AMBER Archive (2009)

Subject: RE: [AMBER] glycopeptide Parametrization

From: Ross Walker (
Date: Fri Jun 12 2009 - 11:09:37 CDT

Hi Carlo,

> Now my parametrization is as simple as that (I am using the bondi
> radii because I want to try an implicit-solvent simulation with
> igb=7, but of course I will also run the explicit-solvent one):

Unless you have specific reasons for using IGB=7, say comparison to previous
results, then I would suggest avoiding it and using IGB=5. I think the
general consensus right now is that IGB=7 does not improve over the previous
GB results and can potentially make things worse.
> xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
> set default PBradii bondi
> source leaprc.glycam04
> x = sequence { NVAL GLU ARG NLN GLY HIS CSER }
> set x tail x.4.11
> set 1GB head 1GB.1.1
> y = sequence { x 1GB }
> savepdb y y.pdb
> saveamberparm y y.crd
> quit
> 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.

> As for the 1-4 scaling factors, I performed my previous simulations
> using the default values, e.g.
> SCNB = 2.0
> SCEF = 1.2
> Are these values appropriate for a glycopeptide simulation ?
> If I explicitly set these values in the .in input files of
> my REMD simulation, will the apply to both the peptide and
> the sugar parts ?

There is a slight mismatch right now between the Glycam force field and the
protein ones. The protein force fields all scale VDW by 2.0 and EEL by 1.2
(I assume you meant SCEE above and not SCEF) which are the defaults. GLYCAM
on the other hand does not do any scaling so would have SCNB = SCEE = 1.0.
AMBER 10 does not support such mixing of different 1-4 scaling factors
(AMBER 11 will support it) and thus at present you have to choose a
compromise. I believe the current 'accepted practice' is just to use the
defaults of 2.0 and 1.2 for everything when doing mixed protein /
carbohydrate simulations.

Good luck,

|\oss Walker

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| San Diego Supercomputer Center |
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