[gmx-users] simulation of heme along with h2o2

[Justin Lemkul]

On 2/18/15 9:18 AM, Sanchaita Rajkhowa wrote:
> Dear all, I am trying to simulate a heme containing protein in high
> concentration (having hydrogen peroxide). However, I do not know which
> forcefield to use. Heme has forcefield in gromos96 but not the forcefield
> of H2O2? Will generating .itp files for H2O2 from swissparam work? Please
> help.
>

SwissParam creates CHARMM-compatible parameters, so no, you can't mix those with 
GROMOS.  CHARMM supports heme, but you have to clean up a lot of auto-generated 
angles and dihedrals that don't belong.

-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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