VMD-L Mailing List

From: vivek sharma (vivek.sharma_at_helsinki.fi)
Date: Tue Dec 07 2004 - 06:23:38 CST

Sir,

Problem appears to be solved but strangely. Actually if you notice the
warnings in the first email I sent, there is word mentioned 'WATE' in each
warning, actually in my original pdb as well as psf (used for solvate
command) this segment name was WATER, but it doesnot read that as WATER
but WATE (is it like that it takes only 4 letters to make name of a
segment?)
To explain; I was using word CHAINA in my psf generating script for the
segment and coordpdb command (like 'coordpdb xxx.pdb chainA' as well as in
command 'segment chainA { pdb xxx.pdb }') and generating the psf and pdb
but solvate package doesnot read 'chainA' word (in either pdb or psf) and
just says cant read 'chai' segment, this means it probably reads only four
letters and cant find that segment in pdb or psf. But if I use 'main' in
my psf generating script (like 'coordpdb xxx.pdb main' as well as in
command 'segment main { pdb xxx.pdb }') and use the generated psf and pdb
(with word 'main') in solvate package, it works fine.

Please explain, if it is like this.
I have tried this on 1.8.2 + Linux and will try on 1.8.3 too.

Thanking you,

sincerely,

Vivek Sharma
 Quoting John Stone <johns_at_ks.uiuc.edu>:

>
> 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