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 -- ================================================== 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 [email protected] | (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 [email protected].
