learning how to do a Cys palmitoyl patch

From: seigneuret_at_cochin.inserm.fr
Date: Tue Aug 02 2005 - 16:24:19 CDT

Dear Namd experts,
I am trying to do MD on a Cys-palmitoylated protein with Namd.
I would like to make a sidechain patch to Cys rather than using
the CYP RESI topology file available in the Namd contribs. The
problem is that the sidechain patches available in the Mackerel
CHARMM topology files are either too simple (e.g. protonated Asp
or Glu) or too complex (e.g. heme liked to His) to be helpful examples.
Could someone direct me to or send me intermediate complexity
exemples (e.g. methylated or phosphorylated sidechains) that i
could use to understand how it is done.

Michel Seigneuret
Institut Cochin
Paris, France

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