Good evening,
I am having difficulty inserting a covalently bound unit within a DNA
helix (it is internal, not terminal). The problem seems the same as
presented in the Amber archives in 2010:
http://archive.ambermd.org/201002/0013.html
I was hoping to solicit clarification of the advice herein. I have a
nucleotide modified in a similar manner to that discussed here, such
that I think the solution is the same as suggested by Dr. Case in 2010.
My specific questions are
1.) It is advised to run antechamber using amber atom types. My
understanding is that this is because the normal nucleic acids are going
to use something akin to ff14SB or ff99SB, and leap would be confused by
a covalently bound (connected) atoms being a mixture of gaff vs. amber
force fields?
2.) I do not believe that this is an option for me; there are "missing
parameters" using "amber" force fields (the GAFF parameters are complete
when I check them). Can this advice be modified for using a nucleotide
with purely GAFF generated parameters? I know that in the preceding
thread (
http://archive.ambermd.org/201002/0005.html) that Dr. Swails
advised against this for the reason stated in #1.
3.) I have thus tried to create a new unit based on the advice on
creating a new unit, but failed. I think this is because I do not
understand why one cannot simply
UNIT_NAME=loadmol2 NAME.mol2
loadamberparams NAME.frcmod
and make sure the pdb name matches NAME for the unit? This fails
terribly, but I do not understand why (because I am not really sure I
understand how leap "recognizes" units and adds in the "right" missing
atoms (like a terminal P or O in a helix, or a missing hydrogen). I get
atoms overlapping ontop of one another.
4.) I do apologize if this information is in the Amber tutorials; to my
knowledge, 2 of them deal with non-connected ligand parameterization,
and one deals with connected-non-standard residue insertion in a protein
(whose process seems very different than for a helix).
--
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 Sun Sep 13 2015 - 17:30:03 PDT
