Re: [Apbs-users] APBS-PyMol on Windows 'pymol-generated.dx' file does not exist
Biomolecular electrostatics software
Brought to you by:
sobolevnrm
From: Roland S. <rol...@gm...> - 2008-12-25 11:52:22
|
# # 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 C:\Users\Roland\Desktop\polyB-Hamada\polyB-Opalp.pqr # read molecule 1 end elec mg-auto dime 129 65 65 # number of find grid points # calculated by psize.py cglen 73.373702 30.231100 30.479300 # coarse mesh lengths (A) fglen 63.161001 30.231100 30.479300 # fine mesh lengths (A) # calculated by psize.py cgcent 2.390500 0.701500 0.250500 # (could also give (x,y,z) form psize.py) #known center fgcent 2.390500 0.701500 0.250500 # (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 sdh # 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 <charge> <conc (M)> <radius> ion 2 0.000000 2.000000 # ion <charge> <conc (M)> <radius> ion -2 0.000000 2.000000 # ion <charge> <conc (M)> <radius> pdie 2.000000 # Solute dielectric sdie 80.000000 # Solvent dielectric chgm spl2 # Charge disc method # 0 is linear splines # 1 is cubic b-splines mol 1 # which molecule to use srfm smol # 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) sdens 10.000000 # Specify the number of grid points per square-angstrom to use in Vacc object. Ignored when srad is 0.0 (see srad) or srfm is spl2 (see srfm). There is a direct correlation between the value used for the Vacc sphere density, the accuracy of the Vacc object, and the APBS calculation time. APBS default value is 10.0. 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 no # 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 no # 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 |