[gmx-users] parameters/references

[Nagy, Peter I.]

Dear GROMACS Users!

   I will have to estimate parameters for a non-standard side chain and for different ligands. I checked the section Force Fields in the 3.1 manual, and found reference 39, which is another manual. Could somebody give me one or more journal references where the parameter estimation for GROMACS/GROMOS96 is described. I mean the ab initio level for obtaining charges, equilibrium bond lengths and bond angles. I read from the manual that the force constant may be estimated from the harmonic approximation. So I would like to know what level
(semiempirical, HF, B3LYP, MP2,...) and basis set was used for calculating the abovementioned parameters.

Thank, Peter Nagy
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