[gmx-users] GROMACS with AMBER heme parameters

[Ebert Maximilian]

Yeah that is what I thought but that’s life. 

One more question.In the [ atomtypes ] section I need the sigma and epsilon value. In found them in the GAFF FF in the MOD4 section. In GROMACS sigma is in nm and epsilon in KJ/mol. In GAFF epsilon is in Kcal/mol and sigma is in angstroem and defined as r0 which is sigma *( the 6th root of 2). 

So I picked an atomtype which is defined in the same way in AMBER and GAFF to see if I am doing the conversion right. A standard carbon CA is similar in both since the definition is taken from OPLS:

GAFF ca          r0: 1.9080  epsilon: 0.0860

If I look in the AMBER FF in GROMACS this changes to 

AMBER FF in GROMACS CA sigma: 3.39967e-01 epsilon: 3.59824e-01

If I convert now the 0.086 kcal/mol into kj/mol I get 3.59824e-01 which is as expected. However, for sigma I get only 1.6998e-01 instead of 3.39967e-01, which is half. Why is the sigma value in GROMACS two times the sigma value in GAFF? Is GAFF using Rmin/2 and GROMACS Rmin? It seems like it but I just wanted to be sure.

Thanks

> On Sep 25, 2015, at 4:43 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> 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
> 
> ==================================================
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