Simulating Protonated base pairs of RNA

From: Monika Sharma (mon_sharma_at_research.iiit.ac.in)
Date: Sat Jul 11 2009 - 07:07:29 CDT

Dear All,

I plan to simulate RNA molecule using CHARMM 27 force fields. One of the
base pair A:C is non-canonical, with the protonated Adenine (N1 is
protonated) pairing with cytosine as W:W cis. The parameter files have
options for neutral bases. I wish to know how to proceed with such base
pairs. I mean setting the charges etc. This may be important feature, since
the base pair is present at the proximity of helix near a junction. If
someone has experiences with such cases. Do I need to parametrize or so??
All suggestions are welcome.

Thanks in advance..

Regards
Monika Sharma

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