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.
/home/pandora/jorgensen/apbs.49875/
I have used PDB2PQR to convert system.pdb into system.pqr
/home/pandora/jorgensen/apbs.49875/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
Christian
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