[gmx-users] boron atom parameter
jalemkul at vt.edu
Sat Oct 18 22:18:59 CEST 2014
On 10/18/14 3:39 PM, fatemeh ramezani wrote:
> Dear gmx users
> I am performing a simulation by gromacs. My ligand molecule has a boron atom and by topology builder softwares such as prodrg, ATB, swiss param, antechamber I get an error that boron atom is not supported by this program.
> Do you have any propose for solute this problem? How can I build a top file for this ligand?
You need to use a force field that supports boron. Most biomolecular force
fields won't, and none of the force fields provided in Gromacs recognize boron.
Perhaps someone has parametrized boron for a suitable force field, and in that
case you will have to extend that force field to add boron, then figure out a
way to generate the topology (probably manually, as servers will clearly not do it).
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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