[gmx-users] Re: Amber to gromacs topology conversion for non-amino acid

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 18 14:05:52 CEST 2010

Please keep all Gromacs-related correspondence on the gmx-users list.  As I have 
said many times, I am not a private tutor.  I am CC'ing this message to the 
list; please continue all further discussion there.

There are a number of topology-generating scripts on the Gromacs website.  Have 
a look there:



swapnil chavan wrote:
> Dear Dr. Lemkul,
> I want to run MD simulation for ligand-protein complex. I can't use
> dundee server for topology files preparation for this ligand. Could
> you please tell me another way by which I can generate that topology
> and forcefield files on my desk (without submission to online server).
> Thank you in advance.


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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