Hello Karl,
Thank you very much for your kind assistance. I will take a look at them.
Stéphane
--------
Stéphane Abel, PhD
CEA Saclay DSV/IbItec-S/SB2SM & CNRS UMR 8221
Bat 528 Door 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60
________________________________________
De : Karl Kirschner [k.n.kirschner.gmail.com]
Envoyé : vendredi 21 février 2014 10:22
À : AMBER Mailing List
Objet : Re: [AMBER] GLYCAM parameters for cis double conformation
Hello again Stéphane,
I have uploaded 2-butene, proop-2-ene, and ethene to the Wolf2Pack
molecular database, with the CT-C2-C2-CT, where the C2 atom type is an sp2
hybridized atom (antechamber automatically assigned this atom type to CM).
These molecules should cover the C=C functionality of your molecule. One
could create a new atom type for these two atoms, and then fit the QM PES
to optimize the parameters that are missing.there are missing (e.g. HA-XX,
XX-XX, HA-XX-HA). If you are going to use the most recent Glycam force
field, once this is accomplished just copy/paste the force field file over
from the browser and alter the atom type naming to be consistent with
Glycam (e.g. XX--> Xx).
Of course you can always check the performance of any existing
force-field parameter by identifiying a molecule within the database that
has the appropriate functionality.
If you have any questions concerning W2P or run into problems, let me
know. There is a Message Board on the website that can easily be used to
W2P topics.
Best regards,
Karl
On Mon, Feb 17, 2014 at 5:00 PM, ABEL Stephane 175950
<Stephane.ABEL.cea.fr>wrote:
> 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
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
> _______________________________________________
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Received on Fri Feb 21 2014 - 03:00:02 PST
