problems with mutation in psfgen

From: L. Michel Espinoza-Fonseca (
Date: Wed Jul 04 2007 - 15:18:45 CDT

Hi all,

Recently I started using psfgen to mutate one or two residues on a
protein. Psfgen performs the tasks and finishes OK. However, when I
visually check the my files, the few crystallographic waters I kept in
my system look like three-membered rings (all of them)! I assume the
problem is related to the psf file, because when I analyze the pdb
alone the system looks fine, but when I load the pdb + psf files, I
get the buggy "cyclic" waters. I'd like to mention that everything
works fine when I don't use "mutate" (i.e., I don't get bad waters or
any other strange thing).

I'm using the standalone version of psfgen (version 1.4.5). Below
please find my input file.

All comments/suggestions will be highly appreciated.


topology toppar/top_all27_prot_na.rtf
pdbalias atom ILE CD1 CD
pdbalias atom GLY OXT OT1
pdbalias residue HIS HSD
segment TIMA { pdb pftim-A.pdb
mutate 120 GLY
coordpdb pftim-A.pdb TIMA
segment TIMB { pdb pftim-B.pdb
mutate 120 GLY
coordpdb pftim-B.pdb TIMB
pdbalias residue HOH TIP3
segment SOLV {
 auto none
 pdb pftim-water.pdb
pdbalias atom HOH O OH2
coordpdb pftim-water.pdb SOLV
writepdb pftim-Y74G.pdb
writepsf pftim-Y74G.psf

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