Massimiliano,
The net charge needs to be integerized by sinking the charge difference onto
a neighboring atom. We're in the process of publishing the N-sulfate
charges so I'd like to discuss the implementation off the list. There was
quite a bit of work that went into generating these charge sets so, for now,
we address these on a case by case basis until the publication is released.
Please email me off-list to discuss this.
Matthew B. Tessier
Complex Carbohydrate Research Center
University of Georgia
+1 (706) 542-3508
mbt3911.uga.edu
matthew.tessier.gmail.com
-----Original Message-----
From: Massimiliano Porrini [mailto:M.Porrini.ed.ac.uk]
Sent: Wednesday, November 30, 2011 2:24 PM
To: AMBER Mailing List
Subject: [AMBER] D-N-Sulfate-glucosamine net charge
Dear Amber users,
I am attempting to do MD simulations of certain glycosaminoglycans (GAG)
interacting with proteins.
With regard to the partial charges, from the Amber archives I understood
that I should use the sulfate.prep file from GLYCAM website, whilst having a
look at the GLYCAM website FAQs I should use the parameters given in J.
Comp. Chem. Huige and Altona, Vol. 16, 56 (1995).
To familiarise with the tleap oligosaccharides building procedure I am
starting from monomer D-N-Acetylglucosamine in which I want to substitute
the acetyl with the sulfate group (at the N atom in position 2).
The total charge of the new sulfated compound should obviously be -1 .
If I implement the partial charges given in "sulfate.prep" file downloaded
from GLYCAM website (
http://glycam.ccrc.uga.edu/ccrc/pages/parameters.html
) I get a net charge equal to
-0.909000
whereas
if I implement the partial charges given in J. Comp. Chem. Huige and Altona,
Vol. 16, 56 (1995), I get a net charge equal to
-0.982000
which is closer to the unit (in this case I implemented the charges derived
for Isopropyl-Sulfamate and I used also the N and H atoms charges in
addition to those of SO_3).
For helping I enclosed the input file I use for tleap (where there are
several comments for clarity).
Am I doing right or missing something here?
Should I recalculate the partial charges through a RESP procedure?
But if this is the case, why is there a sulfate.prep file in GLYCAM website
and how should one use it?
Any hint/suggestion would be really appreciated.
Best,
--
Dr Massimiliano Porrini
Institute for Condensed Matter and Complex Systems School of Physics &
Astronomy The University of Edinburgh James Clerk Maxwell Building The
King's Buildings Mayfield Road Edinburgh EH9 3JZ
Tel +44-(0)131-650-5229
E-mails : M.Porrini.ed.ac.uk
mozz76.gmail.com
maxp.iesl.forth.gr
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Received on Wed Nov 30 2011 - 13:30:03 PST
