Re: AMBER: refinement of NMR struture using AMBER

From: andy ng <>
Date: Fri, 7 Sep 2007 23:42:44 +1000

As you probably know, CYANA structure is a torsion angle dynamics structure,
therefore some of the side chains are not in energy minimum position.
Refinement in explicit solvent model also improve the overall quality of the
CYANA structure. I compared the difference between only minimisation and MD
followed by minimisation, all with NMR constraints. I found that the overall
quality is better if MD is performed and followed by minimisation. As to
your first question 'when we should do only just minimisation', my opinion
is that if your quality of your CYANA structure is very good (lots of NOEs,
more than 15 constraints per residue), then I would think refinement
explicitly without NMR constraints would not make much of the different. But
if your CYANA structure is a medium resolution structure, minimisation
without NMR constraints could lead to significant distortion of the
structure. So, to be safe, I think MD and minimisation with NMR constraints
is the best method to get the minimum energy structure using AMBER and CYANA


On 9/6/07, Prem Prakash Pathak <> wrote:
> 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.
> regards
> 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 - 06:07:30 PDT
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