namdenergy and amber trajectory

From: Alessandro Nascimento (as_nascimento_at_yahoo.com.br)
Date: Wed Jul 30 2008 - 10:06:27 CDT

Hi Everyone

Thanks for the comments and suggestions

I compared the results from NAMDenergy and the results I computed
using the amber script "mm_pbsa.pl" and they matched perfectly. So
that told me that there was an error in my code.
Fortunately, I found it (a vector index). Now everything is fine...

I still want to make some tests with larger molecules to see how the
1-4scaling affect the results in amber ff. If some of you have interest
in this comparison, send me an e-mail and I can let you know my results!

Thanks a lot,

--alessandro

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