Hi Ravi,

if you have only organic molecules the MMFF94(s) and Ghemical work both good though MMFF94 is particularly well suited for organic and "drug" molecules.

The UFF is an all atom force field, so it considers all the atoms in the periodic table. Having transition metal, for example, means to use UFF.

MMFF94 considers the atoms: C, H, N, O, F, Si, P, S, Cl, Br, and ions: Fe+2, Fe+3, F-, Cl-, Br-, Li+, Na+, K+, Zn+2, Ca+2, Cu+1, Cu+2, and Mg+2.

Furthemore MMFF94 has two versions, the MMFF94 and MMFF94(s). If you consider crystal structures, you should use MMFF94s (s=static) while for “docking” simulations, use the MMFF94 variant. The difference between the two is due to a high pyramidal puckering on the N atoms in the MMFF94 when optimizing crystal derived structures. Using the MMFF94s avoids such a problem.

Hope it helps

Marco

very much tahks forthe answer

Please at Dr. Fiorini, thanks for your answer. It was really insightful but please could you provide a publication where one can find more details about this forcefield

How I optimize draw ligand before done docking by Autodock vina.

Plz suggest me.

Thank you