Hi Stephane,
> I would like to simulate a protein with a N-Carboxymethionine at the
> N-term with the AMBER(99SB)12 force fields. This residue plays an
> important in the protein functions, so I can not remove it. Before
> to (re)compute the RESP charges for this particular residue, I would
> like to know if somebody has the RESP charges for this residue.
If you follow the Amber approach to derive RESP charges for amino-acid
fragments you might consider this N-Carboxymethionine as a central
methionine (already known) + a N-Carboxy fragment; i.e. just another
capping group...
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=17753927
i.e. I would first try capping this carboxylate group by a N-acetyl
group, and apply an intra-molecular charge constraint set to zero on
this capping group.
regards, Francois
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Received on Sat Mar 09 2013 - 23:30:02 PST
