VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 26 2006 - 17:32:45 CDT

Ivana,
  From the error log below it looks like you were using
the graphical interface, is this correct? Also, you were running
the final VMD 1.8.4 release, and not a test version, correct?
If that's all correct, then I may need a copy of your test files
to try out locally, as I've never encountered this kind of error before.
It might also be useful if you can send me a screen shot of the parameters
you typed into the solvate interface as well.

  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Jun 24, 2006 at 09:37:57AM -0400, ivana adamovic wrote:
> Hi John,
>
> I am using VMD 1.8.4 for MacOS X (Intel x86) using native OpenGL
> verison and I have tried to build in water box around solute molecule.
> I have uploaded .pdb and .psf files and tried all options: to define
> box size, to use molecule dimensions ...
> Here is the error log from one of the tests:
> while executing
> "error """
> (procedure "solvate_usage" line 19)
> invoked from within
> "solvate_usage "
> (procedure "solvate_core" line 55)
> invoked from within
> "solvate_core /Users/ivana/Desktop/NEW SOLVENT TESTS/WATER
> BOX-explicit solvent/1nkn.ab.psf /Users/ivana/Desktop/Ivana Old
> Laptop-Srba/MY DOCUMENTS/1NK..."
> ("eval" body line 1)
> invoked from within
> "eval solvate_core $args "
> invoked from within
> "if $errflag { error $errMsg $savedInfo $savedCode }"
> (procedure "solvate" line 8)
> invoked from within
> "solvate /Users/ivana/Desktop/NEW SOLVENT TESTS/WATER BOX-explicit
> solvent/1nkn.ab.psf /Users/ivana/Desktop/Ivana Old Laptop-Srba/MY
> DOCUMENTS/1NKN/VMD..."
> ("eval" body line 1)
> invoked from within
> "eval solvate $command_line"
> (procedure "::Solvate::run_solvate" line 76)
> invoked from within
> "::Solvate::run_solvate"
> invoked from within
> ".solvategui.solvate invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 23)
> invoked from within
> "tk::ButtonUp .solvategui.solvate"
> (command bound to event)
>
>
> Could you please explain me how to properly use this function?
>
> Thanks a lot,
>
> Ivana 

-- 
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