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 -- ================================================== 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
