AMBER Archive (2008)

Subject: Re: AMBER: residual dipolar couplings - alignment tensor energy

From: David A. Case (case_at_scripps.edu)
Date: Wed Apr 02 2008 - 12:53:38 CDT

On Wed, Mar 26, 2008, Douglas Kojetin wrote:
>
> (A) Should the alignment tensor information (s11...s23) in the DIPOLE
> restraint file be updated for the last minimization step to reflect
> the minimized (float) alignment tensor from the SA step?

Yes.

> (B) Should I increase the number of steps of either the steepest
> descent or conjugate gradient minimization performed during the last
> minimization step to allow the tensor to float back to the original,
> initial estimate?

Hard to say: you will probably have to experiment some to determine the best
number of steps.

> (C) Should I not specify a DIPOLE restraint file in the minimization
> step?

No, including the DIPOLE information in the final minimization may make sense.
As always with dipolar couplings, you need to be careful about overfitting.
Use the weakest restraints you can get away with. Many people assign a weight
of zero to these terms, just using them to validate (or not!) structures
determined on the basis of other restraints.

...good luck....dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu