Thanks Lachele and Karl for your quick responses
In fact, I would like to simulate sophorolipid with GLYCAM (Figure 1B in the following link [1]). The cis double bond is for C18 alkyl chain. So I wonder if the available GLYCAM's or the karl's parameters are sufficient to favor the cis conformation.
[1]
http://www.biosurfing.ugent.be/sophorolipids.htm
________________________________________
De : Lachele Foley [lf.list.gmail.com]
Envoyé : lundi 17 février 2014 16:33
À : AMBER Mailing List
Objet : Re: [AMBER] GLYCAM parameters for cis double conformation
Thanks, Karl! 06j is the most recent release. Shortcut: glycam.org/params
Do see also the release notes if anything using the glycam parameters will
be bonded to a protein. The j release is designed for ff10, ff13, ff12SB
and ff13SB. The info in GLYCAM_06j.dat should be backward compatible with
older protein ffs, but prep and lib files might not be.
On Mon, Feb 17, 2014 at 10:26 AM, Karl Kirschner <k.n.kirschner.gmail.com>wrote:
> 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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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Mon Feb 17 2014 - 08:30:02 PST
