Manual Generation of APBS Input Files

The APBS input could be set manually as well. Three pqr files ( prot_only.pqr, lig_in_prot.pqr, lig_only.pqr) has to be generated according to the original definition from . For a system that has 800 water molecules, the files could be feed to the object via rocklinc.RocklinCorrection.set_APBS_input()

import rocklinc
rc = rocklinc.RocklinCorrection(box, lig_netq, protein_netq, temp,
                                rocklinc.waters.TIP3P)
rc.set_APBS_input(800, box, lig_netq, protein_netq,)
rocklinc.RocklinCorrection.set_APBS_input(self, NS, box=None, qL=None, qP=None, in_prot_only='prot_only.pqr', in_lig_in_prot='lig_in_prot.pqr', in_lig_only='lig_only.pqr', apbs_in='apbs.in')

Manually set the input file for the APBS calculations.

Parameters

  • NS (int) – The number of solvent molecule in the system.

  • box (array, optional) – The unitcell dimensions of the system [lx, ly, lz] for APBS calculations.

  • qL (float, optional) – The unit charge of the ligand.

  • qP (float, optional) – The unit charge of the protein.

  • in_prot_only (str, optional) – The name of the pqr file where the ligand has no partial charge. (prot_only.pqr)

  • in_lig_in_prot (str, optional) – The name of the pqr file where the protein has no partial charge. (lig_in_prot.pqr)

  • in_lig_only (str, optional) – The name of the pqr file of the ligand. (lig_only.pqr)

  • apbs_in (str, optional) – The input file to the APBS program. (apbs.in)

The next step is to run the APBS calculations.