VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 03 2007 - 13:05:34 CST

Hi,
  I noticed that in your script there's a comment about forcing the
segid of the original structure, followed by a line that's commented
out, perhaps might be part of the problem? You might also ask Lubos Vrbka
since he wrote the original script that yours is based on. Just reading
through the script rapidly, I didn't see any blindingly obvious reason
for the problem, so you may want to ask Lubos what assumptions his
script makes. His email contact info is givenon his web site:
  http://www.lubos.vrbka.net/

  John

On Thu, Dec 21, 2006 at 01:09:59PM +0200, " politr"@huji.ac.il wrote:
> Dear Sir,
>
> My name is Regina and I'm a PhD student. I hope you will be so kind and be
> able to help me with my problem. I need to calculate the number of
> water/glycerol molecules in a predefined radius around the peptide. I have
> a trajectory after simulation. During the simulation my peptide is drifting
> to the PBC borders. When I used the selection "water and within * of
> resid VMD showed the water molecules within the distance, but only
> those inside the box. When I turn on peridoic cell in the direction
> peptide drifting, VMD still wouldn't show those water molecules. Neither
> did they
> appear on the other side of the water box. As I understand
> this is known issue of vmd - it is not 'pbc enabled'.
>
> I have tried to use tcl script from VMD script library (color_coord.tcl)in
> oder to build replicas of
> central box and after that to calculate the the number of molecules
> but the script didn't work. Can you please be so kind and help me with
> this problem. The modified script is attached. You can also see the output
> I'm geting when trying to run it.
>
>
> Best regards
> Regina
>
> shifting by 0.0 0.0 0.0
> building segment R0
> setting patch for first residue to NONE
> setting patch for last residue to NONE
> Info: generating structure...
> Info: segment complete.
>
>
> no residue 5 of segment R0
> ERROR: failed on coord
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> 

-- 
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