Re: [AMBER] tar-MD with custom J-coupling relation

From: Christina Bergonzo <>
Date: Tue, 3 Mar 2020 09:02:34 -0500


I don't know of any way to implement a different Karplus relation for
direct refinement against J coupling constants - in the past I've
translated J coupling constants to torsions and used those as restraints
It seems like you'd need to edit the functional form of the Karplus
equation found at lines 1492-1500 in nmr.F90.


On Tue, Mar 3, 2020 at 8:37 AM Dieter Buyst <> wrote:

> Dear all,
> After going through the manual and looking through the archive, I couldn't
> identify an answer to the following question:
> Given one wants to run time averaged restrained (tar) MD with J-couplings
> as the primary restraints, is it possible to define your own relationship
> that AMBER uses to calculate the possible torsion angle values outside of
> the classical Karplus relation? More specifically, we have parameterized
> our own relation specifically for fluorinated compounds and now want to
> test this relation using MD.
> Previous work (years ago) has been done in the past using the Diez-Donders
> relation but this involved adapting the AMBER source code (specifically the
> nmr.f file) but this falls outside of my programming knowledge for the
> moment.
> If anyone could point me in the right direction or confirm that adapting
> the source code is the only possible way, that would be greatly appreciated!
> Best regards,
> Dieter
> Dieter Buyst
> Department Organic and Macromolecular Chemistry
> Ghent University
> Belgium
> _______________________________________________
> AMBER mailing list

Christina Bergonzo
Research Chemist
Biomolecular Measurement Division, MML, NIST
AMBER mailing list
Received on Tue Mar 03 2020 - 06:30:02 PST
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