AMBER Archive (2006)

Subject: AMBER: Hessian matrix

From: Marie Brut (
Date: Mon Feb 06 2006 - 06:12:53 CST


I have two problems actually.
First, before working on proteins, I'd like to use Amber to test my job on a
little polymer : the PNIPAM, which is not a biological molecule (and so, has not
recognized residues). How can I construct a PDB file which will be recognized,
and what potential must I use ?
Secondly, I only need to minimize my structure and to obtain the Hessian
matrix. Is it an obligation to calculate the normal modes to obtain it ?
A last problem for me in minimization is the convergence criterion : I do my
minimization for 10000 cycles or more, but I never get 1.10-4. Can I hope
getting this accurancy, and is 1.10-4 really necessary to consider a
minimization is good ? Can I be satisfied if I only obtain 1.10-2 for example ?

Thank you in advance for your help,
Best regards,
Marie Brut
Marie Brut
7 avenue du Colonel Roche,
31077 Toulouse

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