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 -- ================================================== 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
