[gmx-users] (no subject)

[Justin Lemkul]

On 9/8/14 5:33 AM, Somayeh Alimohammadi wrote:
> Dear gmx users
> I am performing a simulation by gromacs. for building the ligand itp file
> by Prodrg, I get an error thet boron atom is not supported by this program.
> Do you have any propose for solute this problem?

Choose a force field and parametrization strategy that accounts for B.  The 
Gromos96 parameter sets (by default at least) do not have parameters for B, 
hence PRODRG complains.  Probably the same is true for ATB, for the same reason.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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