VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Feb 15 2006 - 10:34:21 CST

Hi Jacob,
I've been unable to reproduce this error using b11. Could you please
send me your console output leading up to the crash? Also, are you using
psfgen or AutoPSF?
Thanks,
Peter

Jacob Pøhlsgaard wrote:

>Hi John
>
> Yeah this is with the latest beta 11. In fact this seemed even more quirky, giving me "access denied" errors when it tried to delete some temporary files. The beta before that just did the "file not found: c:\Program" error.
> This may be because the psfgen program has been changed in the new beta, in the previous it could build the PSF, solvate and ionize in one go. Now I have to do it in steps, and I think I got the new kind of error in the solvation step.
>
> I haven't really tried exhaustive combinations of file locations and program versions, since it simply works when I use something like c:\vmdstuff as a work dir.
>
>Best regards
>
>Jacob Pøhlsgaard
>Department of Biochemistry and Molecular Biology
>
>Tel. +45 6550 2370
>Fax +45 6550 2467
>Email jacobp_at_bmb.sdu.dk
>Addr. Campusvej 55, 5230 Odense M
>
>UNIVERSITY OF SOUTHERN DENMARK
>_______________________________________________________________
>Campusvej 55 * DK-5230 * Odense M * Tel. +45 6550 1000 * www.sdu.dk
>
>
>-----Original Message-----
>From: John Stone [mailto:johns_at_ks.uiuc.edu]
>Sent: 14. februar 2006 23:12
>To: Jacob Pøhlsgaard; Peter Freddolino; jan.saam_at_charite.de
>Cc: vmd-l_at_ks.uiuc.edu
>Subject: Re: vmd-l: PSF tools in windows and long paths
>
>
>Hi,
> I haven't seen this recently, but we've certainly had this sort of problem before in the test versions. Which version of VMD were you running?
>We had thought that these problems were fixed in b11, so if you're running
>b11 that's very important to know.
>
>Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
>On Tue, Feb 14, 2006 at 10:47:34AM +0100, Jacob Pøhlsgaard wrote:
>
>
>>Hi guys
>>
>> Have anybody else tried using the psf tools (such as psfgen, solvate and ionize) under windows?
>>
>> Mine consistanly fail if any of the files are in directories containing spaces (such as "Program Files", "University of Illinois" or "My Documents"). It looks like the plugins just parse the path until they reach a whitespace, as they will typically output something like "File not found: C:\Program". I've also have "access denied" errors and such.
>>
>> A workaround is to copy all files involed (also the topology file) to a dir not containing spaces.
>>
>>Best regards
>>
>>Jacob Pøhlsgaard
>>Department of Biochemistry and Molecular Biology University of
>>Southern Denmark
>>
>>
>
>--
>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
>
>
>