[gmx-users] boron atom parameter

[Justin Lemkul]

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

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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