AMBER Archive (2006)

Subject: AMBER: DNA tutorial, in vacuo minimization

From: amanda.mccook_at_gatech.edu
Date: Fri Apr 14 2006 - 14:15:31 CDT

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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