Since the heme definition in AMBER uses GAFF atom types how do I get the GAFF FF to work in GROMACS? I would need all the bonded and non bonded definitions of GAFF for the heme in der AMBER FF port in GROMACS right?
Max > On Sep 25, 2015, at 1:36 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 9/25/15 1:32 PM, Ebert Maximilian wrote: >> Hi there, >> >> I am trying to simulate a heme containing protein. I found AMBER heme >> parameters in the mol2 and frcmod file format. I know that I can generate >> .itp files containing the parameters, which I can later add to my .top file. >> However, it would be much easier to use pdb2gmx directly without stripping >> the heme and the cysteine binding the heme and later manually add it again. I >> added the cysteine to the standard amber force field. However, before adding >> the heme manually I wanted to know if there is a way to load an itp file >> while executing pdb2gmx? >> > > pdb2gmx does not need .itp information. grompp does. Add the parameters to > ffbonded.itp or ffnonbonded.itp as needed. > >> How would you add the information from the cysteine in mol2 format and the >> heme in mol2/frcmod format to amber in gromacs? >> > > Charges and connectivity go in the .rtp entry. Heme ligation by His and Cys > is already supported via specbond.dat. > > -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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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-requ...@gromacs.org. -- 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-requ...@gromacs.org.