AMBER Archive (2006)

Subject: AMBER: Free energy perturbation

From: Angelo Pugliese (
Date: Wed Feb 22 2006 - 10:42:06 CST

Dear all,

I am interested to know if somebody performed FEP calculations involving
the topology change double stranded DNA (decamer) versus DNA-RNA hybrid
(essentially mutating one of the DNA strands in RNA and calculating the
difference in free energy). Using a thermodynamic cycle pertubation
approach, I am not sure if may the size of the mutation be too big
(transforming 10 Hydrogens in 10 OH groups) for this kind of
calculations, in addition I am not sure about the reliability of the
single stranded DNA and RNAsimulations. Also, I would be glade to know
how to deal with the increment in the coupling parameter and with the
MD sampling for each LAMBDA value.

Thank you for your always useful suggestions.


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