[gmx-users] Script for coverting ITP and gro file to Autodock pdbqs

Mahnam mahnam at ibb.ut.ac.ir
Wed Nov 29 16:46:52 CET 2006

In God We Trust
Hello Dear raja
I think that the charges in itp of Gromacs don't match with charges in
Autodock.Becase the total charge in Autodock is zero ,but the total
charges in itp of Gromacs are not zero ,then you can't use gromacs charge
for Autodock. 
Sincerely yours
Karim Mahnam
Institute of  Biochemistry  and  Biophysics (IBB)
Tehran University 
P.O.box 13145-1384

-----Original Message-----
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Tue, 28 Nov 2006 12:47:14 +1100
Subject: Re: [gmx-users] Script for coverting ITP and gro file to Autodock

> raja wrote:
> > Hi gmxions,
> > I want to use charge information contained in itp file produced in
> > gromacs for docking purpose (Autodock). Kindly share a script if
> anyone
> > written to convert information content from gromacs protein's itp
> (for
> > charge) and gro (coordinate) information to autodock pdbqs or pdbq
> > formated one.
> This sounds like a good exercise for learning how to use Perl. Get the 
> file format descriptions and read a few chapters of a Perl reference.
> Mark
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