AMBER Archive (2009)

Subject: Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala

From: Wallace Kunin (kunin_at_marshall.edu)
Date: Thu Nov 12 2009 - 02:15:40 CST

I have successfully completed the testing for AmberTools after doing sudo rm
/bin/sh then sudo ln -s /bin/bash /bin/sh. However, there are some tests
that possibly failed and I want to verify that I don't need to make anymore
adjustments

Running test of randomized embedding
>
> 1c1
> < radius of gyration: 7.340
> ---
> > radius of gyration: 7.196
> FAILED (OK if gyration radius is about 7 or 8)
>

Running test to do simple lmod optimization
>
> 1c1
> < Glob. min. E = -122.793 kcal/mol
> ---
> > Glob. min. E = -122.994 kcal/mol
> FAILED (probably OK if energy is -115 to -125)
>

cd antechamber/tp && ./Run.tp
> diffing tp.mol2.save with tp.mol2
> possible FAILURE: check tp.mol2.dif
>
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