Re: angle violation in SANDER simulation

From: David A. Case <>
Date: Wed, 4 Jun 2003 08:17:32 -0700

On Wed, Jun 04, 2003, XU Xingfu wrote:

> I am beginning to learn use AMBER 7 to do energy minimization of
> my protein structure after the NMR calculation by CYANA. I used the 15ps
> simulated annealing protocol without any change of the parameters according
> to the tutorial. The final summary file says that there are some angle
> restraints violations ( > 5 and even 50). The distance restraints have no
> large violation( < 0.25). But using the same restraints files, CYANA
> calculation will not generate any angle violation( > 5). The angle
> violations generated during AMBER refinement are in the loop regions where I
> only set some very loose restraints by TALOS prediction.

There's not much information to go on. You need to look at these particular
violations in detail. What are the penalty energies? You may need to
increase the force constants on these restraints if you want to make it more
likely that they will not be violated. On the other hand, if other (distance)
restraints are better satisfied than in the starting structures, the
simulations may be telling you that the loop has a conformation different than
that predicted by TALOS.

...good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Wed Jun 04 2003 - 16:53:03 PDT
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