Dear Amber community,
I am setting up an MD simulation of a monomolecular DNA G-quadruplex
containing internal 3'-3' and 5'-5' inversion of polarity sites (IPS),
(non-canonical phosphodiester linkages) where two 3'- or two 5'-hydroxyl
groups are connected by a native phosphate group.
I have built the model with the correct connectivity starting from an
existing PDB structure, and I would like to optimize it by MD simulation.
I searched the Amber manual, tutorials, and online archive but could not
find guidance on this specific case.
My questions are:
1. Is there a reasonable protocol in the Amber community for preparing
and running MD simulations of DNA with 3'-3' and/or 5'-5' IPS?
2. In particular, how should the non-canonical junction residues be
handled in tLEaP to ensure a physically correct bonded topology?
Thank you for any guidance or pointer to relevant work.
best regards
Carmen
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Received on Wed Apr 08 2026 - 13:00:02 PDT
