[AMBER] Preparation of i-Motif structures

From: Sruthi Sudhakar <sruthisudhakarraji.gmail.com>
Date: Wed, 10 Feb 2021 03:00:41 +0530

Dear all,

I would like to know how the preparation of i-motifs ( semiprotonated C-C+)
base pairs can be prepared. We could add a hydrogen on to the nitrogen to
make it protonated,but how different would be the forcefield preparation.
Typically for G quadruplexes we could use the OL15 force field, what would
be the case with i-Motifs? Also since there is a semiprotonated cytosine,
do we need any other parametrization to continue with the topology

Thank you for any guidance you can provide.

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Received on Tue Feb 09 2021 - 14:00:02 PST
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