From: vsharma (vsharma_at_mappi.helsinki.fi)
Date: Tue Dec 07 2004 - 08:26:00 CST

Sir,

Actually I just checked the psfgen documentation and it says that segment
name in psfgen script should be of 1-4 characters and I was using more
than four instead. Sorry for
mailing unknowingly.

sincerely,

Vivek Sharma

On Mon, 6 Dec 2004, John Stone wrote:

>
> Vivek,
> Which version of VMD are you using, and on what platform?
> Can you try the test version of VMD 1.8.3 and let me know if you
> encounter the same problem or not? You can download it here:
> http://www.ks.uiuc.edu/Research/vmd/alpha/
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Dec 01, 2004 at 07:58:46PM +0200, vivek sharma wrote:
> > Dear Sir,
> >
> > I am using solvate program via VMD with available psf and pdb files
> > (generated by psfgen). When I run Solvate from tkcon using commands in
> > console,
> >
> > package require solvate
> > solvate xyz.psf xyz.pdb -t 5 -o abc_wat
> >
> > everything goes fine, solvate runs, but warnings are shown in console as
> > shown below for each and every atom of pdb used;
> >
> > ------------------------------------
> > Warning: failed to set coordinate for atom H1 TIP3:15 WATE
> > no segment WATE
> > Warning: failed to set coordinate for atom H2 TIP3:15 WATE
> > no segment WATE
> > Warning: failed to set coordinate for atom OH2 TIP3:17 WATE
> > no segment WATE
> > Warning: failed to set coordinate for atom H1 TIP3:17 WATE
> > no segment WATE
> > -------------------------------------
> > and finally generated abc_wat.pdb file contains solvation water properly
> > but all original protein coordinates are not shown, something of this type
> > is shown,
> >
> > ------------------------
> >
> > ATOM 1 N PHE 2 0.000 0.000 0.000 -1.00 0.00
> > CHAINA
> > ATOM 2 HT1 PHE 2 0.000 0.000 0.000 -1.00 0.00
> > CHAINA
> > ATOM 3 HT2 PHE 2 0.000 0.000 0.000 -1.00 0.00
> > CHAINA
> > ATOM 4 HT3 PHE 2 0.000 0.000 0.000 -1.00 0.00
> > CHAINA
> > ATOM 5 CA PHE 2 0.000 0.000 0.000 -1.00 0.00
> > CHAINA
> > ATOM 6 HA PHE 2 0.000 0.000 0.000 -1.00 0.00
> > CHAINA
> >
> > -------------------------
> >
> > I have checked that solvation water present after the protein atoms in
> > this same pdb has coordinates but these original atoms does not.
> > What can be the reason? Please explain.
> >
> > sincerely,
> >
> > Vivek Sharma
> > --
> > VIVEK SHARMA
> > HBG BI
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>

VIVEK SHARMA
HBG BI