Hello all, I was wondering, is it possible to replace a residue and then continue a simulation using the new parameters/geometry of the new residue? The reason I ask is that I am interested in performing simulations of proteins with tryptophan in its excited state following a lengthy equilibration with TRP in its ground state. I already have reliable excited state atomic charges for the TRP atoms, and I suppose that I will need to change at least some bonded terms to account for the altered geometry of the excited state.
I am still in the middle of reading the information that is out there regarding parameterizing new molecules (since I'm using the CHARMM FF, I've been starting to follow Alexander MacKerell's protocols), but I'm still not quite sure as to how one would practically do this residue replacement in the context of a Gromacs run. Will I need to manually edit my .top file, or is there perhaps another way to update the topology file with the new residue following the ground state equilibration? How about coordinates, will I need to transform the TRP coordinates to the excited state geometry by hand? Perhaps the most important question: is there a better way to do the sort of residue replacement I'm contemplating, or is this something that is just inherently going to be a bit messy? Thanks very much for any insight or guidance you can offer! -- ---------- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists