[gmx-users] boron atom parameter
jalemkul at vt.edu
Sat Oct 18 23:18:34 CEST 2014
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On 10/18/14 5:00 PM, fatemeh ramezani wrote:
> Dear Dr. Justin
> I have boron parameter from a paper. Can I prepare top file by the below method?
> I replace boron atom with carbon in my ligand structure and I get a top file
> from prodrg, then in the top file I replace boron atom again and I put its
> parameter prepared from the paper.
"Parameters for boron" and "parameters for a ligand containing boron" are very
different concepts. First, PRODRG topologies are generally low quality and
require manual reparametrization. Second, the electronic structures of boron
and carbon are different, so the partial charges and other parameters will
inherently be different, so no, I do not believe such a substitution is justified.
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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