AMBER Archive (2004)

Subject: Re: AMBER: Antechamber on cluster with queue?

From: David A. Case (
Date: Wed Oct 06 2004 - 10:24:17 CDT

On Wed, Oct 06, 2004, wrote:
> 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
?? What is that argument?

> I try to run it on 1 processor. I get the following error message (smilar
> when I tried 2 processors):
> Flag not recognized: 1

I suspect that antechamber is trying to process the ${NSLOTS} argument,
which is being expanded to "1", which is not a legal flag for antechamber.

> 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)?

Once you get it working, you can test for yourself!


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