Re: [Rdkit-discuss] AM1-BCC charges for small molecules

[Francois B. <ml...@li...>]

On 12/03/2019 03:55, James T. Metz via Rdkit-discuss wrote:
> RDkit Discussion Group,
> 
>     I am interested in generating and assigning AM1-BCC charges to
> small molecules,

You can do it with Chimera.

Cf. 
http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/addcharge/addcharge.html

Though you would have to create a script to do it efficiently for 
several molecules.

---
#!/usr/bin/python2

# convert a single molecule 3D .sdf with hydrogens to a .mol2 with 
AM1-BCC partial charges

from chimera import runCommand, openModels
from AddCharge import estimateNetCharge
import os, sys

# I need an env. var to pass the input file name, so that chimera 
doesn't
# try to read that file
sdf = os.environ['INPUT_FILE']

runCommand("open " + sdf)
molecule = openModels.list()[0]
net_charge = estimateNetCharge(molecule.atoms)
runCommand("addcharge nonstd #0 " + str(net_charge) + " method am1")
runCommand("write format mol2 #0 " + sdf[:-4] + ".mol2")
runCommand("close all")
---

I also had a shell script on top of that, to process a single molecule.

---
#!/bin/bash

# convert a .sdf to a .mol2 with partial charges assigned by chimera's 
AM1-BCC FF

# trick to pass an input_file to the python script and not having 
chimera
# try to interprete that file
export INPUT_FILE=$1

chimera --nogui --script ~/bin/chimeraAM1-BCC.py
---

Please ask the chimera ML if you need more help.

I don't guarantee those scripts still work.

Regards,
F.

> preferably in batch mode.  I understand this topic has been discussed
> previously, but
> has there been RDkit code written to do this?  Since this relies on
> the results of AM1
> calculations, has anyone perhaps written RDkit code to calculate and
> assign the
> charges if I have already generated a MOPAC output file by some other
> means?
> 
>     I greatly appreciate all the capabilities of RDkit, and not to be
> off-topic, but if
> someone is aware of a non-RDkit way to generate AM1-BCC charges, that
> might work
> for me.  Hence, please let me know.  Thank you.
> 
>     Regards,
> 
>     Jim Metz
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