VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Dec 06 2004 - 09:42:54 CST

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
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