I am trying to parameterize a small organic molecule namely L(+)Lactate and I am having problems with the dihedral fitting procedure. I have 360 degree of torsional scan for each dihedral angle in the molecule. However I cannot calculate the force constants such that it will give QM Energy surface. I did checked the similar molecules and use the periodicities and phase shifts accordingly but still some of the graph does not reproduce the QM Energy surface. How should I approach to such problem ?. Once again forgive my ignorance on the matter. I would much appreciate any detailed explanation. Thank you in advance. By the way some of the torsional scan graphs are attached below.
You can use Paratool program available in VMD.
http://www.ks.uiuc.edu/Research/vmd/plugins/paratool/
The manual is easy and straightforward.
My first suspicion is that you perhaps ran the torsion in such a way that other effects were not excluded, such as a periodic variation in the bending potential or stretching potential. Was the torsion the only factor allowed to vary when you obtained your plots? Similarly, when you say you have torsional scans for every dihedral, do you have a complete dihedral PES surface (360° of values for each dihedral at every possible value of every other dihedral)? I realize that for any significant number of dihedrals, this is quite difficult, but there can be complex interaction between them...
I am not personally familiar with the Paratool program cited above, but upon looking it over, it certainly seems like it would solve your problem if it is capable of reproducing your surface – you might end up with the realization that you don't have enough information to reproduce certain complex interactions.
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