Re: [AMBER] carbon and nitrogen chemical shift restraints

From: Alexandra Balaceanu <>
Date: Fri, 3 Oct 2014 21:03:59 +0200

Thank you for your answer.

It would indeed be very helpful for sander to include such capabilities. My
project however does not focus on methodology, so I cannot invest much time
into implementing such features into sander. I will need to somehow
circumvent this problem.

I was reffering to xplor-nih previously, but indeed camshift does a very
nice job based on simple functions, easily differentiable with respect to
cartesian coordinates.

If you have the time, just out of curiosity, in what way do the data
structures need to be modified?

Best regards,


On 3 Oct 2014 15:32, "David A Case" <> wrote:
> On Fri, Oct 03, 2014, Alexandra Balaceanu wrote:
> >
> > I would like to know if there is any way to perform simulations in
> > Amber using carbon and nitrogen chemical shifts restraints. Or,
> > alternatively, to manually introduce a custom restraint potential that
> > would do the job, namely minimize the difference between observed
> > shifts and those predicted by a chosen method.
> There is no way now to include carbon and nitrogen shift restraints. It
> not be all that difficult to add custom code: you would probably want to
> modify the existing proton-only code in cshf.F90. But it's not all that
> simple, either, since you would have to grok the data structures that are
> being used in sander.
> >
> > I know there are other programs that do refinement using at least 13C
> > shifts, but for my purposes it would be very useful to have this
> > possibility within Amber.
> I agree. Are you thinking of the 13C restraints in nih-xplor? Or is
> something else (CAMSHIFT?) that seems to give good results? It would be
> for sander to have this capability, and I could probably get someone here
> work on that. Of course, that would take time, and hence does not solve
> immediate problem.
> [If you do decide to do this yourself, please consider contributing the
> to the AmberTools code base, so that others can benefit as well. We'll
> sure you get proper credit.]
> ...thanks...dac
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Received on Fri Oct 03 2014 - 12:30:02 PDT
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