AMBER Archive (2007)

Subject: Re: AMBER: refinement of NMR struture using AMBER

From: Seth Lilavivat (sethl_at_gatech.edu)
Date: Thu Sep 06 2007 - 14:20:52 CDT

This is a good question. The protocol that we have been using is
running MD (simulated annealing) with NMR restraints and then
minimizing with NMR restraints. The structure hardly moves because
when minimizing WITH NMR restraints. I have tried minimizing WITH OUT
NMR restraints and the structure moves very slightly. However, even
the slightest change from the minimization WITH OUT restraints creates
some NOE violations so we decided to minimize WITH NMR restraints.

Seth

On 9/5/07, Prem Prakash Pathak <prempolymer_at_gmail.com> 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 <andy810915_at_gmail.com> 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 <prempolymer_at_gmail.com> 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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