AMBER Archive (2003)

Subject: Re: AMBER: Restraints to maintain base pair planarity

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Wed Oct 15 2003 - 11:51:12 CDT

Hi,
> Is there a way to specify planar restraints to maintain base pair
> planarity for NMR refinement using AMBER.
There is a way that works *in principle*:
One can penalize deviation from planarity by adding
'soft bonds' (i.e. distance restraints) between *say* three atoms from
base A and 3 atoms from base B. For 'best performance', bonds should be
added like A1-B1, A1-B2, A1-B3,...,A3-B3.
This is not 'elegant' but it worked for me (not NMR related). You just
need the right 'bond
lengths' to start with. To have good leverage, the atoms
should be chosen such that they form large roughly equilateral triangles.

Hope it helps
(And sorry if that doesn't help for NMR refinement :-)
Andreas

             
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