From: Leonardo Sepulveda Durán (leonardosepulveda_at_gmail.com)
Date: Fri Jun 24 2005 - 09:30:26 CDT
I dont Know what "TYS" is ...it sound like a sulfur Tyrosine???,
anyway psfgen can only read residue tipes defined in your topology
file i.e. top_all22_prot.inp (or something like that). You have to add
it to your topology or create a different topology file for TYS and
read both secuentially. That only can be done "cutting and pasting"
from your normal CHARMM topology if atoms in your residue already have
parameters in CHARMM FF. If not you should create proper parameters
using Ab-Initio quantum mechanical procedures. Take a look in namd
page, there is a tutorial were they parametrize a novel residue from
extant residues in CHARMM FF.
Leonardo
Universidad de Chile
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