AMBER Archive (2008)

Subject: AMBER: Amber10: Problem with tgtmd and ncsu testing

From: Dmitri Nilov (nilovdm_at_gmail.com)
Date: Wed Oct 15 2008 - 08:00:11 CDT

Hi all!
I have a problem with testing basic Amber10 distribution.
After successful Amber Tools installation I`ve installed serial version of
Amber10 (with prior bugfix.all source files patching).
My OS is Suse Linux 9.3 and CPU is Pentium 4 3.20GHz.
While testing Amber10 distribution ("make test") I have similar problem with
"Targeted MD with changing target and restraints" test and "ncsu.serial"
test.
Sander works too long and doesn't finish. It seems like this:
.......................................................
.......................................................
==============================================================
cd tgtmd/change_target.rms && ./Run.tgtmd
SANDER: Targeted MD with changing target and fit/rmsd
        to different regions
diffing tgtmd.out.save with tgtmd.out
PASSED
==============================================================
cd tgtmd/change_target.ntr && ./Run.tgtmd
SANDER: Targeted MD with changing target and restraints

#No error messages, but sander cannot finish..

and like this:
..............................................................
..............................................................
==============================================================
cd amoeba_formbox && ./Run.amoeba_formbox
diffing amoeba_formbox.mdout.save with amoeba_formbox.mdout
PASSED
==============================================================
cd ncsu && ./run-serial.sh
>>>>>>> doing 'abmd_ANALYSIS'

#No error messages, but sander cannot finish..
/test/tgtmd/change_target.ntr/tgtmd.out contains only header and
/test/ncsu/abmd_ANALYSIS/mdout contains only input info.

I`ve comment out lines corresponding to these problem tests in Makefile and
after that
testing was successfully passed.

I`m not going to run Targeted MD and to use ncsu functionality (I suppose
it`s related to Adaptively
biased MD, steered MD, and umbrella sampling with REMD) in my work.
But could these testing problems be sufficient to suppose something wrong
in basic Amber functioning?

Thanks!

Nilov Dmitri,
Lomonosov Moscow State University

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu