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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Received on Sun Apr 16 2006 - 06:07:06 PDT
