Re: Hi,how can I generate a psf file with a pdb file contain some special amino acid like TYS

From: Leonardo Sepulveda Durán (
Date: Fri Jun 24 2005 - 09:30:26 CDT

I dont Know what "TYS" is 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.

Universidad de Chile

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:40:53 CST