Good evening,
I am confused on proper parameterization of units which are covalently
bound. I am going to introduce a modified nucleotide into a DNA crystal
structure of a standard helix properties. I thus need to create a unit
in leap to identify the modified nucleotide. My question is independent
of the nature of modified nucleotide, so I will just frame them in terms
of adenine.
In adenine nucleotide, I would inherently put a hydroxyl group on the
ribose for parameterization. An internal ribose would actually have this
be a linkage to the next phosphate. I am confused how this will be read
properly by leap. When I go to parameterize, it will create a unit with
for parameters for OH bonds, but the unit I load into leap must discard
these parameters? Same logic applies for the OH on the phosphate, which
will in reality make a phosphodiester linkage?
I apologize if this obvious; understanding the answer to this question I
believe will help me load my unit properly.
--
Dr. Robert Molt Jr.
r.molt.chemical.physics.gmail.com
Visiting Associate Professor of Chemistry
Department of Chemistry & Chemical Biology
Indiana University-Purdue University Indianapolis
LD 326
402 N. Blackford St.
Indianapolis, IN 46202
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 16 2015 - 19:00:03 PDT
