AMBER Archive (2009)

Subject: [AMBER] trouble with antechamber

From: Jennifer L. Muzyka (jennifer.muzyka_at_centre.edu)
Date: Tue Nov 24 2009 - 14:13:46 CST

We'd appreciate any insights or advice anybody can offer. Thanks.
-Jennifer

Jennifer Muzyka
Professor of Chemistry
Centre College
Danville, KY 40422

-----Original Message-----
From: Jordan Feigerle
Sent: Tuesday, November 24, 2009 2:04 PM
To: Jennifer L. Muzyka
Subject:

I am using Amber10 and I am having difficulties using antechamber to simulate an organic compound. I attempted to perform the tutorial with the sustiva.pdb file but my pc was not able to finish the calculations. My first question is how long is the calculation on a 32-bit 2.4 GHz PC using Ubuntu. The divconx file provided on the tutorial had a runtime of approximately 40s. I have let the computer run for over 24 hours with the concern that I was not letting the program run long enough. My second question is regarding mopac. I had been having some of the problems other posters have had concerning the "&" in the mopac.sh code. I removed the & and the syntax error went away. However, the terminal will load mopac.sh and just run constantly (using the "top" command shows that mopac is using 100% of the processor). The output file which mopac designates at FOR006 is created with the following message at the bottom: "NO POINT LOWER IN ENERGY THAN THE STARTING POINT COULD BE FOUND IN THE LINE MINIMIZATION."
  I have also changed from using bash to using dash and neither seem to make a difference. Anyone have advice as to what this issue might be?

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