AMBER Archive (2004)

Subject: AMBER: Antechamber on cluster with queue?

From: opitz_at_che.udel.edu
Date: Wed Oct 06 2004 - 10:08:25 CDT

('binary' encoding is not supported, stored as-is) Dear Amber community,

I am trying to run antechamber on a cluster, using a queue system. The
script I use to submit the job is the same I have used to submit sander
jobs, so that should work (it also works with ptraj). My command for the
job is:
${AMBER}/antechamber -i file.pdb -fi pdb -o file.prepin -fo prepi -c bcc
-cf file.charge ${NSLOTS} < /dev/null
I try to run it on 1 processor. I get the following error message (smilar
when I tried 2 processors):
Flag not recognized: 1
Use antechamber -h for command-line syntax
I'm not sure what the error message is trying to tell me. How would I fix
this and be able to run antechamber on the cluster?

Second question I have, the mopac version on teh cluster is 7.01-4, while
on my workstation the version is 5.09. How much would the charges
outputed differ between these two versions (using the bcc command in
antechamber)?

Best Regards,

Armin

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