AMBER Archive (2006)

Subject: Re: AMBER: program to calculate net charge of a ligand for Antechamber

From: David Mobley (dmobley_at_gmail.com)
Date: Mon Jul 10 2006 - 23:18:36 CDT

Probably bad news to do it from a pdb file, unless you are talking
about a pdb file which already has all of the hydrogens, in which case
it probably should be doable. But if you're lacking hydrogens, you
can't infer the protonation state from the pdb file since the pdb
doesn't have bond types.

In terms of a program to do it, I'm not sure.

David Mobley
Dill lab
UCSF

On 7/10/06, Christophe Guilbert <cguilbert_at_picasso.ucsf.edu> wrote:
> Hi,
> Sorry for this question a little bit off topic, but I was wondering if
> anyone know a free software to automaticaly calculate the net charge of
> a ligand from a mol2 or pdb file. Charge I would later use with the -nc
> (net charge) Antechamber option.
>
> Thanks
>
> --
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> Christophe Guilbert, Ph.D.
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