Coloring molecule with RESP charge on pymol #Pymol

To visualize 3D structure of molecule, PyMol is nice tool. What I would like to write on the post is how to visualize calculated RESP charge on pymol ;)
One idea is embed calculated RESP charge to b_factor of molecule pdb. PDB file can make easily from rdkit mol object.
A problem for me is how to edit b_factor of PDB file. I found good tool to solve it today, python package ‘BioPandas’! It can install from pypi or anaconda.
By using biopandas, user can handle pdb file like pandas dataframe.

At first I would like to show examples of biopandas. If you often working with PDB you feel it is very useful I think.
Following code is an example for loading PDB and retrieve protein and ligand data as pandas dataframe.

from biopandas.pdb import PandasPdb
pbdobj = PandasPdb('1atp.pdb')
#Check Atom data
#Check ligand data

Now I can access pdb file as pandas data frame, it means that it is easy to edit and analyze pdb data! More examples are described in official site. So I move to next.

Following example is …
Calculate RESP charge with Psikit and then make pdf file from rdkit mol object and finally replace the b_factor to calculated RESP charge.
At frist load packages.

import os
import sys
from biopandas.pdb import PandasPdb
import pandas as pd
sys.path.append('path for /psikit')
from psikit import Psikit

Then define the function which make pdb file.

def make_pdb_with_Resp(smi, fname=None):
    pk = Psikit()
    charge = pk.resp_charge
    RESP = charge['Restrained Electrostatic Potential Charges']
    if fname == None:
        fname = 'mol'
        fname = fname
    Chem.MolToPDBFile(pk.mol, '{}.pdb'.format(fname))
    pdbobj = PandasPdb().read_pdb('{}.pdb'.format(fname))
   # Following step is editing state, you can see the approach like a pandas method ;)
    pdbobj.df['HETATM']['b_factor'] = RESP

Run the function! After running the code, I could get two files named aceticacid.pdb and tetrazole.pdb

It can load from pymol.


Now I would like to color the molecule with edited b_factor. So I use spectrum command on pymol command line.

spectrum b, blue_red, minimum=-1., maximum=1.
Acetic acid with RESP charge

Acetic acid has negative charge on two oxygen atoms. And carbonyl carbon has the most positive charge.

Tetrazole with RESP charge

The result of tetrazole is strange for me because the nitrogen at position 2 which has hydrogen shows positive. And the nitrogen at position 1 is the most negative. I investigated two protonated state of the tetrazole, 1H-tetrazole and 2H-tetrazole.
But both results shows the nitrogen atom which has hydrogen has positive charge than other nitrogen atoms. I found that BioPandas is useful. But I could not get solution for the last problem. Hmm…


Published by iwatobipen

I'm medicinal chemist in mid size of pharmaceutical company. I love chemoinfo, cording, organic synthesis, my family.

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