Re: [apbs-users] Titration Curves using the single site approximation
Biomolecular electrostatics software
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From: Murga, L. <l....@no...> - 2017-06-27 20:56:50
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Just in case, I am including here the UHBD script that we would use in this case: read mol 1 file "pkaSH.pdb" pdb end ====> coordinates of the protein read mol 2 file "sitesinpr.pdb" pdb end =====> coordinates of the atoms of ionizable residues set charge radii file "pkaS.dat" para mine end edit all charge 0. end edit charge 1. atnum 1 end read grid epsi binary file "coarse.epsi" end read grid epsj binary file "coarse.epsj" end read grid epsk binary file "coarse.epsk" end elec calc mol 1 bcflag 2 solver 0 reps nmap 1.4 nsph 500 maxits 300 temp 293.0 sdie 80.00 pdie 20.00 ionstr 150.000 rion 2.00 end print elec phizero all end print elec phisave all end elec calc mol 1 bcflag 4 solver 0 spacing 1.20 dime 15 15 15 gcenter 24.704 20.926 27.944 nmap 1.4 nsph 500 maxits 300 temp 293.0 sdie 80.00 pdie 20.00 ionstr 150.000 rion 2.00 end print elec phisave all end elec calc mol 1 bcflag 4 solver 0 spacing 0.75 dime 15 15 15 gcenter 24.704 20.926 27.944 nmap 1.4 nsph 500 samsrf maxits 300 temp 293.0 sdie 80.00 pdie 20.00 ionstr 150.000 rion 2.00 end print elec phisave all end elec calc mol 1 bcflag 4 solver 0 spacing 0.25 dime 20 20 20 gcenter 24.704 20.926 27.944 nmap 1.4 nsph 500 samsrf maxits 300 temp 293.0 sdie 80.00 pdie 20.00 ionstr 150.000 rion 2.00 end Thanks! Leonel ________________________________ From: Murga, Leonel <l....@no...> Sent: Tuesday, June 27, 2017 3:46:21 PM To: apb...@li... Subject: [apbs-users] Titration Curves using the single site approximation Hello all, For years our group has been using UHBD to calculate titration curves using the single site approximation. Under this approximation, a +1 charge is located in a particular atom of an ionizable group of a protein (for example at the C of the COOH group of an aspartate or the N of the Lysine) while all the other charges are set to zero; then, the potentials that this charge creates at the other ionizable groups in the protein are calculated via the PB equation. These are sometimes called interaction potential. The process is carried on until all the interaction potentials created by placing at +1 charge on each ionizable group of the protein have been calculated. The potentials are then used for the calculation of titration curves using one of several methodologies available. For large proteins the use of a fine enough grid (~0.25 Ang) is not feasible because of the computational cost it represents. Even more so in the above situation in which the PBE has to be solved once for each ionizable residue in the protein. For these cases UHBD uses focusing. In essence, the PB equation is solved once using a coarse grid (~2.0 to 2.5 Ang) centered at the protein center in an initial step. In additional calculations, increasingly finer grids are placed and centered at the atom where the +1 charge was located and the PB equation is solved. This process is repeated until the finest grid is reached. The electrostatic potentials are then calculated at each atomic position in the protein including where the +1 charge is located. We have tried to implement these algorithm in APBS without success. Here is a section of the input script for APBS for calculating the interaction potentials for the first ionizable group in a protein (this would actually corresponds to the N atom of the N-terminus): read mol pqr pkaSH.pqr ====> protein in its neutral state mol pqr pkaSH_Mod.pqr =====> protein with all charges set to zero except a +1 charge on the first ionizable mol pqr chargeaa_Mod.pqr =======> this is the isolated ionizable used in a later calculation that is not included here. end elec name prot-coarse mg-manual dime 129 129 129 grid 1.00 1.00 1.00 gcent mol 2 mol 2 lpbe bcfl sdh ion charge 1 conc 0.150 radius 2.0 ion charge -1 conc 0.150 radius 2.0 pdie 20.0000 sdie 80.0000 srfm smol chgm spl2 sdens 10.00 srad 1.40 swin 0.30 temp 298.15 calcforce no end elec name prot-fine1 mg-manual dime 97 97 97 grid 0.5 0.5 0.5 gcent 24.704 20.926 27.944 ======> These are the coordinates of the N atom of the first ionizable group mol 2 lpbe bcfl focus ion charge 1 conc 0.150 radius 2.0 ion charge -1 conc 0.150 radius 2.0 pdie 20.0000 sdie 80.0000 srfm smol chgm spl2 sdens 10.00 srad 1.40 swin 0.30 temp 298.15 calcforce no end elec name prot-fine2 mg-manual dime 65 65 65 grid 0.25 0.25 0.25 gcent 24.704 20.926 27.944 mol 2 lpbe bcfl focus ion charge 1 conc 0.150 radius 2.0 ion charge -1 conc 0.150 radius 2.0 pdie 20.0000 sdie 80.0000 srfm smol chgm spl2 sdens 10.00 srad 1.40 swin 0.30 temp 298.15 calcenergy total calcforce no write pot dx pot_mulgr_pr end The pot_mulgr_pr file is written without any problems. We then use the multivalue program in the utils folder asking it to calculate the potentials at all the atomic positions and here is what we get (this is only a small section): 2.622700e+01,1.271200e+01,2.357900e+01,-1.649562e+18 2.608400e+01,1.166200e+01,2.258300e+01,NaN 2.535400e+01,1.046600e+01,2.321300e+01,NaN 2.533700e+01,1.031000e+01,2.443700e+01,NaN 2.711200e+01,1.272300e+01,2.407800e+01,-1.460145e+18 2.480500e+01,9.537000e+00,2.245400e+01,NaN 2.405200e+01,8.386000e+00,2.297400e+01,NaN 2.489700e+01,7.502000e+00,2.384900e+01,NaN 2.450400e+01,7.220000e+00,2.497200e+01,NaN 2.350600e+01,7.549000e+00,2.179300e+01,NaN 2.274100e+01,6.293000e+00,2.218200e+01,NaN 2.224200e+01,5.559000e+00,2.093100e+01,NaN 2.331900e+01,5.176000e+00,2.003700e+01,NaN 2.393100e+01,3.984000e+00,2.008300e+01,NaN 2.362200e+01,3.034000e+00,2.096100e+01,NaN 2.489500e+01,3.751000e+00,1.919900e+01,NaN 2.475500e+01,9.746000e+00,2.147200e+01,NaN 2.345400e+01,5.790000e+00,1.926600e+01,NaN 2.296200e+01,3.182000e+00,2.172500e+01,NaN 2.411300e+01,2.152000e+00,2.095500e+01,NaN 2.535300e+01,2.849000e+00,1.918600e+01,NaN Almost every potential comes as NaN. In UHBD this process works without any problems. What am I doing wrong? Thanks for your help! Leonel Murga |