Lacheley,
Thanks again for your quick response. If I understand you well, I could use
to model for sphohorolipids :
- the Glycam for the carbohydrate portion
- the GAFF or the GLYCAM (from Tessier et al ) parameters for the alkyl
chain with the double bond
- GAFF for the carboxylate part of the molecule
And the RESP charges will be computed according to the GLYCAM rules?
I am correct?
Best
2014-10-21 22:06 GMT+02:00 Lachele Foley <lf.list.gmail.com>:
> You can use GLYCAM for the carbohydrate portions of the molecules.
> You should probably use a lipid force field for those bits. The
> simplest thing to do for any parts not covered by those two force
> fields would be to use GAFF. No matter what you choose, be sure to do
> some testing/validation to make sure the molecules behave well in
> simulation.
>
> If you need help with GAFF or the lipid ff, you might get faster
> service if you change your subject line to represent that.
>
>
>
> On Tue, Oct 21, 2014 at 2:33 PM, sa <sagmx.mail.gmail.com> wrote:
> > Hello Lacheley,
> >
> > Thank you for your response and sorry if was not very clear and complete
> in
> > my previous message. I have chosen to use the GLYCAM parameters instead
> of
> > the others AMBER lipid ffs since I would like to model different neutral
> > and charged linear sphohorolipids [1]. Does GLYCAM can be used for these
> > types of molecules ?
> >
> > *[1] http://www.biosurfing.ugent.be/sophorolipids.htm
> > <http://www.biosurfing.ugent.be/sophorolipids.htm> (Figure 1b)*
> >
> > *Best, *
> >
> > *SA*
> >
> > 2014-10-21 19:44 GMT+02:00 Lachele Foley <lf.list.gmail.com>:
> >
> >> Sorry to take so long responding.
> >>
> >> You *could* do the R-COO- variant, but I'm not sure you should. You'd
> >> definitely need to do some heavy validation. Our parameters are for
> >> carboxylate groups attached to sugars, and there is no guarantee that
> >> the parameters would be appropriate for such a different chemical
> >> environment. For example, we can't use the NHCO parameters from a
> >> peptide backbone for our X-NAc residues. Did you try using one of the
> >> lipid force fields? The GLYCAM lipid force field is decent, but
> >> treats only a few subunits, so you'll probably do better with one of
> >> the other AMBER lipid ff's.
> >>
> >>
> >>
> >> On Mon, Oct 20, 2014 at 11:52 AM, sa <sagmx.mail.gmail.com> wrote:
> >> > Hi
> >> >
> >> > I am wondering if it possible to use the GLYCAM force field model
> R-COOH
> >> > and R-COO- groups (where R is a alkane chain)? If yes, which atom
> types
> >> > should I use ?
> >> >
> >> > Thanks for your response
> >> >
> >> > SA
> >> > _______________________________________________
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> >>
> >>
> >>
> >> --
> >> :-) Lachele
> >> Lachele Foley
> >> CCRC/UGA
> >> Athens, GA USA
> >>
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
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> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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>
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Received on Tue Oct 21 2014 - 14:00:02 PDT
