AMBER Archive (2009)

Subject: RE: [AMBER] glycopeptide Parametrization

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Sat Jun 13 2009 - 02:40:00 CDT

Dear Ross & Carlo,

>> Please let me know if this is what you meant. Which charges I will be
>> using with this parametrization ? Charges based on the Connolly surface
>> for the amino-acid residues and charges based on the CHELPG algorithm
>> for the sugar ?
>
> I would use RESP charges for everything. See: W.D. Cornell, P. Cieplak, C.I.
> Bayly & P.A. Kollman J. Am. Chem. Soc. 1993, 115, 9620-9631.

Just few additional comments:

- For the "peptide" part use RESP charge derivation approach as in
AMBER force fields: This means use the Connolly surface + 2 RESP
stages with qwt=.0005 & qwt=.001.
See also P. Cieplak, W.D. Cornell, C.I. Bayly & P.A. Kollman J.
Comput. Chem. 1995, 16, 1357-1377.

- For the "sugar" part use RESP charge derivation as in the GLYCAM
force field: This means use the CHELPG algo. + 1 RESP stage with qwt =
qwt=.01.
See R.J. Woods & R. Chappelle. J. Mol. Struct. (THEOCHEM) 2000, 527, 149-156

For additional references, see:
http://q4md-forcefieldtools.org/RED/reference.php

All this is automatically set up in R.E.D. and/or R.E.D. Server. You
just pick up the "RESP-A1A" or "RESP-C2" charge models:

-1- RESP-A1A: HF/6-31G* Connolly surface algo., 2 stage RESP fit
qwt=.0005/.001
-5- RESP-C2: HF/6-31G* CHELPG algo., 1 stage RESP fit qwt=.01

This means two different charge derivation approaches for the two
different parts of your molecule (NO am1-bcc and NO gaff):
See http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
     http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#27

regards, Francois

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