Hello Stéphane,
According to Glycam06g-1.dat, double bonds are described by the atom
types Ck and Cj. Depending on what internal coordinate you want to model,
there may be existing torsion parameters (e.g. Os-Ck-Ck-Cg, Cj-Ck-Ck-Cj).
You might want to take a look at the Glycam's groups website (
glycam.ccrc.uga.edu/ccrc/) to obtain the most current force field, which I
think is GLYCAM_06j.dat.
If you are looking for an alternative parameter set for modeling
glycolipids, you could look at the parameters that we optimized and used to
model a gram-negative bacteria's bilayer (
http://dqfnet.ufpe.br/biomat/Software.html).
You are also welcomed to use Wolf2Pack (www.wolf2pack.com) to
test/optimize parameters that should be compatible with Glycam06g-1.dat. If
you do this, you will have to be careful to convert the atom types to the
Glycam's current scheme (i.e. Xy) once you have optimized the parameters,
since W2P uses the older full capitalization version (e.g. XY).
Best regards,
Karl
<
http://glycam.ccrc.uga.edu/ccrc/users/dpage.jsp?contentType=chemical/x-dat&type=Parameter&projectName=glycam06&fileName=GLYCAM_06j.dat>
On Mon, Feb 17, 2014 at 2:35 PM, ABEL Stephane 175950
<Stephane.ABEL.cea.fr>wrote:
> Dear Amber users,
>
> Does anybody know if recent parameters for specific cis double bond for
> GLYCAM were already parametrized? I know those from Tessier et al JCC 2008
> for phospholipids, but they are quite old.
>
> Thank you
>
> Stéphane
>
>
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Received on Mon Feb 17 2014 - 07:30:02 PST
