[Apbs-users] reading dx files From: - 2009-10-12 23:15:27 Attachments: Message as HTML ```Hello, My problem, is to calculate solvation energy from a charge, placed in a center of a sphere. The easiest way to do this, would simply be to add an ion with a certain radius in the pqr file. My goal however, is to change the shape of the sphere in the future. As far as I understand, this requires a change in potential maps - dx files. I generate a dx file - a space, where dielectric constant equals 80 (solvent), with a bowl, where dielectric constant equals 1 (solute). Later, I implement such map in apbs input file, together with the pqr file, so that the charge is placed in the center of the bowl. As I run APBS calculation, everything seems to be fine. The problem occures later: nomather how I change the shape of my solute (my dx file), the energy remains the same. It seems that APBS is not reading my maps although it says it does. Since I am a newbie, perhaps I am missing something obvious in my calculations. below, I include my APBS input file and the pqr file. I would be grateful for any help Przemek pqr: ATOM 1 I ION 1 4.000 4.000 4.000 1.00 3 input file: read mol pqr ion.pqr diel dx xBowl_65_1_80.dx yBowl_65_1_80.dx zBowl_65_1_80.dx # diel dx xElips_33_1_80.dx yElips_33_1_80.dx zElips_33_1_80.dx end elec name solv # Electrostatics calculation on the solvated state mg-manual # Specify the mode for APBS to run dime 129 129 129 # The grid dimensions nlev 4 # Multigrid level parameter grid 0.33 0.33 0.33 # Grid spacing gcent mol 1 # Center the grid on molecule 1 mol 1 # Perform the calculation on molecule 1 lpbe # Solve the linearized Poisson-Boltzmann # equation bcfl mdh # Use all multipole moments when calculating the # potential pdie 1.0 # Solute dielectric sdie 80 # Solvent dielectric chgm spl2 # Spline-based discretization of the delta # functions srfm mol # Molecular surface definition srad 1.4 # Solvent probe radius (for molecular surface) swin 0.3 # Solvent surface spline window (not used here) sdens 10.0 # Sphere density of accessibility object temp 298.15 # Temperature gamma 0.105 # Apolar energy surface coefficient (not used here) calcenergy total # Calculate energies calcforce no # Do not calculate forces #write pot dx potential-RADIUS # Write out the potential #write dielx dx mapax end elec name ref # Calculate potential for reference (vacuum) state mg-manual dime 129 129 129 nlev 1 grid 0.33 0.33 0.33 gcent mol 1 mol 1 lpbe bcfl mdh pdie 1.0 # The solvent and solute dielectric constants are # equal sdie 1.0 # The solvent and solute dielectric constants are # equal chgm spl2 srfm mol srad 1.4 swin 0.3 sdens 10.0 temp 298.15 gamma 0.105 calcenergy total calcforce no # write diely dx mapay # write dielz dx mapaz # write kappa dx kappa end print energy solv - ref end quit ```

 [Apbs-users] reading dx files From: - 2009-10-12 23:15:27 Attachments: Message as HTML ```Hello, My problem, is to calculate solvation energy from a charge, placed in a center of a sphere. The easiest way to do this, would simply be to add an ion with a certain radius in the pqr file. My goal however, is to change the shape of the sphere in the future. As far as I understand, this requires a change in potential maps - dx files. I generate a dx file - a space, where dielectric constant equals 80 (solvent), with a bowl, where dielectric constant equals 1 (solute). Later, I implement such map in apbs input file, together with the pqr file, so that the charge is placed in the center of the bowl. As I run APBS calculation, everything seems to be fine. The problem occures later: nomather how I change the shape of my solute (my dx file), the energy remains the same. It seems that APBS is not reading my maps although it says it does. Since I am a newbie, perhaps I am missing something obvious in my calculations. below, I include my APBS input file and the pqr file. I would be grateful for any help Przemek pqr: ATOM 1 I ION 1 4.000 4.000 4.000 1.00 3 input file: read mol pqr ion.pqr diel dx xBowl_65_1_80.dx yBowl_65_1_80.dx zBowl_65_1_80.dx # diel dx xElips_33_1_80.dx yElips_33_1_80.dx zElips_33_1_80.dx end elec name solv # Electrostatics calculation on the solvated state mg-manual # Specify the mode for APBS to run dime 129 129 129 # The grid dimensions nlev 4 # Multigrid level parameter grid 0.33 0.33 0.33 # Grid spacing gcent mol 1 # Center the grid on molecule 1 mol 1 # Perform the calculation on molecule 1 lpbe # Solve the linearized Poisson-Boltzmann # equation bcfl mdh # Use all multipole moments when calculating the # potential pdie 1.0 # Solute dielectric sdie 80 # Solvent dielectric chgm spl2 # Spline-based discretization of the delta # functions srfm mol # Molecular surface definition srad 1.4 # Solvent probe radius (for molecular surface) swin 0.3 # Solvent surface spline window (not used here) sdens 10.0 # Sphere density of accessibility object temp 298.15 # Temperature gamma 0.105 # Apolar energy surface coefficient (not used here) calcenergy total # Calculate energies calcforce no # Do not calculate forces #write pot dx potential-RADIUS # Write out the potential #write dielx dx mapax end elec name ref # Calculate potential for reference (vacuum) state mg-manual dime 129 129 129 nlev 1 grid 0.33 0.33 0.33 gcent mol 1 mol 1 lpbe bcfl mdh pdie 1.0 # The solvent and solute dielectric constants are # equal sdie 1.0 # The solvent and solute dielectric constants are # equal chgm spl2 srfm mol srad 1.4 swin 0.3 sdens 10.0 temp 298.15 gamma 0.105 calcenergy total calcforce no # write diely dx mapay # write dielz dx mapaz # write kappa dx kappa end print energy solv - ref end quit ```
 Re: [Apbs-users] reading dx files From: Nathan Baker - 2009-10-13 12:59:55 Attachments: Message as HTML ```Hello -- It appears that you've forgotten to include the "usemap" http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#usemap command in your input file. -- Nathan On Oct 12, 2009, at 6:15 PM, wrote: > Hello, > > My problem, is to calculate solvation energy from a charge, placed > in a center of a sphere. > The easiest way to do this, would simply be to add an ion with a > certain radius in the pqr file. My goal however, is to change the > shape of the sphere in the future. > As far as I understand, this requires a change in potential maps - > dx files. > I generate a dx file - a space, where dielectric constant equals 80 > (solvent), with a bowl, where dielectric constant equals 1 (solute). > Later, I implement such map in apbs input file, together with the > pqr file, so that the charge is placed in the center of the bowl. > > As I run APBS calculation, everything seems to be fine. > The problem occures later: nomather how I change the shape of my > solute (my dx file), the energy remains the same. It seems that APBS > is not reading my maps although it says it does. > > Since I am a newbie, perhaps I am missing something obvious in my > calculations. > > below, I include my APBS input file and the pqr file. > > I would be grateful for any help > Przemek > > > pqr: > ATOM 1 I ION 1 4.000 4.000 4.000 1.00 3 > > input file: > > read > mol pqr ion.pqr > diel dx xBowl_65_1_80.dx yBowl_65_1_80.dx zBowl_65_1_80.dx > # diel dx xElips_33_1_80.dx yElips_33_1_80.dx zElips_33_1_80.dx > end > > elec name solv # Electrostatics calculation on the > solvated state > > mg-manual # Specify the mode for APBS to run > dime 129 129 129 # The grid dimensions > nlev 4 # Multigrid level parameter > grid 0.33 0.33 0.33 # Grid spacing > gcent mol 1 # Center the grid on molecule 1 > mol 1 # Perform the calculation on molecule 1 > lpbe # Solve the linearized Poisson-Boltzmann > # equation > bcfl mdh # Use all multipole moments when > calculating the > # potential > pdie 1.0 # Solute dielectric > sdie 80 # Solvent dielectric > chgm spl2 # Spline-based discretization of the delta > # functions > srfm mol # Molecular surface definition > srad 1.4 # Solvent probe radius (for molecular > surface) > swin 0.3 # Solvent surface spline window (not used > here) > sdens 10.0 # Sphere density of accessibility object > temp 298.15 # Temperature > gamma 0.105 # Apolar energy surface coefficient (not > used here) > calcenergy total # Calculate energies > calcforce no # Do not calculate forces > #write pot dx potential-RADIUS > # Write out the potential > #write dielx dx mapax > > end > > elec name ref # Calculate potential for reference > (vacuum) state > > mg-manual > dime 129 129 129 > nlev 1 > grid 0.33 0.33 0.33 > gcent mol 1 > mol 1 > lpbe > bcfl mdh > pdie 1.0 # The solvent and solute dielectric > constants are > # equal > sdie 1.0 # The solvent and solute dielectric > constants are > # equal > chgm spl2 > srfm mol > srad 1.4 > swin 0.3 > sdens 10.0 > temp 298.15 > gamma 0.105 > calcenergy total > calcforce no > > # write diely dx mapay > # write dielz dx mapaz > # write kappa dx kappa > > end > > print > > energy solv - ref > > end > > quit > > > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart > your > developing skills, take BlackBerry mobile applications to market and > stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference_______________________________________________ > apbs-users mailing list > apbs-users@... > https://lists.sourceforge.net/lists/listinfo/apbs-users — Nathan Baker (baker@...) Associate Professor, Dept. of Biochemistry and Molecular Biophysics Director, Computational and Molecular Biophysics Graduate Program Center for Computational Biology, Washington University in St. Louis Web: http://bakergroup.wustl.edu/ ```
 Re: [Apbs-users] reading dx files From: Gernot Kieseritzky - 2009-10-14 08:29:33 ```Hi! Am Dienstag, den 13.10.2009, 01:15 +0200 schrieb przemekbartha@...: > Hello, > > As I run APBS calculation, everything seems to be fine. > The problem occures later: nomather how I change the shape of my > solute (my dx file), the energy remains the same. It seems that APBS > is not reading my maps although it says it does. It's not enough to just load the maps: You forgot to use the "usemap" keyword: http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#usemap Adding the line "usemap diel 1" in both "ELEC" sections of your example should solve the problem. Best regards, Gernot Kieseritzky ```