vmd-l: No APBS output: 'cannot access output file' error

From: Christian Jorgensen (christian.jorgensen_at_merton.ox.ac.uk)
Date: Mon Jul 18 2011 - 18:44:07 CDT

Hi all, I am trying to perform an MM/APBS calculation on a ligand
I have the APBS executable located in a directory with permissions to read and write

I have VMD installed in a similar directory

I am writing to a directory with the correct permissions.

I have used PDB2PQR to convert system.pdb into system.pqr

I perform the MM/PBSA calculation to obtain the electrostatic potential
but I get:
apbsrun) Cannot access output file

The full error shows that the file containing the calculated electrostatic potential has not been
written to the directory:

Info) Finished with coordinate file /home/pandora/jorgensen/apbs.5950/apbs.55245/system.pqr.
apbsrun) Output files pot
apbsrun) Cannot access output file /home/pandora/jorgensen/apbs.5950/apbs.55245/pot.dx

When running the calculation remotely on BioCoRE I get the following error:

apbsrun) Running job mode=biocore
apbsrun) dir is /home/pandora/jorgensen/apbs.5950
apbsrun) using VMD radii
apbsrun) using pqrplugin for /home/pandora/jorgensen/apbs.5950/system.pqr
Info) Opened coordinate file /home/pandora/jorgensen/apbs.5950/system.pqr for writing.
Info) Finished with coordinate file /home/pandora/jorgensen/apbs.5950/system.pqr.
exectool) getAccountsForJob Error: <Partial User Where Full Registrant Required> <isValidBiocoreResponse
    (procedure "isValidBiocoreResponse" line 163)
    invoked from within
"isValidBiocoreResponse $strResponse result iServerVersion"
    (procedure "::biocore::getAccountsForJob" line 14)
    invoked from within
"::biocore::getAccountsForJob $biocore_job_type "> <-1>
apbsrun) biocore_config_run error -2
apbsrun) Error -2 detected in biocore_config_run

I cannot see why the program should fail to write an output

Any help is much appreciated

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:35 CST