Re: [Apbs-users] 1ucu.pdb with parallel calculation

[Todd D. <to...@cc...>]

Hi Volodya -

It sounds like you're trying to run APBS using parallel focusing - if
this is the case, you'll need to modify your .in file for a parallel
run, as the PDB2PQR server only returns mg-auto input files.

Help for creating a parallel input file can be found here:

http://agave.wustl.edu/apbs/doc/html/user-guide/x594.html#mg-para

You can also automatically generate parallel .in files using the Python
inputgen.py script found in apbs/tools/manip:

inputgen.py --METHOD=para [other options] <PQR filename>

This will hopefully fix your problems - if not, let me know.

Todd

On Tue, 2004-10-26 at 04:22, Valodymyr Nechyporuk-Zloy wrote:
> Dear APBS users,
> 
> I have compiled APBS on cluster. The software works fine with APO files from
> the tutorial. Now, I submitted 1ucu. pdb to PDB2PQR server for generation of
> pqr and in files.
> Unfortunately, I have some problems with my calculation. I attached all files.
> I tried to submit job to 64 nodes with 2 processors.
> Thank you very much for your future help.
> 
> Volodya