VMD-L Mailing List

From: Charles McCallum (mmccallum_at_pacific.edu)
Date: Sat Jun 24 2006 - 18:24:16 CDT

where did the PDB and PSF come from?
Did you use the 'solvate' plugin, or the solvent GUI?

Cheers,

Mike

On Jun 24, 2006, at 6:37 AM, 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 

--
C. Michael McCallum           http://www.pacific.edu/college/ 
chemistry/McCallum/cmccallum.html
Associate Professor
Department of Chemistry, UOP
mmccallum .at. pacific .dot. edu                (209) 946-2636 v  /  
(209) 946-2607 fax