VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu May 14 2009 - 20:45:17 CDT

Maxim,
  Yes, I've heard this from another user also.
Which platform are you running on? I assume you're on
a Windows platform as this error shouldn't be possible on
Unix or MacOS X systems (their filesystems work differently).
Adding the "waitfor all" is likely the right fix, though
I will have to look over the code carefully to be sure.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, May 14, 2009 at 08:06:32PM -0400, Maxim Paliy. wrote:
> Dear VMD authors
>
> I'm posting this here 'cause I have not found author's name in solvate.tcl
>
> I got a small bug while running solvate 1.3 from the new VMD 1.7:
>
> error deleting "combine.pdb": permission denied
> it is traced back to the line
> "file delete combine.pdb" in the solvate.tcl
>
> Apparently this is because on slower machines and for huge files an
> operation just above
> "mol addfile combine.pdb" cannot finish in time.
>
> Modification "mol addfile combine.pdb waitfor all" does the trick for me.
>
> However, there some other attempts to delete files throughout the text
> (it is related to the rotation), so probably they have to be corrected
> as well...
>
> Regards, Maxim
>
> 

-- 
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