[gmx-users] Ligand breaks during energy minimization

Justin Lemkul jalemkul at vt.edu
Sat Mar 26 04:29:55 CET 2016

On 3/25/16 8:03 PM, Soumya Lipsa Rath wrote:
> Dear Justin and Nikhil,
> Many thanks for your suggestions. Justin, I had optimized the parameters
> using VMD's FFTK toolkit, so I just replaced my results in the *.str file
> obtained from paramchem.
> I tried minimizing the ligand in vaccum and in a solvent box, in both
> cases, the molecule just scatters apart (pardon me, the bond doesn't
> break).
> I think there might be something wrong with the topology. However, I just
> followed the general steps.

Well, when relying on automated methods fails, you have to roll your sleeves up 
and do the work yourself :)

If you can provide the stream file and coordinates of the ligand, I will try to 
offer suggestions; if you can share them publicly across the list it may be 
informative for others to listen in on the conversation.

Note, though, that the CGenFF paper is itself a tutorial on how to parametrize 
small molecules, and there are even more detailed CGenFF tutorials available 
online (check our website).



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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