Hi,
> 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,
Thomas
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
