AMBER Archive (2007)

Subject: Re: AMBER: NMR refinement

From: David A. Case (case_at_scripps.edu)
Date: Wed Sep 26 2007 - 17:03:01 CDT

On Wed, Sep 26, 2007, Wenyong Tong wrote:
>
> Could you please give some suggestions about the
> following results from NMR refinement? Please note
> that the final temperature did not get down.

You should examine the beginning of the input file, where the program prints
out the weight change information: be sure it seems to do what you want.

I don't see anything obviously wrong with the input, but I'm probably missing
something. But try some short(!) test cases to make sure annealing is doing
what you want -- something like 1,000 to 10,000 times shorter than what you
showed here.

>
> NMR restraints: Bond = 0.045 Angle = 0.000
> Torsion = 0.000

Note that even without cooling, you have essentially zero restraint
violations. I have no idea whether this means that your structures are really
good, or that your restraints are too weak, but it is something to look into.

...dac

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