AMBER Archive (2004)

Subject: AMBER: DNA

From: Beale, John (jbeale_at_stlcop.edu)
Date: Mon Feb 02 2004 - 07:31:51 CST

At the bottom of the md.in file for the production run of the polyA-polyT molecule in the DNA tutorial there is a set of numbers. I wonder if someone could tell me what they mean:

58.3501205 39.8315298 39.8315298 90.0000000 90.0000000 90.0000000
60 40 40 4 0 0 0
0.00001

I recognize that the first string of numbers is the box size for the run. What do the "60 40 40 4 0 0 0" and "0.00001" indicate? Is sander actually reading the box size from this file and using these values in the run? I couldn't find reference to this in the manual.

Thanks!

John Beale

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