VMD-L Mailing List

From: Andrea Kirkpatrick (ak52_at_caltech.edu)
Date: Mon Jul 09 2012 - 17:31:35 CDT

Hi all,

  I have run MD with NAMD, but now I want to continue the run with one
of my residues mutated. What is the best way to make this happen? At the
moment I made a .pdb from the NAMD .dcd snapshot, and I was trying to
use the "mutate" command from psfgen. However, it seems to dislike the
fact that I have multiple chains going on. This is the .pgn file I was
using (the pdb is called ge_j.3.pdb, and I'm mutating R348Q on chain A):

package require psfgen
topology top_all27_prot_lipid.inp
segment A {pdb ge_j.3.pdb
mutate resid 348 GLN}
coordpdb ge_j.3.pdb A
guesscoord
writepdb ge_j.R348Q.pdb
writepsf ge_j.R348Q.psf
exit

Am I doing anything wrong? Is going through a .pdb just completely
backwards since I already have a .psf of the system for the MD run?

Thank you!
Andrea