Re: [apbs-users] cgcent and fgcent
Biomolecular electrostatics software
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From: Baker, N. <Nat...@pn...> - 2011-10-12 21:38:43
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Hello – I’m sorry but I didn’t write that tutorial and therefore can’t comment on the expected results. I would recommend trying one of the examples distributed with APBS and/or provided at http://www.poissonboltzmann.org/ to get started with the software. Thanks, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: 509-375-3997 http://kdi.pnl.gov/bios/baker.stm From: susie [mailto:sus...@gm...] Sent: Tuesday, October 11, 2011 10:34 AM To: apb...@go... Subject: Re: [apbs-users] cgcent and fgcent Thank you for your reply. I calculated the electrostatic energy for a sodium ion and a cloride ion at several distances along the pore (like in the tutorial) and obtained two plots with the same shape, and completely different shape from the one in the tutorial. I was wondering what am I doing wrong? This is my input file: (I also attached one of the profiles with the energies). Many thanks in advance. read mol pqr pore.pqr mol pqr ion.pqr mol pqr complex.pqr end elec name pore mg-auto dime 161 161 161 cglen 110.0000 110.0000 115.0000 fglen 10 10 10 cgcent mol 3 fgcent mol 2 mol 1 lpbe bcfl sdh 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 write pot dx pot end elec name na mg-auto mol 2 dime 161 161 161 cglen 110.000000 110.000000 115.000000 fglen 10 10 10 cgcent mol 3 fgcent mol 2 # NaCl ionic strength in mol/l ion 1 0.15 0.95 # sodium ions ion -1 0.15 1.81 # chloride ions lpbe bcfl mdh pdie 2.0 # protein and faux-lipid sdie 78.5 # Eisenberg and Crothers Phys. Chem. book 1979 srfm smol chgm spl2 srad 1.4 swin 0.3 sdens 10.0 temp 300 # gamma 0.105 # Uncomment for old versions of APBS -- deprecated for APBS 1.0.0 calcenergy total calcforce no end elec name cpx mg-auto mol 3 dime 161 161 161 cglen 110.000000 110.000000 115.000000 fglen 10 10 10 cgcent mol 3 fgcent mol 2 # NaCl ionic strength in mol/l ion 1 0.15 0.95 # sodium ions ion -1 0.15 1.81 # chloride ions lpbe bcfl mdh pdie 2.0 # protein and faux-lipid sdie 78.5 # Eisenberg and Crothers Phys. Chem. book 1979 srfm smol chgm spl2 srad 1.4 swin 0.3 sdens 10.0 temp 300 # gamma 0.105 # Uncomment for old versions of APBS -- deprecated for APBS 1.0.0 calcenergy total calcforce no end print energy cpx - na - pore end quit |