AMBER Archive (2007)

Subject: AMBER: Normal Mode Analysis

From: Kresimir Sikic (kresimir.sikic_at_fer.hr)
Date: Mon Aug 13 2007 - 10:12:59 CDT

Hi,

 

I have one particular question related to Amber's NMA - I would like to do
the following: take part of a protein (e.g. one HELIX) in .pdb format load
it into Amber's NMA (Nmode program) and get the following output:

a.) stable conformation with a minimum of potential energy (new coordinates
of all atoms, and total potential energy of new structure)

b.) potential energy of input structure (structure before energy
minimization).

 

Is the above possible? If so, please can you give me couple hints how to do
it using Amber (what is the procedure for doing that?).

 

Thank you in advance.

 

Best regards,

Kreso

 

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