Good afternoon,
I was hoping to please be advised where in the documentation it
clarifies when leap chooses to add an Ho atom.
When searching through the Amber user forums, I found several posts, but
none seemed to apply to my case. For example, D. Case once stated
"With just an obvious phosphate force field, bad things can happen with the
terminal H atom. We "cheated" by adding an artificial P--H bond to keep the
geometry of the terminal P-O-H group fixed (as in TIP3P water, for
example)."
In my particular case, I see Ho atoms added to non-terminal phosphates
as well as to alcohol groups coming off of terminal ribose units. I am
unsure what causes leap to add these to my PDB (it leaves other
phosphates in the DNA backbone alone, just some get a Ho).
These are the mysterious atoms that entered my produced PDB file that I
formerly thought were resultant from a prepgen error.
--
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
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Received on Wed Oct 14 2015 - 12:00:03 PDT
