Re: CCL:Amber parameters and charges

 Bernard Pirard of Zeneca inquired about the availability of AMBER
 parameters for treating generic organic molecules.  The primary
 reference for the "official" AMBER force field is:
   CORNELL WD; CIEPLAK P; BAYLY CI; GOULD IR; and others.
      A SECOND GENERATION FORCE FIELD FOR THE SIMULATION OF PROTEINS, NUCLEIC
    ACIDS, AND ORGANIC MOLECULES.
      JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1995 MAY 17, V117 N19:5179-5197.
 The set of parameters described therein represents a complete set
 for modelling proteins and nucleic acids containing standard residues.
 The force field is also described as being appropriate for organic
 molecules, however, the set of parameters available for modelling
 such molecules is far from complete.
 When studying the interactions between small molecules and proteins
 or nucleic acids, bonded parameters can often be borrowed from other
 force fields.  Charges for a new molecule, however, need to be calculated
 from an ab initio generated HF/6-31G* wave function using the RESP protocol
 as described in these references:
    BAYLY CI; CIEPLAK P; CORNELL WD; KOLLMAN PA.
      A WELL-BEHAVED ELECTROSTATIC POTENTIAL BASED METHOD USING CHARGE
    RESTRAINTS FOR DERIVING ATOMIC CHARGES - THE RESP MODEL.
      JOURNAL OF PHYSICAL CHEMISTRY, 1993 OCT 7, V97 N40:10269-10280.
    CORNELL WD; CIEPLAK P; BAYLY CI; KOLLMAN PA.
      APPLICATION OF RESP CHARGES TO CALCULATE CONFORMATIONAL ENERGIES, HYDROGEN
    BOND ENERGIES, AND FREE ENERGIES OF SOLVATION.
      JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1993 OCT 20, V115 N21:9620-9631.
 Variations of the AMBER force field have been implemented in various
 modelling packages and typically include the bonded and VDW parameters
 but use charges derived using a simpler and less costly approach.
 These implementations may be quite useful but it should be noted that
 they differ from the original force field.  The "bona fide" AMBER
 force field was optimized to perform well at calculating relative energies
 of interaction in solution rather than, for example, screening large
 sets of compounds in a DOCKing procedure.
 For those who want to carry out MD studies in solution involving
 functional groups for which parameters are not available in the
 JACS reference, members of the Kollman research group as well as
 other members of the AMBER community often have derived such parameters.
 We are currently working on developing additional parameters, however,
 it will still fall to the user to calculate charges for a new molecule.
 Cheers,
 =Wendy Cornell
 _________________________________________________________________________________
 Wendy D. Cornell, Ph.D.
 Senior Scientist
 Biomolecular Structure and Drug Design Chemistry
 Parke-Davis Research
 Ann Arbor, MI  48105  USA