AMBER Archive (2009)
Subject: Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala
From: Mark Williamson (mjw_at_sdsc.edu)
Date: Mon Nov 16 2009 - 11:37:18 CST
Wallace Kunin wrote:
> cd tgtmd/change_target.ntr && ./Run.tgtmd
>> SANDER: Targeted MD with changing target and restraints
> Does anyone have an idea of what might be causing this or what other info do
> you guys need to figure this out? Thanks.
Can you run the command explicitly that is being wrapped by this test
script (./Run.tgtmd) ?
Generally, these test scripts will:
1) Write a set of inputs in that directory.
2) Run a compiled binary from $AMBERHOME/exe/ using the above inputs.
3) Compare the just generated outputs against a known correct output.
4) Delete the inputs that were generated in 1.
To aid debugging, you can comment out the command in the Run.tgtmd
script that cleans up:
#/bin/rm -f tgtmd.trj tgtmd.info tgtmd.restrt dummy
then run the script again (to generate the inputs in that directory),
followed by the actual command that may be failing:
../../../exe/sander -O \
-i tgtmd.in \
-o tgtmd.out \
-p prmtop \
-c inpcrd \
-ref refcrd \
-x tgtmd.trj \
-inf tgtmd.info \
and see if there is any more information from that. It may be a good
idea to look in the tgtmd.out file.
Mark Williamson, Post Doc
Walker Molecular Dynamics Group
San Diego Supercomputer Center
9500 Gilman Drive
La Jolla, CA 92093-0505
Email: mjw at sdsc.edu
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