[gmx-users] topology of ligand contains boron

Justin Lemkul jalemkul at vt.edu
Mon Nov 30 13:40:31 CET 2015

On 11/30/15 3:19 AM, Low Chen Fei wrote:
> Dear,
> im currently running MD simulation of protein-ligand complex. but the
> ligand that im running contain boron. i failed to obtain the ligand
> topology from PRODRG, thus my analysis cant progress since then. would like
> to ask for opinion how can i solve this situation.?

I don't know of a biomolecular force field (at least in GROMACS) that supports 
boron.  Either you'll have to parametrize it completely from scratch, or change 
your approach.



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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