VMD-L Mailing List

From: Per Jr. Greisen (greisen_at_binf.ku.dk)
Date: Tue Mar 13 2007 - 13:32:04 CDT

Hi,

I am running the APBS analysis as an extension from the VMD menu but it
seems that something goes wrong.

I start by generating the *.pqr file from the webserver as prescribed from
the tutorial. I load the *.pqr file into vmd and go to the APBS, select
the molecule, edit in order to see if the default parameters are okay -
than I press "RUN APBS" and than the program starts to crash. The
vmd-console displays apbsrun) Running job mode=normal and if I go into the
"top" I see that vmd is running - I never see apbs executed which I find
rather strange.
And than it just keeps on running until I kill the job. If I execute the
abps outside of VMD it takes no time to do the calculations.

How to fix so it can be executed within VMD. Any help or advices
appreciated. Thanks in advance

Best Regards

Per