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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>> 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 - 13:30:05 PDT
