From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Jul 04 2007 - 15:29:49 CDT
Comment out the H-H bond in the TIP3P water in your topology file.
It's unnecessary for NAMD and leads to funny looking waters.
On Jul 4, 2007, at 3:18 PM, L. Michel Espinoza-Fonseca wrote:
> 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.
>
> Thanks!
> Michel
>
> 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
> guesscoord
> writepdb pftim-Y74G.pdb
> writepsf pftim-Y74G.psf
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