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

From: Mark Williamson <>
Date: Wed, 07 Feb 2007 20:25:19 +0000

WANG,YING wrote:

> | New format PARM file being parsed.
> | Version = 1.000 Date = 02/06/07 Time = 11:40:55
> mpirun: killing job...

Dear Ying,

I still do not understand why the mpirun related error message is here,
yet you say you are not specifying it in your command line, hence it may
be an issue with with the PBS queuing system. Perhaps, at the queuing
level, every job command is being prefixed with mpirun? I do not know.

A second thing to look at is that some queuing systems sometimes run in
other directories that submitted. Hence use full paths in all files
being operated on.

Overall, I think the the problem lies somewhere with your cluster. As
it has been mentioned, ambpdb is not designed to be run in parallel. I
think you should talk to your cluster administrator since the I feel
problem is in a realm over which we have no control or knowledge.


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Received on Sun Feb 11 2007 - 06:07:11 PST
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