Good evening,
I have a confusion regarding prepgen's mc file. In particular, I am
confused whether one needs to list the main_chain atoms.
1.) In tutorial5, the authors list several main chain atoms.
However, the manual states, on p.275, "By default, the program generates
a mainchain itself. However, you may also specify the main-chain atoms
in the main chain file..." through to the end of the top of p.276.
I am confused: it says the program generates the mainchain
automatically. Either my interpretation of the manual is flawed or the
tutorial was just writing this for the fun of it?
2.) If I do need to specify the mainchain in entirety /explicitly/, do I
need to specify ALL atoms? For example, if I have a nucleotide, I need
to specify the entirety of the ribose or the nucleic acid? Obviously, I
can pick a connectivity between head-tail that ignores half the ribose
and all of the nucleic acid.
3.) I would assume that, if a PDB DNA strand is written 5' to 3', the
"head" will be defined as oxygen ester nearest the methylene outside the
ribose (and the tail is thus what was the ribose alcoholic oxygen before
dehydration synthesis)? This is my understanding of biochemistry, but
perhaps I do not know if the implicit terminal caps of leap DNA strands
somehow change what is my perception of how this works.
---
Dr. Robert Molt Jr.
r.molt.chemical.physics.gmail.com
Department of Chemistry & Chemical Biology
Indiana University-Purdue University Indianapolis
LD 326
402 N. Blackford St.
Indianapolis, IN 46202
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Received on Mon Sep 21 2015 - 19:00:03 PDT
