[gmx-users] Re. Generating topology for Tetrahydrofolate within CHARMM ff
jalemkul at vt.edu
Fri May 13 13:33:43 CEST 2016
On 5/13/16 5:04 AM, zeineb SI CHAIB wrote:
> @ Justin
> Dear Justin,
> Thank you very much for the website.
> I tried to generate my topology from the website. After many problems in my input file, it finally generated the .str file with no error/warnings found but unfortunately some penalties were not good at all (> 50 and between 10 and 50)!
> How can I fix the file?
You'll need to manually parametrize/refine anything that has bad penalties.
Spend some time with the CGenFF paper and tutorial:
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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