AMBER Archive (2006)

Subject: RE: AMBER: DNA tutorial, in vacuo minimization

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Apr 14 2006 - 14:34:32 CDT

Hi Amanda,

This sounds like the installation you have of Amber 8 is broken. It is
probably best to speak to the person who installed it and find out what they
did. Did they successfully run all the test cases after completeing the
compilation?

Also note that if the executable was built for mpi you cannot use it for
single processor runs where you don't use mpirun to run the code. I suggest
that you ask your administrator to build you a complete single processor
version of AMBER 8 in a different directory. Make sure they run all of the
tests to verify that it was built correctly.

All the best
Ross

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|\oss Walker

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of amanda.mccook_at_gatech.edu
> Sent: Friday, April 14, 2006 12:16
> To: amber_at_scripps.edu
> Subject: AMBER: DNA tutorial, in vacuo minimization
>
>
> I am unable to run 'in vacuo' minimization for the DNA
> tutorial. When running
> the minimization script from the webpage (below), I get a
> "Segmentation fault
> (core dumped)" error. The output file I get is attached. I
> am running Amber 8
> on SGI/Irix 6.5. I am told it was set up for MPI, but I am
> only attempting a
> single processor run.
>
> Interestingly, by changing only "igb=0" to "igb=1", the
> minimization does run
> completely; but this is no longer vacuum. Please help me
> find a way to make
> this work in vacuo.
>
> Thank you,
> Amanda
>
>
>
> ***minimization script from DNA tutorial
> *** http://amber.scripps.edu/tutorial/polyA-polyT_New/minandmd1.html
>
> polyA-polyT 10-mer: initial minimisation prior to MD
> &cntrl
> imin = 1,
> maxcyc = 500,
> ncyc = 250,
> ntb = 0,
> igb = 0,
> cut = 12
> /
>
> --
>

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