Charmm scripts to use the Merck Molecular Force Field (MMFF).


Scripts provided by Prof. Alex MacKerell Jr. Further explanations are given in the inputs.

  1. Create structure using CHARMM topology file and minimize with MMFF.

    mmff_charmm_input.inp
    ---mmff_setup.str
    ------mmffsup.par
    ------mmffprop.par
    ------mmffsymb.par
    ------mmffdef.par
    ------mmffbndk.par
    ------mmffhdef.par
    ------mmffarom.par
    ------mmffvdw.par
    ------mmffbond.par
    ------mmffchg.par
    ------mmffpbci.paf
    ------mmffang.par
    ------mmffstbn.par
    ------mmffdfsb.par
    ------mmffoop.par
    ------mmfftor.par

  2. Read Merck format sturcture, insert in a waterbox and perform energy minimization.

    mmff_solvate.inp
    ---mmff_setup.str
    ---am07a.mrk
    ---wat125.crd

  3. Read MOL2 format structures, minimize and do vibrational analysis.

    mmff_mol2.inp
    ---mmff_setup.str

  4. Read compounds from a MOL2 database, minimize and perform vibrational analysis.

    mmff_database.inp
    ---mmff_setup.str
    ---test_db.dat
    ---mmff_db.mol2

  5. Read protein in pdb format and write out in Merck format.

    mmff_prot.inp
    ---mmff_setup.str
    ---top_all22_prot_mmff.inp
    ---asv_charmm.pdb

  6. Read compounds from a MOL2 database which have been previously DOCKed into ASV integrase, read ASV integrase structure (from mmff_prot.inp), minimize each compound in protein, perform analysis and output information to a datafile.

    mmff_complex.inp
    ---mmff_setup.str
    ---top_all22_prot_mmff.inp
    ---mmff_db_2.mol2
    ---mmff_db_2.list
    ---asvin.mrk