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
>> >> > _______________________________________________
>> >> > 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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>> >> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Tue Oct 21 2014 - 14:00:02 PDT
