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 - 11:30:02 PST
