[AMBER] MMGBSA on Protein-DNA/RNA complex

From: Muthukumaran R <kumaran.bicpu.edu.in>
Date: Tue, 23 Jun 2015 16:02:15 +0530

Dear amber users,
I found from literature and mailing list that implicit simulations for
nucleic acids is not properly parameterized. I have done explicit solvent
simulations for protein-DNA and protein-RNA complexes. I want to study the
specificity of protien towards DNA/RNA, in this regard I have performed
binding energy calculations using mmgbsa (AMBER 12 and Amber tools 13)

Input used:
  startframe=20000, endframe=25000,interval=50,
  verbose=2, keep_files=1,


1. is it possible to study specificity using MM-GBSA.
2. As it is a relative method, is it meaningful to compare the binding
energies of DNA and RNA?
3. In regard to the gb model, I have adopted igb=5 (modified OBC model) as
used in "A Computational Study of Nucleosomal DNA Flexibility by Jory Z.
Ruscio and Alexey Onufriev". is this still an accepted model for studying
nucleic acids.

Apart from MM-GBSA, is there any other analysis/method for studying the
specificity of Protein towards DNA and RNA.??
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Received on Tue Jun 23 2015 - 04:00:02 PDT
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