Re: AMBER: refinement of NMR struture using AMBER

From: Prem Prakash Pathak <>
Date: Wed, 5 Sep 2007 19:31:41 +0530

I want to do restrained energy minimization for ensemble of conformers
obtaind from CYANA.
I have tried doing minimization without any NMR constraints , and i
did MD in explicite solvent.
I wanted to know very basics ,
1. when we should do only just minimization,
2. when we should do minimization with NMR constraints
3. When should we do minimization after running MD and also along with
NMR constraints.

On 9/5/07, andy ng <> wrote:
> I believe it is all depending on what is your purpose. Some will just do
> minimisation explicitly on the structure using NMR constraint using the
> input file from DYANA, CYANA structure. So that the structure deposited into
> PDB data bank would be energy minimised structure. Some would do
> minimisation followed by MD and minimisation using the same DYANA/CYANA
> structure. Others would also build the structure from the scratch and do MD
> with constraint and followed by minimisation with constraint to get the
> energy minimised structure. Hope this help a little bit. If you are not
> after the energy minimised structure, then don't worry about minimisation
> after the MD.
> Andy
> On 8/29/07, Prem Prakash Pathak <> wrote:
> >
> > Dear AMBER user,
> > What do we mean by refinement of struture using amber?
> >
> > Will any one explain me, what are the step followed to refine an NMR
> > structure using AMBER?
> > Does refinement means, minimization using the NMR constraint,
> > or it includes the molecular simulation using the NMR constraints?
> >
> > PREM

> >
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Received on Sun Sep 09 2007 - 06:07:09 PDT
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