Re: [AMBER] NMR distance restrained MD

From: Christina Bergonzo <>
Date: Thu, 2 Jan 2020 08:45:30 -0500

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!

On Thu, Jan 2, 2020 at 2:57 AM maya nair <> 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

Christina Bergonzo
Research Chemist
Biomolecular Measurement Division, MML, NIST
AMBER mailing list
Received on Thu Jan 02 2020 - 06:00:03 PST
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