Re: AMBER: Help!! I cannot perform the ambpdb

From: Mark Williamson <>
Date: Wed, 07 Feb 2007 16:08:41 +0000

Looking through your recent thread of emails, you initially use the
subject of "problems in xleap" but the actual body of the email (and the
error messages generated) pertain to issues with the ambpd. Inaccurate /
wrong subjects will increase the time taken for a problem to be solved.
Hence in addition to Carlos' correct advice, you should not be using any
form of mpi wrapper for ambpdb.

You do not give any indication of what command line parameters are being
used and my hunch from looking at your error messages is that you
probably have omitted the "<" , ">" redirectors when using ambpdb. Since
you are using this in a non interactive environment i.e. a queuing
system, this problem may not reveal itself clearly. Therefore, you
should be using ambpdb in a similar fashion as below:

$AMBERHOME/exe/ambpdb -pqr -p prmtop < inpcrd > output.pdb

Try modifying your PBS submission script to reflect this. Or, even
better for debugging, try running the command on an interactive node on
your cluster or on actually on a standalone machine with the AMBER suite


Mark Williamson
The AMBER Mail Reflector
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Received on Sun Feb 11 2007 - 06:07:08 PST
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