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

From: Dieter Buyst <Dieter.Buyst.UGent.be>
Date: Tue, 3 Mar 2020 13:37:30 +0000

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 Buyst
Department Organic and Macromolecular Chemistry
Ghent University

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Received on Tue Mar 03 2020 - 06:00:02 PST
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