[gmx-users] GROMACS with AMBER heme parameters
m.ebert at umontreal.ca
Fri Sep 25 22:22:59 CEST 2015
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?
> On Sep 25, 2015, at 1:36 PM, Justin Lemkul <jalemkul at 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 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
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