Hi James -
We've seen this error before, although we're still not sure what the exact cause is - it looks to be a VMD error. I do have a couple of suggestions for you:
1. Since it looks like you're running Windows, you might want to try just running APBS from the command line without VMD.
2. Assuming that works, make sure that you're using a PQR file instead of a PDB file - while I believe that VMD can convert from one to the other, if we're trying to isolate the problem it'd be useful to start with a PQR file. You can use pdb2pqr ( http://pdb2pqr.sourceforge.net) to do so.
3. Copy your PQR file and the executable to C:/ (or a subdirectory without a space). This might resolve conflicts that could arise from spaces in the file names, particularly when calling APBS.
4. First load your molecule into VMD, then open the APBS electrostatics pane, and edit the settings to point to the correct APBS location. You may also want to set the working directory to the same directory, as I don't think VMD can write to the /tmp directory in Windows.
Hopefully this works! We've seen issues with spaces in the filenames with other Windows visualization programs, so that might be the key problem here. I believe the VMD people are aware of this issue, so hopefully it will be resolved soon.
Please let me know how it goes!
I get the following error while running the
latest greatest APBS version under VMD 1.8.4 windows version:
Main console display active (Tcl8.4.1 / Tk8.4.1)
apbsrun: using VMD radii
apbsrun: using pqrplugin for /tmp/1PTR.pqr
apbsrun: error running C:/Program Files/APBS/apbs.exe
apbsrun: error occurred while running APBS:
can't read "apbs_fd": no such variable
(George Orr) 1 %
Is there a fix for the current version of APBS or VMD
to correct this?
Dr. James C. Ianni, MSc., Ph.D.
Department of Chemistry,
University of Pennsylvania, mailbox #254
231 South 34th Street, Philadelphia, PA 19104, USA
tel.: 001 215-573-4249 (lab)
001 215-573-6741 (office)
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