[gmx-developers] Regarding Amber topology and co-ordinate file

Justin Lemkul jalemkul at vt.edu
Mon Apr 21 19:57:24 CEST 2014

Please ask usage questions on the gmx-users mailing list.  The development list 
is for coding and planning discussions; this post is not appropriate here.  I am 
CC'ing this message over to gmx-users.  Please post anything further there.

On 4/21/14, 10:28 AM, MOHD HOMAIDUR RAHMAN wrote:
> Dear Gromacs User
> I have ILs system in small box that is running on Amber 12 MD package. Now I
> want to use Gromacs MD package for my bigger system (Large no of molecules with
> proteins) with the same parameter.
> So, it is possible to convert Amber topology format to gromacs topology format.
> I have also prep and frcmod file for that molecules. which is use in tleap to
> generate topology file and Co-ordinate file to direct use in Amber MD package.

There are various scripts floating around the web that do such conversions; 
amb2gmx.pl comes to mind.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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