[gmx-users] simulation of heme along with h2o2
srajkhowa18 at gmail.com
Thu Feb 19 05:13:24 CET 2015
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
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
> 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 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
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users