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]> wrote:
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 Hackbusch
PhD Candidate
Department of Chemistry
University of the Pacific