Re: [AMBER] carbon and nitrogen chemical shift restraints

From: David A Case <>
Date: Fri, 3 Oct 2014 09:32:15 -0400

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 would
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 there
something else (CAMSHIFT?) that seems to give good results? It would be good
for sander to have this capability, and I could probably get someone here to
work on that. Of course, that would take time, and hence does not solve your
immediate problem.

[If you do decide to do this yourself, please consider contributing the result
to the AmberTools code base, so that others can benefit as well. We'll make
sure you get proper credit.]


AMBER mailing list
Received on Fri Oct 03 2014 - 07:00:03 PDT
Custom Search