Hello Yohanna,

Thank you for your offer to help!

I think I will first try to use the approximation you recommend and compare
the results to QM computations to verify it is a good enough approximation.
If I understand the Glycam06 paper correctly, I will need to generate a
rotational energy curve for the rotation about the Cg-Os bond for my
molecule at the B3LYP/6-31++G(2d,2p)//HF/6-31G* level of theory and then to
compare this curve to the GLYCAM06 result.
--Can you explain how I generate the rotational energy curve from the
GLYCAM06 parameters?

If I were to have to develop my own parameters, would it be correct to use
two simple compounds (methyl methoxyacetate and tetrahydro-2H-pyran-2-yl
acetate) as a training set to generate the parameters?
Here, I am not completely clear on how the fitting of the parameter terms
was performed (in terms of the math involved) and how the rotational energy
curve was divided into the respective atomic sequences (as opposed to using
just a single atomic sequence in GLYCAM93).

Thank you again!

On Fri, Sep 16, 2016 at 7:17 AM, Yohanna White <[log in to unmask]>

> 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.
> Thanks,
> Yohanna
> 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
>> --
>> Sven Hackbusch
>> PhD Candidate
>> Department of Chemistry
>> University of the Pacific


Sven Hackbusch
PhD Candidate
Department of Chemistry
University of the Pacific