 > ATOM 78 H SER A 30 22.723 23.030 18.600 0.272 0.600 > ATOM 79 HA SER A 30 20.284 24.548 18.006 0.084 1.387 > ATOM 80 HB2 SER A 30 20.866 23.850 20.319 0.035 1.387 > ATOM 81 HB3 SER A 30 20.509 25.571 20.216 0.035 1.387 > ATOM 82 N MET A 31 23.053 26.083 17.540 -0.416 1.824 > ATOM 83 CA MET A 31 23.689 27.330 17.000 -0.024 1.908 > ATOM 84 C MET A 31 23.345 27.428 15.549 0.597 1.908 > ATOM 85 O MET A 31 22.943 28.475 15.021 -0.568 1.661 > ATOM 86 CB MET A 31 25.217 27.123 17.193 0.034 1.908 > ATOM 87 CG MET A 31 25.435 27.429 18.679 0.002 1.908 > ATOM 88 SD MET A 31 26.027 29.166 18.675 -0.274 2.000 > ATOM 89 CE MET A 31 27.784 28.762 18.463 -0.054 1.908 > ATOM 90 HE3 MET A 31 28.115 29.086 17.476 0.068 1.387 > ATOM 91 H MET A 31 23.631 25.278 17.735 0.272 0.600 > ATOM 92 HA MET A 31 23.355 28.242 17.494 0.088 1.387 > ATOM 93 HB2 MET A 31 25.786 27.809 16.566 0.024 1.487 > ATOM 94 HG2 MET A 31 26.183 26.763 19.109 0.044 1.387 > ATOM 95 HE2 MET A 31 27.924 27.685 18.559 0.068 1.387 > ATOM 96 HB3 MET A 31 25.548 26.123 16.913 0.024 1.487 > ATOM 97 HG3 MET A 31 24.535 27.288 19.278 0.044 1.387 > ATOM 98 HE1 MET A 31 28.369 29.273 19.228 0.068 1.387 > ATOM 99 N GLU A 32 23.528 26.285 14.864 0.000 0.000 > ATOM 100 C GLU A 32 23.054 26.425 13.417 0.000 0.000 > ATOM 101 C GLU A 32 21.595 26.777 13.352 0.000 0.000 > ATOM 102 O GLU A 32 21.176 27.692 12.606 0.000 0.000 > ATOM 103 C GLU A 32 23.341 25.159 12.644 0.000 0.000 > ATOM 104 C GLU A 32 24.793 24.655 12.660 0.000 0.000 > ATOM 105 H GLU A 32 25.138 24.507 11.637 0.000 0.000 > ATOM 106 H GLU A 32 23.927 25.443 15.255 0.000 0.000 > ATOM 107 H GLU A 32 23.608 27.243 12.957 0.000 0.000 > ATOM 108 H GLU A 32 23.063 25.336 11.605 0.000 0.000 > ATOM 109 H GLU A 32 24.844 23.710 13.201 0.000 0.000 > ATOM 110 H GLU A 32 22.763 24.382 13.143 0.000 0.000 > ATOM 111 H GLU A 32 25.427 25.391 13.154 0.000 0.000 > ATOM 112 N PHE A 33 20.752 26.053 14.131 -0.416 1.824 > ATOM 113 CA PHE A 33 19.304 26.419 14.182 -0.002 1.908 > ATOM 114 C PHE A 33 19.109 27.896 14.516 0.597 1.908 > ATOM 115 O PHE A 33 18.325 28.634 13.848 -0.568 1.661 > ATOM 116 CB PHE A 33 18.492 25.486 15.111 -0.034 1.908 > ATOM 117 CG PHE A 33 17.001 25.776 15.157 0.012 1.908 > ATOM 118 CD1 PHE A 33 16.208 25.535 14.025 -0.126 1.908 > ATOM 119 CD2 PHE A 33 16.394 26.279 16.298 -0.126 1.908 > ATOM 120 CE1 PHE A 33 14.857 25.777 14.038 -0.170 1.908 > ATOM 121 CE2 PHE A 33 15.024 26.522 16.361 -0.170 1.908 > ATOM 122 CZ PHE A 33 14.255 26.274 15.213 -0.107 1.908 > ATOM 123 HZ PHE A 33 13.182 26.467 15.230 0.130 1.459 > ATOM 124 H PHE A 33 21.100 25.274 14.671 0.272 0.600 > ATOM 125 HA PHE A 33 18.901 26.267 13.181 0.098 1.387 > ATOM 126 HB2 PHE A 33 18.889 25.583 16.122 0.030 1.487 > ATOM 127 HD1 PHE A 33 16.673 25.148 13.118 0.133 1.459 > ATOM 128 HD2 PHE A 33 17.008 26.491 17.173 0.133 1.459 > ATOM 129 HE1 PHE A 33 14.255 25.587 13.149 0.143 1.459 > ATOM 130 HE2 PHE A 33 14.562 26.894 17.276 0.143 1.459 > ATOM 131 HB3 PHE A 33 18.597 24.480 14.704 0.030 1.487 > ATOM 132 N CYS A 34 19.723 28.330 15.596 -0.416 1.824 > ATOM 133 CA CYS A 34 19.703 29.767 15.995 0.021 1.908 > ATOM 134 C CYS A 34 19.908 30.765 14.838 0.597 1.908 > ATOM 135 O CYS A 34 19.143 31.752 14.648 -0.568 1.661 > ATOM 136 CB CYS A 34 20.718 29.985 17.127 -0.123 1.908 > ATOM 137 SG CYS A 34 20.701 31.739 17.619 -0.312 2.000 > ATOM 138 HG CYS A 34 21.752 32.367 17.074 0.193 0.600 > ATOM 139 H CYS A 34 20.224 27.669 16.173 0.272 0.600 > ATOM 140 HA CYS A 34 18.694 29.985 16.346 0.112 1.387 > ATOM 141 HB2 CYS A 34 21.715 29.713 16.781 0.111 1.387 > ATOM 142 HB3 CYS A 34 20.452 29.363 17.982 0.111 1.387 > ATOM 143 N PHE A 35 20.901 30.534 13.997 -0.416 1.824 > ATOM 144 CA PHE A 35 21.305 31.507 12.929 -0.002 1.908 > ATOM 145 C PHE A 35 20.390 31.361 11.743 0.597 1.908 > ATOM 146 O PHE A 35 20.027 32.391 11.201 -0.568 1.661 > ATOM 147 CB PHE A 35 22.813 31.268 12.588 -0.034 1.908 > ATOM 148 CG PHE A 35 23.662 31.873 13.708 0.012 1.908 > ATOM 149 CD1 PHE A 35 23.510 33.247 13.990 -0.126 1.908 > ATOM 150 CD2 PHE A 35 24.558 31.066 14.411 -0.126 1.908 > ATOM 151 CE1 PHE A 35 24.241 33.795 15.049 -0.170 1.908 > ATOM 152 CE2 PHE A 35 25.318 31.616 15.473 -0.170 1.908 > ATOM 153 CZ PHE A 35 25.118 32.979 15.758 -0.107 1.908 > ATOM 154 HZ PHE A 35 25.681 33.421 16.580 0.130 1.459 > ATOM 155 H PHE A 35 21.410 29.665 14.077 0.272 0.600 > ATOM 156 HA PHE A 35 21.205 32.539 13.267 0.098 1.387 > ATOM 157 HB2 PHE A 35 23.057 31.747 11.640 0.030 1.487 > ATOM 158 HD1 PHE A 35 22.838 33.867 13.396 0.133 1.459 > ATOM 159 HD2 PHE A 35 24.673 30.016 14.144 0.133 1.459 > ATOM 160 HE1 PHE A 35 24.126 34.846 15.315 0.143 1.459 > ATOM 161 HE2 PHE A 35 26.024 31.012 16.042 0.143 1.459 > ATOM 162 HB3 PHE A 35 23.013 30.200 12.501 0.030 1.487 > ATOM 163 N ASP A 36 19.885 30.157 11.532 -0.516 1.824 > ATOM 164 CA ASP A 36 18.776 30.042 10.532 0.038 1.908 > ATOM 165 C ASP A 36 17.586 30.883 10.914 0.537 1.908 > ATOM 166 O ASP A 36 16.975 31.568 10.060 -0.582 1.661 > ATOM 167 CB ASP A 36 18.408 28.591 10.259 -0.030 1.908 > ATOM 168 CG ASP A 36 19.407 27.873 9.364 0.799 1.908 > ATOM 169 OD1 ASP A 36 20.298 28.500 8.781 -0.801 1.661 > ATOM 170 OD2 ASP A 36 19.262 26.643 9.326 -0.801 1.661 > ATOM 171 HB2 ASP A 36 17.431 28.566 9.777 -0.012 1.487 > ATOM 172 H ASP A 36 20.233 29.348 12.025 0.294 0.600 > ATOM 173 HA ASP A 36 19.146 30.447 9.590 0.088 1.387 > ATOM 174 HB3 ASP A 36 18.406 28.074 11.218 -0.012 1.487 > ATOM 175 N VAL A 37 17.163 30.722 12.174 -0.416 1.824 > ATOM 176 CA VAL A 37 15.980 31.547 12.617 -0.087 1.908 > ATOM 177 C VAL A 37 16.291 33.048 12.486 0.597 1.908 > ATOM 178 O VAL A 37 15.433 33.885 12.098 -0.568 1.661 > ATOM 179 CB VAL A 37 15.557 31.095 14.043 0.299 1.908 > ATOM 180 CG1 VAL A 37 14.559 32.074 14.645 -0.319 1.908 > ATOM 181 CG2 VAL A 37 14.944 29.674 14.023 -0.319 1.908 > ATOM 182 HG23 VAL A 37 14.798 29.326 15.046 0.079 1.487 > ATOM 183 H VAL A 37 17.617 30.075 12.802 0.272 0.600 > ATOM 184 HA VAL A 37 15.120 31.381 11.968 0.097 1.387 > ATOM 185 HB VAL A 37 16.456 31.077 14.659 -0.030 1.487 > ATOM 186 HG13 VAL A 37 14.364 32.878 13.935 0.079 1.487 > ATOM 187 HG22 VAL A 37 15.617 28.995 13.500 0.079 1.487 > ATOM 188 HG12 VAL A 37 14.969 32.492 15.564 0.079 1.487 > ATOM 189 HG21 VAL A 37 13.984 29.700 13.508 0.079 1.487 > ATOM 190 HG11 VAL A 37 13.628 31.552 14.867 0.079 1.487 > ATOM 191 N PHE A 38 17.483 33.411 12.929 -0.416 1.824 > ATOM 192 CA PHE A 38 17.911 34.841 12.926 -0.002 1.908 > ATOM 193 C PHE A 38 17.806 35.454 11.516 0.597 1.908 > ATOM 194 O PHE A 38 17.258 36.547 11.372 -0.568 1.661 > ATOM 195 CB PHE A 38 19.318 34.985 13.540 -0.034 1.908 > ATOM 196 CG PHE A 38 19.672 36.438 13.773 0.012 1.908 > ATOM 197 CD1 PHE A 38 18.970 37.189 14.703 -0.126 1.908 > ATOM 198 CD2 PHE A 38 20.695 37.035 12.992 -0.126 1.908 > ATOM 199 CE1 PHE A 38 19.276 38.541 14.938 -0.170 1.908 > ATOM 200 CE2 PHE A 38 21.001 38.397 13.223 -0.170 1.908 > ATOM 201 CZ PHE A 38 20.318 39.142 14.194 -0.107 1.908 > === message truncated ===> # > # Note that most of the comments here were taken from sample > # input files that came with APBS. You can find APBS at > # http://agave.wustl.edu/apbs/ > # Note that APBS is GPL'd code. > # > read > mol pqr pymol-generated.pqr # read molecule 1 > end > elec > mg-auto > dime 193 193 161 # number of find grid points > # calculated by psize.py > cglen 111.564202 104.211702 79.228498 # coarse mesh lengths (A) > fglen 85.626001 81.301001 66.604999 # fine mesh lengths (A) > # calculated by psize.py > cgcent 13.830001 30.882500 25.519499 # (could also give (x,y,z) form > psize.py) #known center > fgcent 13.830001 30.882500 25.519499 # (could also give (x,y,z) form > psize.py) #known center > npbe # solve the full nonlinear PBE with npbe > #lpbe # solve the linear PBE with lpbe > bcfl 1 # Boundary condition flag > # 0 => Zero > # 1 => Single DH sphere > # 2 => Multiple DH spheres > # 4 => Focusing > # > #ion 1 0.000 2.0 # Counterion declaration: > ion 1 0.000000 2.000000 # Counterion declaration: > ion -1 0.000000 2.000000 # ion > ion 2 0.000000 2.000000 # ion > ion -2 0.000000 2.000000 # ion > pdie 20.000000 # Solute dielectric > sdie 80.000000 # Solvent dielectric > chgm 1 # Charge disc method > # 0 is linear splines > # 1 is cubic b-splines > mol 1 # which molecule to use > srfm 1 # Surface calculation method > # 0 => Mol surface for epsilon; > # inflated VdW for kappa; no > # smoothing > # 1 => As 0 with harmoic average > # smoothing > # 2 => Cubic spline > srad 1.400000 # Solvent radius (1.4 for water) > swin 0.3 # Surface cubic spline window .. default 0.3 > temp 310.000000 # System temperature (298.15 default) > gamma 0.105 # Surface tension parameter for apolar forces (in > kJ/mol/A^2) > # only used for force calculations, so we don't care, > but > # it's always required, and 0.105 is the default > calcenergy 0 # Energy I/O to stdout > # 0 => don't write out energy > # 1 => write out total energy > # 2 => write out total energy and all > # components > calcforce 0 # Atomic forces I/O (to stdout) > # 0 => don't write out forces > # 1 => write out net forces on molecule > # 2 => write out atom-level forces > write pot dx pymol-generated # What to write .. this says write the > potential in dx > # format to a file. > end > quit > > > _______________________________________________ > apbs-users mailing list > apbs-users@... > http://cholla.wustl.edu/mailman/listinfo/apbs-users > -- Assistant Professor, Dept. of Biochemistry and Molecular Biophysics Washington University in St. Louis http://cholla.wustl.edu ```
 Re: [Apbs-users] apbs-pymol plugin From: Michael George Lerner - 2005-06-28 18:06:42 ```Hi all, This is fixed in the current PyMOL source tree, and it'll be fixed in the next released version of PyMOL. In the meantime, you can download the current version here: http://www-personal.umich.edu/~mlerner/PyMOL/apbs_tools.py There are installation instructions at the top of http://www-personal.umich.edu/~mlerner/PyMOL/ but it boils down to "replace your \$PYMOL_PATH/modules/pmg_tk/startup/apbs_tools.py with the current one." There are a few other new features, including: - More reasonable starting dielectric constants - The ability to set a maximum number of grid points - The ability to display solvent accessible surfaces as well as molecular surfaces - Better warnings when PyMOL is unable to generate appropriate parameters in the PQR file. Sometime soon, I'll probably also change the .in file to say things like "bcfl sdh" instead of "bcfl 1" etc. Given that the PyMOL/APBS Plugin is getting updated a bit, please let me know if there are any features/changes you'd like. thanks, -michael -- http://www.umich.edu/~mlerner | _ |Michael Lerner This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan it's a cheer-ocracy. | - against HTML email X | Biophysics -Torrence, Bring It On| / \ | mlerner@... On Mon, 20 Jun 2005, Nathan Baker wrote: > Hi Joel -- > > This is a problem with chain IDs; they need to be removed from the PQR file > prior to input to APBS. > > Thanks, > > Nathan > > --- Joel Tyndall wrote: > >> Hi folks, >> >> I finally got around to installing apbs. I've tried to run it thru the >> pymol plugin and I get an error. It seems to run ok but then can't read >> in the map file (see below). any help would be welcome >> >> J >> >> set grid >> >> coarsedim is [111.56420230865479, 104.21170161962509, 79.228497600555414] >> finedim is [85.626001358032227, 81.301000952720642, 66.604998588562012] >> center is [13.830000877380371, 30.882500469684601, 25.5194993019104] >> finegridpoints is [193, 193, 161] >> radiobutton said to generate it Use PyMOL generated PQR and PyMOL >> generated Hydrogens and termini so i am returning pymol-generated.pqr >> radiobutton said to generate it Use PyMOL generated PQR and PyMOL >> generated Hydrogens and termini so i am returning pymol-generated.pqr >> WARNING: 124 atoms did not have formal charges assigned >> WARNING: 264 atoms did not have properties assigned >> >> ---------------------------------------------------------------------- >> APBS -- Adaptive Poisson-Boltzmann Solver >> Version 0.3.2 >> >> ....... >> >> information about PMG and FEtk may be found at ;. >> ---------------------------------------------------------------------- >> >> >> This executable compiled on Nov 10 2004 at 11:39:22 >> >> Parsing input file pymol-generated.in... >> parsePBE: Warning -- parsed deprecated "bcfl 1" statement >> parsePBE: Please use "bcfl sdh" instead. >> NOsh: Warning -- parsed deprecated statment "chgm 1". >> NOsh: Please use "chgm spl2" instead! >> parsePBE: Warning -- parsed deprecated "srfm 1" statement. >> parsePBE: Please use "srfm smol" instead. >> parsePBE: Warning -- parsed deprecated "calcenergy 0" statement. >> parsePBE: Please use "calcenergy no" instead. >> parsePBE: Warning -- parsed deprecated "calcforce 0" statement. >> parsePBE: Please use "calcforce no" instead. >> Parsed input file. >> Got PQR paths for 1 molecules >> Reading PQR-format atom data from pymol-generated.pqr. >> Valist_readPDB: Unable to parse resSeq token (A) as int! >> Valist_readPDB: Error while parsing residue name! >> Valist_readPQR: Error parsing ATOM field! >> Error while reading molecule from pymol-generated.pqr >> Error reading molecules! >> ObjectMapLoadDXFile-Error: Unable to open file! >> >> -- >> Joel Tyndall, PhD >> >> Lecturer >> National School of Pharmacy >> University of Otago >> PO Box 913 Dunedin >> New Zealand >> >> Pukenga >> Te Kura Taiwhanga Putaiao >> Te Whare Wananga o Otago >> Pouaka Poutapeta 913 Otepoti >> Aotearoa >> >> Ph / Waea +64 3 4797293 >> Fax / Waeawhakaahua +64 3 4797034 >> >> >>> ATOM 1 C ACE A 23 24.288 17.826 14.313 0.000 0.000 >> ATOM 2 O ACE A 23 24.917 18.906 14.298 0.000 0.000 >> ATOM 3 C ACE A 23 22.864 17.702 13.793 0.000 0.000 >> ATOM 4 H ACE A 23 22.472 16.715 14.037 0.000 0.000 >> ATOM 5 H ACE A 23 22.858 17.839 12.712 0.000 0.000 >> ATOM 6 H ACE A 23 22.240 18.465 14.258 0.000 0.000 >> ATOM 7 N GLY A 24 24.767 16.666 14.754 -0.416 1.824 >> ATOM 8 CA GLY A 24 26.114 16.416 15.194 -0.025 1.908 >> ATOM 9 C GLY A 24 26.119 16.275 16.728 0.597 1.908 >> ATOM 10 O GLY A 24 26.108 15.189 17.316 -0.568 1.661 >> ATOM 11 HA3 GLY A 24 26.756 17.246 14.900 0.070 1.387 >> ATOM 12 H GLY A 24 24.125 15.887 14.783 0.272 0.600 >> ATOM 13 HA GLY A 24 26.488 15.499 14.738 0.070 1.387 >> ATOM 14 N SER A 25 26.082 17.456 17.330 -0.416 1.824 >> ATOM 15 CA SER A 25 26.050 17.650 18.768 -0.025 1.908 >> ATOM 16 C SER A 25 25.103 18.838 19.026 0.597 1.908 >> ATOM 17 O SER A 25 24.852 19.618 18.088 -0.568 1.661 >> ATOM 18 CB SER A 25 27.481 18.052 19.186 0.212 1.908 >> ATOM 19 OG SER A 25 27.632 19.358 18.606 -0.655 1.721 >> ATOM 20 HG SER A 25 27.486 20.027 19.279 0.428 0.000 >> ATOM 21 H SER A 25 26.076 18.280 16.746 0.272 0.600 >> ATOM 22 HA SER A 25 25.720 16.765 19.313 0.084 1.387 >> ATOM 23 HB2 SER A 25 28.217 17.356 18.784 0.035 1.387 >> ATOM 24 HB3 SER A 25 27.632 18.041 20.265 0.035 1.387 >> ATOM 25 N ILE A 26 24.639 18.867 20.260 -0.416 1.824 >> ATOM 26 CA ILE A 26 23.549 19.815 20.576 -0.060 1.908 >> ATOM 27 C ILE A 26 24.058 21.261 20.462 0.597 1.908 >> ATOM 28 O ILE A 26 23.209 22.114 20.153 -0.568 1.661 >> ATOM 29 CB ILE A 26 22.962 19.478 21.981 0.130 1.908 >> ATOM 30 CG1 ILE A 26 21.788 20.471 22.340 -0.043 1.908 >> ATOM 31 CG2 ILE A 26 23.978 19.371 23.126 -0.320 1.908 >> ATOM 32 CD1 ILE A 26 20.527 20.085 21.481 -0.066 1.908 >> ATOM 33 HD13 ILE A 26 20.179 19.093 21.771 0.019 1.487 >> ATOM 34 H ILE A 26 25.018 18.258 20.971 0.272 0.600 >> ATOM 35 HA ILE A 26 22.737 19.717 19.856 0.087 1.387 >> ATOM 36 HB ILE A 26 22.576 18.463 21.886 0.019 1.487 >> ATOM 37 HG12 ILE A 26 22.089 21.494 22.114 0.024 1.487 >> ATOM 38 HG23 ILE A 26 24.295 18.334 23.235 0.088 1.487 >> ATOM 39 HD12 ILE A 26 20.793 20.083 20.424 0.019 1.487 >> ATOM 40 HG13 ILE A 26 21.552 20.401 23.402 0.024 1.487 >> ATOM 41 HG22 ILE A 26 23.518 19.710 24.054 0.088 1.487 >> ATOM 42 HD11 ILE A 26 19.734 20.812 21.654 0.019 1.487 >> ATOM 43 HG21 ILE A 26 24.844 19.994 22.902 0.088 1.487 >> ATOM 44 N GLY A 27 25.346 21.441 20.740 -0.416 1.824 >> ATOM 45 CA GLY A 27 25.967 22.810 20.689 -0.025 1.908 >> ATOM 46 C GLY A 27 25.881 23.325 19.252 0.597 1.908 >> ATOM 47 O GLY A 27 25.258 24.368 18.941 -0.568 1.661 >> ATOM 48 HA3 GLY A 27 27.010 22.754 20.999 0.070 1.387 >> ATOM 49 H GLY A 27 25.916 20.646 20.989 0.272 0.600 >> ATOM 50 HA GLY A 27 25.439 23.486 21.361 0.070 1.387 >> ATOM 51 N ALA A 28 26.464 22.566 18.365 -0.416 1.824 >> ATOM 52 CA ALA A 28 26.464 22.821 16.913 0.034 1.908 >> ATOM 53 C ALA A 28 25.054 22.924 16.353 0.597 1.908 >> ATOM 54 O ALA A 28 24.728 23.841 15.561 -0.568 1.661 >> ATOM 55 CB ALA A 28 27.204 21.691 16.230 -0.183 1.908 >> ATOM 56 HB3 ALA A 28 27.330 21.925 15.173 0.060 1.487 >> ATOM 57 H ALA A 28 26.950 21.745 18.697 0.272 0.600 >> ATOM 58 HA ALA A 28 26.955 23.776 16.728 0.082 1.387 >> ATOM 59 HB2 ALA A 28 26.634 20.768 16.333 0.060 1.487 >> ATOM 60 HB1 ALA A 28 28.183 21.566 16.693 0.060 1.487 >> ATOM 61 N ALA A 29 24.207 21.956 16.745 -0.416 1.824 >> ATOM 62 CA ALA A 29 22.835 21.972 16.180 0.034 1.908 >> ATOM 63 C ALA A 29 22.040 23.179 16.660 0.597 1.908 >> ATOM 64 O ALA A 29 21.285 23.769 15.836 -0.568 1.661 >> ATOM 65 CB ALA A 29 22.109 20.655 16.465 -0.183 1.908 >> ATOM 66 HB3 ALA A 29 21.958 20.548 17.539 0.060 1.487 >> ATOM 67 H ALA A 29 24.494 21.243 17.401 0.272 0.600 >> ATOM 68 HA ALA A 29 22.923 22.068 15.098 0.082 1.387 >> ATOM 69 HB2 ALA A 29 22.708 19.822 16.097 0.060 1.487 >> ATOM 70 HB1 ALA A 29 21.142 20.657 15.961 0.060 1.487 >> ATOM 71 N SER A 30 22.130 23.529 17.952 -0.416 1.824 >> ATOM 72 CA SER A 30 21.294 24.711 18.383 -0.025 1.908 >> ATOM 73 C SER A 30 21.772 26.016 17.762 0.597 1.908 >> ATOM 74 O SER A 30 21.040 26.949 17.447 -0.568 1.661 >> ATOM 75 CB SER A 30 21.212 24.798 19.907 0.212 1.908 >> ATOM 76 OG SER A 30 22.528 25.088 20.378 -0.655 1.721 >> ATOM 77 HG SER A 30 22.868 24.333 20.864 0.428 0.000 >> ATOM 78 H SER A 30 22.723 23.030 18.600 0.272 0.600 >> ATOM 79 HA SER A 30 20.284 24.548 18.006 0.084 1.387 >> ATOM 80 HB2 SER A 30 20.866 23.850 20.319 0.035 1.387 >> ATOM 81 HB3 SER A 30 20.509 25.571 20.216 0.035 1.387 >> ATOM 82 N MET A 31 23.053 26.083 17.540 -0.416 1.824 >> ATOM 83 CA MET A 31 23.689 27.330 17.000 -0.024 1.908 >> ATOM 84 C MET A 31 23.345 27.428 15.549 0.597 1.908 >> ATOM 85 O MET A 31 22.943 28.475 15.021 -0.568 1.661 >> ATOM 86 CB MET A 31 25.217 27.123 17.193 0.034 1.908 >> ATOM 87 CG MET A 31 25.435 27.429 18.679 0.002 1.908 >> ATOM 88 SD MET A 31 26.027 29.166 18.675 -0.274 2.000 >> ATOM 89 CE MET A 31 27.784 28.762 18.463 -0.054 1.908 >> ATOM 90 HE3 MET A 31 28.115 29.086 17.476 0.068 1.387 >> ATOM 91 H MET A 31 23.631 25.278 17.735 0.272 0.600 >> ATOM 92 HA MET A 31 23.355 28.242 17.494 0.088 1.387 >> ATOM 93 HB2 MET A 31 25.786 27.809 16.566 0.024 1.487 >> ATOM 94 HG2 MET A 31 26.183 26.763 19.109 0.044 1.387 >> ATOM 95 HE2 MET A 31 27.924 27.685 18.559 0.068 1.387 >> ATOM 96 HB3 MET A 31 25.548 26.123 16.913 0.024 1.487 >> ATOM 97 HG3 MET A 31 24.535 27.288 19.278 0.044 1.387 >> ATOM 98 HE1 MET A 31 28.369 29.273 19.228 0.068 1.387 >> ATOM 99 N GLU A 32 23.528 26.285 14.864 0.000 0.000 >> ATOM 100 C GLU A 32 23.054 26.425 13.417 0.000 0.000 >> ATOM 101 C GLU A 32 21.595 26.777 13.352 0.000 0.000 >> ATOM 102 O GLU A 32 21.176 27.692 12.606 0.000 0.000 >> ATOM 103 C GLU A 32 23.341 25.159 12.644 0.000 0.000 >> ATOM 104 C GLU A 32 24.793 24.655 12.660 0.000 0.000 >> ATOM 105 H GLU A 32 25.138 24.507 11.637 0.000 0.000 >> ATOM 106 H GLU A 32 23.927 25.443 15.255 0.000 0.000 >> ATOM 107 H GLU A 32 23.608 27.243 12.957 0.000 0.000 >> ATOM 108 H GLU A 32 23.063 25.336 11.605 0.000 0.000 >> ATOM 109 H GLU A 32 24.844 23.710 13.201 0.000 0.000 >> ATOM 110 H GLU A 32 22.763 24.382 13.143 0.000 0.000 >> ATOM 111 H GLU A 32 25.427 25.391 13.154 0.000 0.000 >> ATOM 112 N PHE A 33 20.752 26.053 14.131 -0.416 1.824 >> ATOM 113 CA PHE A 33 19.304 26.419 14.182 -0.002 1.908 >> ATOM 114 C PHE A 33 19.109 27.896 14.516 0.597 1.908 >> ATOM 115 O PHE A 33 18.325 28.634 13.848 -0.568 1.661 >> ATOM 116 CB PHE A 33 18.492 25.486 15.111 -0.034 1.908 >> ATOM 117 CG PHE A 33 17.001 25.776 15.157 0.012 1.908 >> ATOM 118 CD1 PHE A 33 16.208 25.535 14.025 -0.126 1.908 >> ATOM 119 CD2 PHE A 33 16.394 26.279 16.298 -0.126 1.908 >> ATOM 120 CE1 PHE A 33 14.857 25.777 14.038 -0.170 1.908 >> ATOM 121 CE2 PHE A 33 15.024 26.522 16.361 -0.170 1.908 >> ATOM 122 CZ PHE A 33 14.255 26.274 15.213 -0.107 1.908 >> ATOM 123 HZ PHE A 33 13.182 26.467 15.230 0.130 1.459 >> ATOM 124 H PHE A 33 21.100 25.274 14.671 0.272 0.600 >> ATOM 125 HA PHE A 33 18.901 26.267 13.181 0.098 1.387 >> ATOM 126 HB2 PHE A 33 18.889 25.583 16.122 0.030 1.487 >> ATOM 127 HD1 PHE A 33 16.673 25.148 13.118 0.133 1.459 >> ATOM 128 HD2 PHE A 33 17.008 26.491 17.173 0.133 1.459 >> ATOM 129 HE1 PHE A 33 14.255 25.587 13.149 0.143 1.459 >> ATOM 130 HE2 PHE A 33 14.562 26.894 17.276 0.143 1.459 >> ATOM 131 HB3 PHE A 33 18.597 24.480 14.704 0.030 1.487 >> ATOM 132 N CYS A 34 19.723 28.330 15.596 -0.416 1.824 >> ATOM 133 CA CYS A 34 19.703 29.767 15.995 0.021 1.908 >> ATOM 134 C CYS A 34 19.908 30.765 14.838 0.597 1.908 >> ATOM 135 O CYS A 34 19.143 31.752 14.648 -0.568 1.661 >> ATOM 136 CB CYS A 34 20.718 29.985 17.127 -0.123 1.908 >> ATOM 137 SG CYS A 34 20.701 31.739 17.619 -0.312 2.000 >> ATOM 138 HG CYS A 34 21.752 32.367 17.074 0.193 0.600 >> ATOM 139 H CYS A 34 20.224 27.669 16.173 0.272 0.600 >> ATOM 140 HA CYS A 34 18.694 29.985 16.346 0.112 1.387 >> ATOM 141 HB2 CYS A 34 21.715 29.713 16.781 0.111 1.387 >> ATOM 142 HB3 CYS A 34 20.452 29.363 17.982 0.111 1.387 >> ATOM 143 N PHE A 35 20.901 30.534 13.997 -0.416 1.824 >> ATOM 144 CA PHE A 35 21.305 31.507 12.929 -0.002 1.908 >> ATOM 145 C PHE A 35 20.390 31.361 11.743 0.597 1.908 >> ATOM 146 O PHE A 35 20.027 32.391 11.201 -0.568 1.661 >> ATOM 147 CB PHE A 35 22.813 31.268 12.588 -0.034 1.908 >> ATOM 148 CG PHE A 35 23.662 31.873 13.708 0.012 1.908 >> ATOM 149 CD1 PHE A 35 23.510 33.247 13.990 -0.126 1.908 >> ATOM 150 CD2 PHE A 35 24.558 31.066 14.411 -0.126 1.908 >> ATOM 151 CE1 PHE A 35 24.241 33.795 15.049 -0.170 1.908 >> ATOM 152 CE2 PHE A 35 25.318 31.616 15.473 -0.170 1.908 >> ATOM 153 CZ PHE A 35 25.118 32.979 15.758 -0.107 1.908 >> ATOM 154 HZ PHE A 35 25.681 33.421 16.580 0.130 1.459 >> ATOM 155 H PHE A 35 21.410 29.665 14.077 0.272 0.600 >> ATOM 156 HA PHE A 35 21.205 32.539 13.267 0.098 1.387 >> ATOM 157 HB2 PHE A 35 23.057 31.747 11.640 0.030 1.487 >> ATOM 158 HD1 PHE A 35 22.838 33.867 13.396 0.133 1.459 >> ATOM 159 HD2 PHE A 35 24.673 30.016 14.144 0.133 1.459 >> ATOM 160 HE1 PHE A 35 24.126 34.846 15.315 0.143 1.459 >> ATOM 161 HE2 PHE A 35 26.024 31.012 16.042 0.143 1.459 >> ATOM 162 HB3 PHE A 35 23.013 30.200 12.501 0.030 1.487 >> ATOM 163 N ASP A 36 19.885 30.157 11.532 -0.516 1.824 >> ATOM 164 CA ASP A 36 18.776 30.042 10.532 0.038 1.908 >> ATOM 165 C ASP A 36 17.586 30.883 10.914 0.537 1.908 >> ATOM 166 O ASP A 36 16.975 31.568 10.060 -0.582 1.661 >> ATOM 167 CB ASP A 36 18.408 28.591 10.259 -0.030 1.908 >> ATOM 168 CG ASP A 36 19.407 27.873 9.364 0.799 1.908 >> ATOM 169 OD1 ASP A 36 20.298 28.500 8.781 -0.801 1.661 >> ATOM 170 OD2 ASP A 36 19.262 26.643 9.326 -0.801 1.661 >> ATOM 171 HB2 ASP A 36 17.431 28.566 9.777 -0.012 1.487 >> ATOM 172 H ASP A 36 20.233 29.348 12.025 0.294 0.600 >> ATOM 173 HA ASP A 36 19.146 30.447 9.590 0.088 1.387 >> ATOM 174 HB3 ASP A 36 18.406 28.074 11.218 -0.012 1.487 >> ATOM 175 N VAL A 37 17.163 30.722 12.174 -0.416 1.824 >> ATOM 176 CA VAL A 37 15.980 31.547 12.617 -0.087 1.908 >> ATOM 177 C VAL A 37 16.291 33.048 12.486 0.597 1.908 >> ATOM 178 O VAL A 37 15.433 33.885 12.098 -0.568 1.661 >> ATOM 179 CB VAL A 37 15.557 31.095 14.043 0.299 1.908 >> ATOM 180 CG1 VAL A 37 14.559 32.074 14.645 -0.319 1.908 >> ATOM 181 CG2 VAL A 37 14.944 29.674 14.023 -0.319 1.908 >> ATOM 182 HG23 VAL A 37 14.798 29.326 15.046 0.079 1.487 >> ATOM 183 H VAL A 37 17.617 30.075 12.802 0.272 0.600 >> ATOM 184 HA VAL A 37 15.120 31.381 11.968 0.097 1.387 >> ATOM 185 HB VAL A 37 16.456 31.077 14.659 -0.030 1.487 >> ATOM 186 HG13 VAL A 37 14.364 32.878 13.935 0.079 1.487 >> ATOM 187 HG22 VAL A 37 15.617 28.995 13.500 0.079 1.487 >> ATOM 188 HG12 VAL A 37 14.969 32.492 15.564 0.079 1.487 >> ATOM 189 HG21 VAL A 37 13.984 29.700 13.508 0.079 1.487 >> ATOM 190 HG11 VAL A 37 13.628 31.552 14.867 0.079 1.487 >> ATOM 191 N PHE A 38 17.483 33.411 12.929 -0.416 1.824 >> ATOM 192 CA PHE A 38 17.911 34.841 12.926 -0.002 1.908 >> ATOM 193 C PHE A 38 17.806 35.454 11.516 0.597 1.908 >> ATOM 194 O PHE A 38 17.258 36.547 11.372 -0.568 1.661 >> ATOM 195 CB PHE A 38 19.318 34.985 13.540 -0.034 1.908 >> ATOM 196 CG PHE A 38 19.672 36.438 13.773 0.012 1.908 >> ATOM 197 CD1 PHE A 38 18.970 37.189 14.703 -0.126 1.908 >> ATOM 198 CD2 PHE A 38 20.695 37.035 12.992 -0.126 1.908 >> ATOM 199 CE1 PHE A 38 19.276 38.541 14.938 -0.170 1.908 >> ATOM 200 CE2 PHE A 38 21.001 38.397 13.223 -0.170 1.908 >> ATOM 201 CZ PHE A 38 20.318 39.142 14.194 -0.107 1.908 >> > === message truncated ===> # >> # Note that most of the comments here were taken from sample >> # input files that came with APBS. You can find APBS at >> # http://agave.wustl.edu/apbs/ >> # Note that APBS is GPL'd code. >> # >> read >> mol pqr pymol-generated.pqr # read molecule 1 >> end >> elec >> mg-auto >> dime 193 193 161 # number of find grid points >> # calculated by psize.py >> cglen 111.564202 104.211702 79.228498 # coarse mesh lengths (A) >> fglen 85.626001 81.301001 66.604999 # fine mesh lengths (A) >> # calculated by psize.py >> cgcent 13.830001 30.882500 25.519499 # (could also give (x,y,z) form >> psize.py) #known center >> fgcent 13.830001 30.882500 25.519499 # (could also give (x,y,z) form >> psize.py) #known center >> npbe # solve the full nonlinear PBE with npbe >> #lpbe # solve the linear PBE with lpbe >> bcfl 1 # Boundary condition flag >> # 0 => Zero >> # 1 => Single DH sphere >> # 2 => Multiple DH spheres >> # 4 => Focusing >> # >> #ion 1 0.000 2.0 # Counterion declaration: >> ion 1 0.000000 2.000000 # Counterion declaration: >> ion -1 0.000000 2.000000 # ion >> ion 2 0.000000 2.000000 # ion >> ion -2 0.000000 2.000000 # ion >> pdie 20.000000 # Solute dielectric >> sdie 80.000000 # Solvent dielectric >> chgm 1 # Charge disc method >> # 0 is linear splines >> # 1 is cubic b-splines >> mol 1 # which molecule to use >> srfm 1 # Surface calculation method >> # 0 => Mol surface for epsilon; >> # inflated VdW for kappa; no >> # smoothing >> # 1 => As 0 with harmoic average >> # smoothing >> # 2 => Cubic spline >> srad 1.400000 # Solvent radius (1.4 for water) >> swin 0.3 # Surface cubic spline window .. default 0.3 >> temp 310.000000 # System temperature (298.15 default) >> gamma 0.105 # Surface tension parameter for apolar forces (in >> kJ/mol/A^2) >> # only used for force calculations, so we don't care, >> but >> # it's always required, and 0.105 is the default >> calcenergy 0 # Energy I/O to stdout >> # 0 => don't write out energy >> # 1 => write out total energy >> # 2 => write out total energy and all >> # components >> calcforce 0 # Atomic forces I/O (to stdout) >> # 0 => don't write out forces >> # 1 => write out net forces on molecule >> # 2 => write out atom-level forces >> write pot dx pymol-generated # What to write .. this says write the >> potential in dx >> # format to a file. >> end >> quit >> >>> _______________________________________________ >> apbs-users mailing list >> apbs-users@... >> http://cholla.wustl.edu/mailman/listinfo/apbs-users >> > > > -- > Assistant Professor, Dept. of Biochemistry and Molecular Biophysics > Washington University in St. Louis > http://cholla.wustl.edu > _______________________________________________ > apbs-users mailing list > apbs-users@... > http://cholla.wustl.edu/mailman/listinfo/apbs-users > > > ```