Dear Sir:
Following your suggestions, I’m getting the dihedral torsion function by GAUSSIAN98, but I can’t make sure that whether my results are correct or not, because the relative energies are larger than that reported in literatures, sometimes the energy values can be more than 100 kcal/mol at a special dihedral degree in my results. My protocal for doing this is like this:
1) based on the optimized structure of a biomecule (e.g. GAL:galactose),I optimized it again by fixing a dihedral angle (e.g. O3-C3-C4-O4 of GAL)to 0 degree, and get the relative energy of 0 degree.
2) Then always based on the optimized structure of 0 degree, I optimized it again by fixing the dihedral angle to other degrees respectively, and get other relative energies of other degrees. (I want to emphasize here that I did them one by one independently, but not through the function of “relaxed potential energy surface scan” of GAUSSIAN98, so I did not remove other dihedral angles involving C3-C4 bond in every work like “relaxed potential energy surface scan” of GAUSSIAN98.I think that the ab initio calculations should be the same as that of CHARMM showed in your tutorials. Is it right?)
Is my protocal right, why are my values so large? Because I still does not start the CHARMM calculations, I can not judge it, Would you please give your judgement? Thanks a lot!