hi, We need to calculate a MD of the protein with a small molecule. So, We calculated point charges of small molecule using gaussian and resp (in amber) . To run MD, We also need bond, angle, torsion, improper torsion and VDW parameters of a small molecule. Does anyone know any information (e.g. web or paper) for beginners that indicate how to calculate it? K, Watanabe. Hitachi ulsi systems co. ltd.