From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Wed Jul 04 2007 - 15:58:41 CDT
Hi JC,
Thank you for your reply. Although this change on the topology file
will solve my problem, I still wonder why the water molecules look
fine when I don't invoke "mutate" within my segment. This is exactly
what surprised me when I built systems.
Cheers,
Michel
2007/7/4, JC Gumbart <gumbart_at_ks.uiuc.edu>:
> 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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