VMD-L Mailing List

From: ivana adamovic (iadamovic_at_gmail.com)
Date: Sat Jun 24 2006 - 08:37:57 CDT

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