AMBER Archive (2004)

Subject: AMBER: Antechamber on cluster with queue?

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

Best Regards,


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to