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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Received on Tue Oct 21 2014 - 12:00:02 PDT
