Re: [AMBER] NMR distance restrained MD

From: David Case <>
Date: Thu, 2 Jan 2020 13:41:00 +0000

On Thu, Jan 02, 2020, maya nair wrote:

>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?

Use the LISTOUT=POUT command command to see the violations you are
getting for each individual distance. Are most satistified, but just a
few are bad? Is everything bad? Can you do a trial calculation with
just a few distance restraints, and gradually add more to see which ones
might be causing the problem?

If you have lots of restraints, the "sviol" program will format the
info into a nicer format, making it easier to visualize. This is
helpful if most the of restraints are being satisfied, and only a few
are causing problems. It is less useful if basically all the restraints
are causing problems.


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Received on Thu Jan 02 2020 - 06:00:03 PST
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