AMBER Archive (2007)

Subject: RE: AMBER: Help!! I cannot perform the ambpdb

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Feb 07 2007 - 09:21:13 CST

Hi Wang,

> mpirun: killing job...
>
> I del my job and run again but it didn't work. I log out and log
> in the PBS systerm again but it didn't work too........... :(
> Could you help me?.......... Sorry, really sorry to trouble
> you....

The only software in the Amber package that is parallel and needs mpirun is
pmemd and sander.MPI (and it's derivatives). All other programs are serial
and should NOT be run with mpirun. Ambpdb is a very simple program that
should take seconds at most to run. Thus there is no point in submitting
this via queuing system such as pbs unless it is part of some elaborate
script. You can simply run it from the command line as:

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

All the best
Ross

/\
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|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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