Re: [AMBER] NMR distance restrained MD

From: maya nair <>
Date: Wed, 29 Jan 2020 13:14:59 +0530

I checked my distances, which are not much varying from B-DNA distances .
But after MD it shows huge variations and the penalities shows a variation.
For slight differences , sometimes higher penality and vice versa. Another
problem I saw is that in dist file sometime H2'' is accepted and sometimes
H2' 2 and the second 2 is taken as the distance. I removed such distances
and checked, then it gives penalities for new one which are not there
Without restraints , structure is correct and after equilibration also the
structure is intact, eventhogh penalty is high.

On Tue, Jan 28, 2020 at 8:34 PM David Case <> wrote:

> On Tue, Jan 28, 2020, maya nair wrote:
> >Dear Prof David,
> Please send amber-related questions to the mail reflector,
> and not to me personally. That way, many people can see your question and
> try
> to help, and the answers can help others with similar questions. See
> for information on how to
> subscribe.
> >the distance penalty is high.
> There could be lots of reasons here. Try picking a particular distance
> that has large violations. Visualize you structures (all the way from
> the beginning to the when things fall apart) in the area of this
> distance: do you see anything that could be causing problems? Does the
> structure stay approximately "correct" if you have no NMR restraints?
> If so, add one or a few structures at a time to see what happens.
> Debugging things like this is pretty much something you have to do
> yourself. I'm assuming that you removed the bad restraint I pointed out
> earlier, but did you also try to figure out how/why that got there in
> the first place? Maybe there are other bad entries that are arising
> from the same reason.
> ...good luck....dac

Maya S Nair
Assistant Professor
Department of Biotechnology
IIT Roorkee
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Received on Wed Jan 29 2020 - 00:00:02 PST
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