Running APBS calculations

APBS input Generation

After System Setup, APBS calculations are performed to obtain the relevant information. The input of the APBS calculations can be generated either automatically or manually.

Generation of APBS Input

Run APBS calculations and load the result

After the generation of the APBS input file (apbs_in='apbs.in'), the APBS calculation could be perfomed with rocklinc.RocklinCorrection.run_APBS() and the result is loaded to the object via rocklinc.RocklinCorrection.read_APBS().

For automatic APBS calculation:

import rocklinc
rc = rocklinc.RocklinCorrection(box, lig_netq, protein_netq, temp,
                                rocklinc.waters.TIP3P)
rc.make_APBS_input(u, 'resname LIG',)
rc.run_APBS()
rc.read_APBS()

For manual APBS calculation:

import rocklinc
rc = rocklinc.RocklinCorrection(box, lig_netq, protein_netq, temp,
                                rocklinc.waters.TIP3P)
rc.set_APBS_input(800, box, lig_netq, protein_netq,)
rc.run_APBS()
rc.read_APBS()
rocklinc.RocklinCorrection.run_APBS(self, apbs_exe='/opt/local/bin/apbs', apbs_in='apbs.in')

Running the APBS calculations, which is the same as

apbs apbs.in
Parameters

  • apbs_exe (str, optional) – The path to the APBS program. (/opt/local/bin/apbs)

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

  • apbs_out (str, optional) – The output file for the APBS calculation. (apbs.out)

rocklinc.RocklinCorrection.read_APBS(self, ligand_RIP_het='ligand_RIP_het.dx', protein_RIP_het='protein_RIP_het.dx', ligand_RIP_hom='ligand_RIP_hom.dx', IP=None, mean_IP=None)

Read the result from the APBS calculations.

Parameters

  • ligand_RIP_het (str, optional) – The APBS program output (ligand_RIP_het.dx).

  • protein_RIP_het (str, optional) – The APBS program output (protein_RIP_het.dx).

  • ligand_RIP_hom (str, optional) – The APBS program output (ligand_RIP_hom.dx).

  • IP (float, optional) – If system only has ligand, set the integrated potential of protein to 0.

After loading the results from APBS calculation, the result is summarised and can be written into a text file.