[gmx-users] simulation of heme along with h2o2

[Sanchaita Rajkhowa]

Dear Justin, thank you for the reply. However, I would like to know if
there is any server which can generate parameters for heme to be used in
OPLS-aa? We have already tried in swissparam with failed results. Please
help.

On 18 February 2015 at 21:15, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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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