Re: [AMBER] relative binding free energy - tutorial a9

From: <>
Date: Sun, 4 Dec 2011 14:57:54 -0500 (EST)


> You broken up each transformation into three substeps : 1) Remove charges
> from BNZ 2) Transform BNZ into PHN and 3) Add charges to PHN.
> I want to know should I use 3 substeps also?

You don't need to, since Amber11 can also do onestep transformations
without first removing charges. Check Steinbrecher, Joung, Case, 2011, J
Comp Chem (I think). However, it may be advantageous to do it in multiple
steps. mutating DNA is a big change, so make sure that you have good
experience using the TI code on smaller changes before you tackle such a
big problem.

Kind Regards,


Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Sun Dec 04 2011 - 12:00:05 PST
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