[gmx-users] GROMACS with AMBER heme parameters

Justin Lemkul jalemkul at vt.edu
Fri Sep 25 19:37:06 CEST 2015

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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