OK, Lachele I will try your suggestions.
Thanks
2014-10-21 22:57 GMT+02:00 Lachele Foley <lf.list.gmail.com>:
> You could use that combination. Developing charges according to
> GLYCAM rules would be good, but it might be hard to get a
> conformational ensemble for something that large and flexible. You
> could break it into smaller pieces, but figuring out a good way to do
> that and then piece them back together might or might not be easy.
>
> But, no matter what you choose, definitely test/validate because you
> are making a novel model.
>
>
> On Tue, Oct 21, 2014 at 4:32 PM, sa <sagmx.mail.gmail.com> wrote:
> > 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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> >> >>
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> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> --
> >> :-) Lachele
> >> Lachele Foley
> >> CCRC/UGA
> >> Athens, GA USA
> >>
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> >> 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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Received on Tue Oct 21 2014 - 14:30:02 PDT
