Hello Sven,

You have several options for this case. You can either make approximations
and make a guess on the torsion terms, develop your own parameters, or we
can develop the parameters for you and guide you through it (but this will
take us about 6 weeks to get to).

So if you'd like to make some approximations, you could set  the Os-Cg-Os-C
to the same term as a Cg-Cg-Os-C, assuming that if this were a hexane, its
torsion term would be similar. And you can set the H2-Cg-Os-C to 0 so it
won't have a torsion term.

Let us know if which plan works best for you.


On Tue, Sep 13, 2016 at 9:30 PM, Sven Hackbusch <[log in to unmask]>

> Dear GLYCAM developers and users,
> I am interested in simulating a sugar that is acetylated at the 1
> position, specifically 1,6-Ac2-alpha-D-Glc, with the GLYCAM forcefield in
> Amber.
> It would appear that there exist no partial charges for this compound (the
> online builder did not let me place an acetyl derivative at position 1), so
> I am using the general protocol for deriving the partial charges.
> However, in generating the prmtop file using xleap I am encountering the
> following errors:
>  ** No torsion terms for Os-Cg-Os-C
>  ** No torsion terms for H2-Cg-Os-C
> Presumably, GLYCAM is missing the dihedral angle parameters for the
> O5-C1-O1-C(acetyl) and H1-C1-O1-C(acetyl) dihedral angles.
> Can anyone advise a way to overcome this roadblock?
> Thank you very much for your help!
>   -Sven
> --
> Sven Hackbusch
> PhD Candidate
> Department of Chemistry
> University of the Pacific