Dear AMBER users,
I want to do a free energy analysis using the
MMPBSA.py script for my DNA G quadruplex system similar to the analysis of
Stefl et. al. (Biophys J. 2003 September; 85(3): 1787–1804. ) I would like
to compare the free energies of a quadruplex having a vacant stem with one
in which the stem contains the requisite number of ions. I was wondering
whether it would be correct to treat the G quadruplex as the receptor and
the channel bound ions as the ligand in this case. Any suggestions would be
extremely helpful.
Best Regards,
Debayan Chakraborty,
PhD Student,
Department of Chemistry,
University of Cambridge
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Received on Tue May 14 2013 - 05:30:03 PDT
