Treatment of a Neutral N-terminus

From: Maria Bagonis (
Date: Fri Jul 20 2007 - 11:51:32 CDT

Dear all,

In my current simulation it is necessary for me to treat the N-terminus of an
amino acid as deprotonated/neutral. I was wondering if anyone had any
suggestions about the best way to do such. I don't believe such a patch is
included in the CHARMM file that I am using (The standard combined All-Hydrogen
Topology File for CHARMM22 Proteins and CHARMM27 Lipids). I have found a patch
in the AMINOH.RTF file (the topology file for CHARMM version 22 (All
Hydrogens)). However, I am unsure if this is the best way to characterize the
group, or if it is even valid to combine these two files.
Any insight into the best way to proceed would be greatly appreciated. (I'm
assuming this problem is likely encountered fairly frequently). Thanks!


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