Re: [AMBER] Thermodynamic Integration (transformation of --H in to ---CH3) atom naming doubt

From: <>
Date: Fri, 15 Jan 2010 13:17:22 -0500 (EST)


ok, it seems as if treating the whole sugar as one residue is not how your
parameter files are set up. As I said, this should not be a problem for
running your simulation. Unless you want to exercise how Amber residues
are built and construct the sugars as single residues yourself, you will
have to keep the setup as it is.

Make sure about one thing though, namely that all atoms that are not in
your scmask are in the same order in both prmtop files (they dont have to
have the same atom numbers nor the same charges or names, but must appear
in the same order). This is not automatically given for different
molecules, unless someone built them specifically with Amber TI
calculations in mind.

Kind Regards,

Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Fri Jan 15 2010 - 10:30:05 PST
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