AMBER Archive (2009)

Subject: Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala

From: Mark Williamson (
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.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 \
  -o tgtmd.out \
  -p prmtop \
  -c inpcrd \
  -ref refcrd \
  -x tgtmd.trj \
  -inf \
  -r tgtmd.restrt

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
Room 395E
San Diego Supercomputer Center
9500 Gilman Drive
La Jolla, CA 92093-0505
Email:  mjw at
Office: 858-246-0827

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