[gmx-users] Replacing a residue and continuing a simulation run

J. Nathan Scott scottjn at chemistry.montana.edu
Tue Mar 15 22:01:35 CET 2011

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

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