Stefane,
Partial charges in GLYCAM06 are obtained through a series of steps and are
molecule-dependant, not necessarily atom type dependent. With that being
said, the "HC" atom-type in sugars is an exception to this. These atom
types have a zero charge because in sugars the charge fluctuation on
aliphatic hydrogens (type HC) is around zero. All the sugars in the
GLYCAM06 prep file have charges already developed for them. If you need to
create your own, here is a general overview of the process.
1. A QM structure is optimized at HF/6-31G* (add diffuse functions for
anionic systems - do this everytime in the development process)
2. Obtain single point energy at HF/6-31G* and calculate initial charges
using a RESP weight of 0.010 and zero charge on the aliphatic hydrogens.
3. Run a MD simulation of the fully solvated structure and extract 100
snapshots (equally dispersed).
4. Using the optimized valence terms from the QM, add hydroxyl and exocyclic
torsions from the 100 snapshots. Freeze these torsions, and re-optimize the
structure at HF/6-31G*.
5. Obtain single point energies for all 100 optimized snapshots and again
use a RESP weight of 0.010 and a zero charge on the aliphatic hydrogens to
calculate charges. Then use the average of all 100 as your final charge
set.
Hopefully this answers your question.
Matthew Tessier
mbt3911.uga.edu
matthew.tessier.gmail.com
Woods' Lab Room 1092
Complex Carbohydrate Research Center - University of Georgia
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Stephane Abel
Sent: Thursday, November 20, 2008 10:40 AM
To: amber.scripps.edu
Subject: AMBER: CG and HC atoms partial charges in AMBER
Hi AMBER users
I would like to simulate a dodecan chain with the AMBER force field
but *without* the AMBER code (i use an other MD package). So I construct
manually the topology and the parameter for this molecule. For
subsequent simulations, I will use GLYCAM_06. So I have a little
question about the partial charge of the carbon (CG) and hydrogen atoms
(HC). How to obtain them ?
Thank you for your help
Stefane
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Received on Fri Dec 05 2008 - 16:10:12 PST
