Thank you very much for the reply.
Since there is no crystal structure available, I started with a docked
structure and that structure is very much seemed to satisfying nmr
structure (position of ligand almost to a position which satisfies the NOE
distance). Can you give a suggestion of how much distance penalty can be
taken for a valid structure?
Regards,
Maya
On Thu, Jan 2, 2020 at 7:15 PM Christina Bergonzo <cbergonzo.gmail.com>
wrote:
> Hello Prof. Nair,
>
> There is plenty that can be going on to cause distortions in a structure
> when NMR distance restraints are active.
> The two things I would check first are:
> Does your initial conformation violate any NOE restraints? Which ones? A
> large number of violations may indicate that the docked position doesn't
> reflect the position sampled in the experiment, and forcing it to change
> via activating NMR restraints could cause many distortions and ultimately
> vlimit errors/simulations crashing.
> The second thing I would check is to make sure the distance restraints were
> generated using the same structure you are simulating. If the atom
> numbering is off, the restraints will be incorrectly applied.
>
> Hope this is helpful!
> -Christina
>
>
> On Thu, Jan 2, 2020 at 2:57 AM maya nair <mayasnair1.gmail.com> wrote:
>
> > Dear Prof. David,
> > I am trying to do the NMR restrained MD for a DNA-ligand complex. I
> started
> > with a docked structure. Minimized it and the MD was run . When adding
> > distance file, the structure is getting very much distorted. I followed
> the
> > tutorial A4 in structure refinement in Amber and also followed the MD
> > tutorial and added dist file into them. But my structure is getting
> > distorted. What are the precautions to be taken to avoid this/ Can you
> give
> > some suggestions to workout this?
> >
> > Thank you
> > Maya
> > --
> > Maya S Nair
> > Assistant Professor
> > Department of Biotechnology
> > IIT Roorkee
> > India
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> -----------------------------------------------------------------
> Christina Bergonzo
> Research Chemist
> Biomolecular Measurement Division, MML, NIST
> -----------------------------------------------------------------
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Maya S Nair
Assistant Professor
Department of Biotechnology
IIT Roorkee
India
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Received on Mon Jan 06 2020 - 04:30:01 PST
