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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