[gmx-users] Conversion of gromacs trajectory file

aiswarya.pawar at gmail.com aiswarya.pawar at gmail.com
Wed Aug 24 14:07:37 CEST 2011

Hi Justin,

Thank for the quick response. I would try out your script for the conversion.

------Original Message------
From: Justin A. Lemkul
To: Aiswarya Pawar
To: Discussion list for GROMACS users
ReplyTo: jalemkul at vt.edu
Subject: Re: [gmx-users] Conversion of gromacs trajectory file
Sent: 24 Aug 2011 5:35 PM

aiswarya.pawar at gmail.com wrote:
> Hello Everyone,
> Any idea how one can convert gromacs trajectory file to amber file. So as to use the amber tools.

The key is finding a compatible intermediate that can be converted.  I've found 
that PDB format is pretty universal.  I have a script that does the opposite 
(mdcrd to .xtc) linked from my site:


It's a bit awkward, but does the job.  Perhaps you can reverse-engineer it for 
your purpose.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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