To develop torsion terms for missing terms in GLYCAM06, you will need to generate QM energy profile for that specific torsion. To do that, optimize the molecule with that torsion restrained in QM (HF/6-31G*), then single point energy calculation with the
optimized structure (B3LYP/6-31G*). We usually vary the torsion angle every 30 degrees.
Once we have QM optimized structures (targeted torsion restrained), perform MM energy minimization with targeted torsion restrained as well. For parameters you use in MM energy minimization, set V terms for that specific torsion to 0. You will have the MM energies without rotational energy corrections ("torsion energies"). The differences between QM and MM (without rotational energy corrections) energies are what "torsion energies" are supposed to be. Then, develop V terms to make sure rotational energies (sum from cosine functions) match the previous energy differences.
It is not complicated, but it will take some time. The logic behind torsion terms development is that torsion terms (rotational energies) are corrections in MM energy calculations. Therefore, if the similar terms are fairly small, it means you could either copy from similar terms or set the V terms to 0. Besides finding similar terms in GLYCAM06, you can also search similar ones in parm and gaff, which are available in AMBER.
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:
Thank you very much for your help!Can anyone advise a way to overcome this roadblock?Presumably, GLYCAM is missing the dihedral angle parameters for the O5-C1-O1-C(acetyl) and H1-C1-O1-C(acetyl) dihedral angles.** No torsion terms for H2-Cg-Os-C** No torsion terms for Os-Cg-Os-CHowever, in generating the prmtop file using xleap I am encountering the following errors: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.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.
Sven Hackbusch PhD Candidate Department of Chemistry University of the Pacific