AMBER Archive (2008)

Subject: Re: AMBER: relative weight of RDC constraints

From: David A. Case (
Date: Mon Dec 15 2008 - 10:44:19 CST

On Mon, Dec 15, 2008, David Witte wrote:

> I'm recently trying to use RDC constraints for a NMR structure
> refinement with Amber10. I'm performing a simulated annealing
> calculation with a following energy minimization. Currently, I'm using
> dwt=0.01 for the simulated annealing and dwt=0.5 for the energy
> minimization.

> If I use dwt>0.01 for simulated annealing Amber crashes.

More information please! Is there any output before the crash? Are you
saying it works with dwt=0.01 but not with 0.02? etc.

> If I use dwt=0.01 for the energy minimization Amber doesn't seem to
> include the RDCs in the calculation. In this case all calculated RDCs
> have a value near 0.

Why do you say "Amber doesn't seem to include the RDCs"? The minimization
you report shows a penalty function being applied:

> Residual dipolar splittings:
> ----------------------------------------------------------------------------
> First atom Last atom curr. value target deviation penalty dista
> ----------------------------------------------------------------------------
> N LEU 5 -- H LEU 5: -0.061 -2.150 2.089 0.025 1.041
> Total align constraint: 114.79

This looks to me like you had penalties active, with a total alignment
constraint energy of 114 kcal/mol. So, from what you have sent so far, it
looks to me like the constaints *are* being included.

I agree that it is funny that all of the calculated values are near to zero,
but I can't say much more, given that I know so little about what you did --
how many steps of minimization were run? Did you set the "iscale" variable?
And so on: basically, the portion of the output file you supplied is not
enough to allow the problem to be diagnosed.


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