[gmx-users] GROMACS with AMBER heme parameters

[Justin Lemkul]

On 9/25/15 4:40 PM, Ebert Maximilian wrote:
> I read that and this is the way I added the cysteine to AMBER which connects to the heme. Now I am adding the heme but the FF definition for bonds, angles, etc are all in lower case for the GAFF FF. From you answer I guess I need to add these lower case atom types and the bonds, angles, etc definition from the GAFF FF to the AMBER FF manually.
>

Indeed, which is what steps 3 and 4 tell you.  Adding a residue is simple, but 
if that residue involves modifications to the force field, then there is more 
work to be done.

-Justin

> Not much fun but I will share the work here in the end. Maybe this will help people who want to simulate heme containing proteins in GROMACS and AMBER99SB-ILDN.
>
> Have a good weekend,
> Max
>
>
> On Sep 25, 2015, at 4:25 PM, Justin Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:
>
>
>
> On 9/25/15 4:22 PM, Ebert Maximilian wrote:
> 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?
>
>
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>
> -Justin
>
> Max
>
> On Sep 25, 2015, at 1:36 PM, Justin Lemkul <jalemkul at vt.edu<mailto: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
>
> --
> ==================================================
>
> 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<mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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> --
> ==================================================
>
> 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<mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
==================================================

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

==================================================