[gmx-users] boron atom parameter

Justin Lemkul jalemkul at vt.edu
Sat Oct 18 23:18:34 CEST 2014

Please keep the discussion on the gmx-users mailing list.

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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