Re: [AMBER] Antechamber trouble with COA-acyl chain

From: M. L. Dodson <>
Date: Thu, 14 Jul 2011 10:28:36 -0500

OK, I have a design question about how best to approach new residue
generation for complex molecules, (re: the acetyl-CoA discussion current
on the list).

I see two ways of going about this:

1. Treat the whole structure as one molecule.

   a. This has the virtue of simplicity.
   b. Dihedrals between natural substructures may or may not be well
   c. There is so much flexibility (due to the flatter energy surface
   for the dihedrals I mentioned) that QM programs would likely be slow
   to converge.

2. Treat the structure as composed of "residues" (substructures) like we
do for nucleic acid and protein components.

   a. For acetyl-CoA these would be (countless introductory biochemistry
   textbooks break it down this way):
                acetyl group - beta-mercaptoethylamine - pantothenic acid -
   b. Each one can be treated as a residue, the QM for each likely
   converges quite rapidly, and you have a family of "residues" that
   make analogs of, e.g., acetyl-CoA easy to define in LEaP. The only
   problematic residue is the 3'-5'-ADP because of the extremely high
   negative charge. This argues for its further subdivision into
   adenosine, interior pyrophosphate, and 3'-terminal phosphate.
   c. LEaP has facilities to set the dihedrals as desired and thorough
   FF development will tell you the energetics (i.e., probabilities) of
   the dihedral values.
   d. I'm almost positive the RED people would recommend this course.
   They can correct me if I am wrong.

It seems to me that method 2 is better in almost every way (although not
likely so obvious to an AMBER novice.)

What say the experts?

Bud Dodson
M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
Gmail: mlesterdodson-at-gmail-dot-com
Phone: eight_three_two-five_63-386_one
AMBER mailing list
Received on Thu Jul 14 2011 - 08:30:03 PDT
Custom Search