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

From: WANG,YING <>
Date: Wed, 7 Feb 2007 14:49:46 -0500 (EST)

Hi, Dear Mark,
I'm so sorry for all the troubles I bring to you and others... :(
yes, in the last last mail I forgot to change the subject. It is
not the problem under the xleap interface.
My problem is: AMBER is installed in the computer center of our
university. So I only can use it through the SSH client and submit
my jobs through the PBS. I don't know how to control "ambpdb"
directly. My oringinal command line is "$AMBERHOME/exe/ambpdb -p
prmtop < inpcrd > output.pdb". And I change the command line to
your version "$AMBERHOME/exe/ambpdb -pqr -p prmtop < inpcrd >
output.pdb" but it doesn't work too........... The error message
report the same problem, as below.
| New format PARM file being parsed.
| Version = 1.000 Date = 02/06/07 Time = 11:40:55
mpirun: killing job...
WARNING: A process refused to die!

Host: hpc112.local
PID: 22429

This process may still be running and/or consuming resources.
And the run time of my job is always 0, the output pdb file is 0
I don't know what's happen. Could you help me? Thanks very
much!!!! Indeed appreciate all the help come from you and

On Wed Feb 07 11:08:41 EST 2007, Mark Williamson
<> wrote:

> 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 installed.
> regards,
> Mark Williamson
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Feb 11 2007 - 06:07:10 PST
Custom Search