AMBER Archive (2008)

Subject: Re: AMBER: NMR refinement

From: David A. Case (
Date: Sat Jan 19 2008 - 12:39:08 CST

On Fri, Jan 18, 2008, Wenyong Tong wrote:
> Was this recommended to you for sugars or something?
> No.

Unless you have good reasons for changing the offset from its default value, I
would strongly recommend against doing it.

> There are some distances with high penalty. I deleted about 10 violations. I
> got the following results. I wonder whether it is appropriate to delete
> them. I know two NOE assignments are ambiguous, but how about others? Should
> the final Eptot be minus?

Only you can decide what constraints to use. There is no reason to expect
Eptot have any particular sign: it depends entirely upon the problem at hand.
(Molecular mechanics energies are only meaningful as relative numbers, not as
absolute numbers.)


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