[gmx-users] Modifying the protein chain in GROMACS

[Justin Lemkul]

On 9/9/14 8:51 AM, Tim Stauch wrote:
> Dear all,
>
> I am currently trying to “mutate" a protein by changing its backbone directly, i.e. I am not interested in changing a specific amino acid against another (I’ve found out that you can use VMD or Pymol for this purpose), but I am rather interested in changing certain atoms in the backbone by another functional group. In other words, I would like to replace, e.g., the NH-C=O-CR unit of a certain amino acid by a couple of other atoms which do not comprise a peptide bond (e.g. a small aromatic ring). After this, I would like to run MD simulations.
>
> How would I do this? Is this actually possible? I would really appreciate your help, because I have no idea how to do the first steps of setting up the calculation (generating an input file that pdb2gmx can read, etc.). Neither an extensive Google search nor the GROMACS manual were useful to me in this respect.
>

The solution is here: 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

The key issues are (1) generating the .rtp entry, (2) deriving suitable 
parameters for whatever the residue(s) is(are), and (3) building a coordinate 
file for pdb2gmx to read.

-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 601
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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