24 September 2015 3 3K Report

Hi all,

I am trying to provide the force constants and distance/angles in frcmod.user for a SECOND (follow-up) submission to R.E.D server so I have a complete amber force field. 

Unfortunately I have no experimental detail about the structure, all I have is the ab initio optimised structure from the original (first) R.E.D. run. Thankfully, there are only five bonds which are unknown to ff99sb, but that is around 20 dihedral angles. 

For the bond length and angles I simply measured the bond length and angles from the ab initio structure, and found the nearest matching set of element bond pair or angle triplets and used the force constant (V kcal...) for those. This makes sense, providing the atom element is the same then the force constant is relative to the distance/angle. 

Unfortunately I do not know how to match dihedral angles to known dihedrals. In the ff99sb force field every dihedral angle is either a 0 or 180. This is really not the cae with my ab initio structure. Any suggestions regarding making a good approximation of the force constants from the force field dihedral angles would be great.

Thanks

Anthony

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