On Thu, Feb 13, 2003, Tian-Xiang Xiang wrote:
>
> I have simulated a peptide in a box of solvent molecules using Sander. I
> need to know the intra-molecular Interaction of the peptide and the
> inter-molecular interaction of the peptide with surrounding solvents. What
> is the best program to do this? The only program I know that might be able
> to do this is
>
> ???Anal???, but I don???t have an example input file that I can modify to my
> need. The manual is pretty hard to follow.
>
There are sample anal input files in $AMBERHOME/test/vac_rna. Maybe those
will help. Don't be afraid to do some trial and error.
..good luck...dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Thu Feb 13 2003 - 15:21:15 PST
