Re: [AMBER] sander bomb and maxpr question

From: Andrew Olson <>
Date: Wed, 24 Mar 2010 07:08:15 -0700 (PDT)

you were right, i was trying to refine using all 20 structures from cyana. i did it again with one structure and it works fine. I do have a couple questions regarding the simulated annealing for the NMR refinement:

1) the tutorial has the heating up phase going up to 600K for the DNA complex, is this normal, even for proteins?
2) the penalties of NMR refinment are printed in kcal/mol, is there a standard for how big a penalty should be before you consider taking that constraint out?



From: case <>
To: AMBER Mailing List <>
Sent: Wed, March 17, 2010 7:36:14 PM
Subject: Re: [AMBER] sander bomb and maxpr question

On Wed, Mar 17, 2010, Andrew Olson wrote:

> This may be a dumb question but isnt this what this NMR structure
> refinement is supposed to do, take my not so good structure from CYANA
> and get rid of the VDW clashes.
> I changed those values from 30,000,000 down to 3 then to 2 then to 1 and
> it didnt help, so i will give the pmemd a shot. Do you have any advice
> for trying to refine an NMR structure from CYANA? THanks again.

I suspect that something is quite wrong with the structure, not just a few
vdW clashes. Have you visualized the input structure? Does it all look
OK? Finding way too many nonbonded contacts suggests that Amber thinks
there are all kinds of atoms really close to each other, way outside the
normal range one would have for a reasonable structure. Make sure the
coordinates are really being read in correctly.


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