[gmx-users] simulate a multimer with one component has covalently attached prosthetic group

[Justin Lemkul]

On 4/1/15 1:49 PM, Debajyoti Dutta wrote:
>
> Hi all,
>
> I am trying to simulate a dimer (say A2) where another protein is docked (say B) which is covalently attached with a prosthetic group.
>
> My question is how to do that.
>
> so far what i did ...
>
> I generate a gro and itp file from PRODRG corresponding to that molecule and modified the charges based on the protocol mentioned in the paper
>
> http://pubs.acs.org/doi/abs/10.1021/ci100335w
>
> but,
>
> 1) the atom which has to be linked with the protein B has taken a H which needed to be stripped; then how to generate the link with protein B.
>

Parameters can change substantially upon deprotonation.  You should parametrize 
the prosthetic group with an appropriate model of the link itself.

> 2) The prosthetic group has a S atom in thioester form; I did not find a place that how and what charge to be assigned to that atom.
>

You need some suitable model compound that you can parametrize against free 
energy of hydration and the neat liquid state, per GROMOS convention.

> 3) to to generate .rtp file for GROMOS 96 43a2 force field?

See http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

-Justin

-- 
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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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