Thread: [Apbs-users] Unusually large potential values
Biomolecular electrostatics software
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From: safwat abdel-a. <saf...@gm...> - 2011-09-01 09:55:53
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Hi APBS users, I am trying to calculate the solvation contribution to the ligand binding, I had this warning: focusFillBound: WARNING! Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! I tried linear and non-linear solutions also I used 1.2.1 and 1.3 version of APBS. Best regards Safwat Here is my input: read mol pqr holo-wt-ral-qmmm-mini-complex.pqr mol pqr Ral.pqr mol pqr holo-wt-ral-qmmm-mini-receptor.pqr end # COMPLEX -- SOLVATED STATE (FOCUSING) elec name complex-solv mg-auto dime 161 193 161 # number of find grid points cglen 112.757597 130.386602 125.512701 # coarse mesh lengths (A) fglen 86.327998 96.698001 93.831000 # fine mesh lengths (A) cgcent mol 2 fgcent mol 2 mol 1 npbe bcfl mdh ion charge 1 conc 0.150 radius 2.0 ion charge -1 conc 0.150 radius 2.0 pdie 2.0000 sdie 78.5400 srfm smol chgm spl2 sdens 10.00 srad 1.40 swin 0.30 temp 298.15 calcenergy total calcforce no end elec name complex-ref mg-auto dime 161 193 161 # number of find grid points cglen 112.757597 130.386602 125.512701 # coarse mesh lengths (A) fglen 86.327998 96.698001 93.831000 # fine mesh lengths (A) cgcent mol 2 fgcent mol 2 mol 1 npbe bcfl mdh ion charge 1 conc 0.150 radius 2.0 ion charge -1 conc 0.150 radius 2.0 pdie 2.0000 sdie 2.000 srfm smol chgm spl2 sdens 10.00 srad 1.40 swin 0.30 temp 298.15 calcenergy total calcforce no end # DMSO -- SOLVATED STATE (FOCUSING) elec name lig-solv mg-auto dime 161 193 161 # number of find grid points cglen 112.757597 130.386602 125.512701 # coarse mesh lengths (A) fglen 86.327998 96.698001 93.831000 # fine mesh lengths (A) cgcent mol 2 fgcent mol 2 mol 2 npbe bcfl mdh ion charge 1 conc 0.150 radius 2.0 ion charge -1 conc 0.150 radius 2.0 pdie 2.0000 sdie 78.5400 srfm smol chgm spl2 sdens 10.00 srad 1.40 swin 0.30 temp 298.15 calcenergy total calcforce no end elec name lig-ref mg-auto dime 161 193 161 # number of find grid points cglen 112.757597 130.386602 125.512701 # coarse mesh lengths (A) fglen 86.327998 96.698001 93.831000 cgcent mol 2 fgcent mol 2 mol 2 npbe bcfl mdh ion charge 1 conc 0.150 radius 2.0 ion charge -1 conc 0.150 radius 2.0 pdie 2.0000 sdie 2.000 srfm smol chgm spl2 sdens 10.00 srad 1.40 swin 0.30 temp 298.15 calcenergy total calcforce no end # 1D7H -- SOLVATED STATE (FOCUSING) elec name ptn-solv mg-auto dime 161 193 161 # number of find grid points cglen 112.757597 130.386602 125.512701 # coarse mesh lengths (A) fglen 86.327998 96.698001 93.831000 cgcent mol 2 fgcent mol 2 mol 3 npbe bcfl mdh ion charge 1 conc 0.150 radius 2.0 ion charge -1 conc 0.150 radius 2.0 pdie 2.0000 sdie 78.5400 srfm smol chgm spl2 sdens 10.00 srad 1.40 swin 0.30 temp 298.15 calcenergy total calcforce no end elec name ptn-ref mg-auto dime 161 193 161 # number of find grid points cglen 112.757597 130.386602 125.512701 # coarse mesh lengths (A) fglen 86.327998 96.698001 93.831000 cgcent mol 2 fgcent mol 2 mol 3 npbe bcfl mdh ion charge 1 conc 0.150 radius 2.0 ion charge -1 conc 0.150 radius 2.0 pdie 2.0000 sdie 2.000 srfm smol chgm spl2 sdens 10.00 srad 1.40 swin 0.30 temp 298.15 calcenergy total calcforce no end # COMPLEX SOLVATION ENERGY print elecEnergy complex-solv - complex-ref end # DMSO SOLVATION ENERGY print elecEnergy lig-solv - lig-ref end # 1D7H SOLVATION ENERGY print elecEnergy ptn-solv - ptn-ref end # CHANGE IN SOLVATION ENERGY UPON BINDING print elecEnergy complex-solv - complex-ref - lig-solv + lig-ref - ptn-solv + ptn-ref end quit -- ----------------------------------------------------------- Safwat Abdel-Azeim, PhD Computational Chemistry Laboratoire de Biologie et Pharmacologie Appliquées (LBPA) Ecole Normale Supérieure de Cachan 61, avenue du Président Wilson 94235 Cachan cedex Tel: +33(0)147407749 Cell phone: +33(0)6 29 68 18 71 WEB: http://www.lbpa.ens-cachan.fr/version-francaise/equipes/bioinformatique-modelisation-et-dynamique-moleculaire-bimodym-/ |
From: Baker, N. <Nat...@pn...> - 2011-09-02 00:25:41
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Hello - Did the calculation converge to a reasonable answer? You might check this by making small changes to the grid lengths and see if the changes in energies are correspondingly small. If so, then this warning can be safely ignored. Thanks, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: 509-375-3997 http://kdi.pnl.gov/bios/baker.stm From: safwat abdel-azeim [mailto:saf...@gm...] Sent: Thursday, September 01, 2011 2:56 AM To: apb...@li... Subject: [Apbs-users] Unusually large potential values Hi APBS users, I am trying to calculate the solvation contribution to the ligand binding, I had this warning: focusFillBound: WARNING! Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! I tried linear and non-linear solutions also I used 1.2.1 and 1.3 version of APBS. Best regards Safwat Here is my input: read mol pqr holo-wt-ral-qmmm-mini-complex.pqr mol pqr Ral.pqr mol pqr holo-wt-ral-qmmm-mini-receptor.pqr end # COMPLEX -- SOLVATED STATE (FOCUSING) elec name complex-solv mg-auto dime 161 193 161 # number of find grid points cglen 112.757597 130.386602 125.512701 # coarse mesh lengths (A) fglen 86.327998 96.698001 93.831000 # fine mesh lengths (A) cgcent mol 2 fgcent mol 2 mol 1 npbe bcfl mdh ion charge 1 conc 0.150 radius 2.0 ion charge -1 conc 0.150 radius 2.0 pdie 2.0000 sdie 78.5400 srfm smol chgm spl2 sdens 10.00 srad 1.40 swin 0.30 temp 298.15 calcenergy total calcforce no end elec name complex-ref mg-auto dime 161 193 161 # number of find grid points cglen 112.757597 130.386602 125.512701 # coarse mesh lengths (A) fglen 86.327998 96.698001 93.831000 # fine mesh lengths (A) cgcent mol 2 fgcent mol 2 mol 1 npbe bcfl mdh ion charge 1 conc 0.150 radius 2.0 ion charge -1 conc 0.150 radius 2.0 pdie 2.0000 sdie 2.000 srfm smol chgm spl2 sdens 10.00 srad 1.40 swin 0.30 temp 298.15 calcenergy total calcforce no end # DMSO -- SOLVATED STATE (FOCUSING) elec name lig-solv mg-auto dime 161 193 161 # number of find grid points cglen 112.757597 130.386602 125.512701 # coarse mesh lengths (A) fglen 86.327998 96.698001 93.831000 # fine mesh lengths (A) cgcent mol 2 fgcent mol 2 mol 2 npbe bcfl mdh ion charge 1 conc 0.150 radius 2.0 ion charge -1 conc 0.150 radius 2.0 pdie 2.0000 sdie 78.5400 srfm smol chgm spl2 sdens 10.00 srad 1.40 swin 0.30 temp 298.15 calcenergy total calcforce no end elec name lig-ref mg-auto dime 161 193 161 # number of find grid points cglen 112.757597 130.386602 125.512701 # coarse mesh lengths (A) fglen 86.327998 96.698001 93.831000 cgcent mol 2 fgcent mol 2 mol 2 npbe bcfl mdh ion charge 1 conc 0.150 radius 2.0 ion charge -1 conc 0.150 radius 2.0 pdie 2.0000 sdie 2.000 srfm smol chgm spl2 sdens 10.00 srad 1.40 swin 0.30 temp 298.15 calcenergy total calcforce no end # 1D7H -- SOLVATED STATE (FOCUSING) elec name ptn-solv mg-auto dime 161 193 161 # number of find grid points cglen 112.757597 130.386602 125.512701 # coarse mesh lengths (A) fglen 86.327998 96.698001 93.831000 cgcent mol 2 fgcent mol 2 mol 3 npbe bcfl mdh ion charge 1 conc 0.150 radius 2.0 ion charge -1 conc 0.150 radius 2.0 pdie 2.0000 sdie 78.5400 srfm smol chgm spl2 sdens 10.00 srad 1.40 swin 0.30 temp 298.15 calcenergy total calcforce no end elec name ptn-ref mg-auto dime 161 193 161 # number of find grid points cglen 112.757597 130.386602 125.512701 # coarse mesh lengths (A) fglen 86.327998 96.698001 93.831000 cgcent mol 2 fgcent mol 2 mol 3 npbe bcfl mdh ion charge 1 conc 0.150 radius 2.0 ion charge -1 conc 0.150 radius 2.0 pdie 2.0000 sdie 2.000 srfm smol chgm spl2 sdens 10.00 srad 1.40 swin 0.30 temp 298.15 calcenergy total calcforce no end # COMPLEX SOLVATION ENERGY print elecEnergy complex-solv - complex-ref end # DMSO SOLVATION ENERGY print elecEnergy lig-solv - lig-ref end # 1D7H SOLVATION ENERGY print elecEnergy ptn-solv - ptn-ref end # CHANGE IN SOLVATION ENERGY UPON BINDING print elecEnergy complex-solv - complex-ref - lig-solv + lig-ref - ptn-solv + ptn-ref end quit -- ----------------------------------------------------------- Safwat Abdel-Azeim, PhD Computational Chemistry Laboratoire de Biologie et Pharmacologie Appliquées (LBPA) Ecole Normale Supérieure de Cachan 61, avenue du Président Wilson 94235 Cachan cedex Tel: +33(0)147407749 Cell phone: +33(0)6 29 68 18 71 WEB:http://www.lbpa.ens-cachan.fr/version-francaise/equipes/bioinformatique-modelisation-et-dynamique-moleculaire-bimodym-/ |