Compiling Results

After the APBS calculations, the result could be return via the rocklinc.RocklinCorrection.compute() and the detailed break down could be written to a text file with rocklinc.RocklinCorrection.write().

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()
result = rc.compute()
rc.write('correction.txt')

result is the correction energy and ‘correction.txt’ has the format:

The total correction energy is: 2.62 kJ/mol or 0.63 kCal/mol
= ΔΔG_ANA(L): 2.62 kJ/mol + ΔΔG_DSC(L): 0.00 kJ/mol
ΔΔG_ANA(L) = ΔΔG_NET(L) + ΔΔG_USV(L) + ΔΔG_RIP(L) + ΔΔG_EMP(L)
ΔΔG_NET(L) = 98.55 kJ/mol
ΔΔG_NET(L) + ΔΔG_USV(L) = 1.02 kJ/mol
ΔΔG_RIP(L) = 1.61 kJ/mol
ΔΔG_EMP(L) = -0.00 kJ/mol

rocklinc.RocklinCorrection.compute(self, NS=None)

Compute the result.

Parameters

NS (int, optional) – Rest the number of solvent molecules.

Returns

results – The total correction free energy in cal/mol.

Return type

float

rocklinc.RocklinCorrection.write(self, outfile)

Write the decomposed results

Parameters

outfile (str) – The output file name.