AMBER Archive (2004)

Subject: Re: AMBER: single amino acid energy

From: Holger Gohlke (
Date: Tue May 18 2004 - 10:23:26 CDT

> Helios Chen schrieb:
> Dear all, I wonder to calculate the single amino acid energy at the
> minimiz status in whole protein, how can I do? For example, a protein
> included 200 amino acid, and I want to calculate the minimized
> energy of 40th amino acid. Could anyone help me? Thanks in advance.

You might want to take a look at the mm_pbsa section, in particular the
decomposition part. You can feed mm_pbsa your restart file from the
minimization, provided you rename it as PREFIX_rec.crd.1 (where PREFIX
is specified in the file).

Best regards


Dr. Holger Gohlke

J.W. Goethe-Universität Fachbereich Biologie und Informatik Institut für Mikrobiologie Marie-Curie-Str. 9 60439 Frankfurt/Main Germany

Tel.: (+49) 69-798-29411; Fax: (+49) 69-798-29826 Email: URL: ++++++++++++++++++++++++++++++++++++++++++++++++++ ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to