LMOD Tutorial


In this tutorial you will learn how to set up a protein/ligand complex for a Macromodel/LMOD search, starting from separate .mol2 files for the protein and ligand structures.

The first part (Praeludium) of the setup procedure deals with the generation of a complex from individual files for the protein and ligand, and with the assignment of Macromodel atom types and MPEOE partial atomic charges. The second part (Fuge) deals with the generation of Macromodel .com and .sbc files for the complex built in the first part. If an old-style (mmio) Macromodel structure files is already available, one may skip the first part, read in the Macromodel structure file of the complex, and proceed directly to the second part (Fuge).
 

Praeludium: set up a protein/ligand complex with Macromodel atom types and MPEO charges
 

- 1 - Read in .MOL2 file with the structure of the protein (L-Arabinose Binding Protein):

- 2 - Read in .MOL2 file with the structure the ligand (alpha-L-Arabinose: arabinose.mol2):


- 3 - Manually move the ligand into the binding site of the protein:

- 4 - Merge protein and ligand structures to form protein / ligand complex:
    Wit!P> build
    Build> freeze /arabinose
    Build> move -flat /arabinose -done /1abe/L/ARA_1
    Build> modify molecule name 1abe complex
- 5 - Assign Macromodel atom types and MPEO partial atomic charges:
    Build> modify
    what: atom ligance current *
    what: atom type
    type: automatic mmod *
    type: done
    what: atom q * -done MPEOE
    what: done
    Build> end

    Note: Partial atomic charges (q) need to be computed only if the LMOD search is set up to use charges specified in the input structure file (c.f. CHGF Macomodel command), and only if the input .mol2 files of the protein and ligand do not already contain valid partial atomic charges.
     

Fuge: the LMOD specific part..
 

- 6 - Define atom setmobile , chiralcomparison , and  mols:

    Wit!P> define set /complex/mobile
    atoms: /complex -rzone 5 /complex/L -done

    Wit!P> define set /complex/chiral
    atoms: /complex -atom match C(X)(X)(X)
    atoms: -not /complex -atom match C(C(H)(H)H)C(H)(H)H
    not atoms: -done

    Wit!P> define set /complex/chiral
    atoms: /complex/chiral -pzone 1 /complex/mobile -done

    Wit!P> define set /complex/comparison
    atoms: /complex/L -not * -atom symbol H -done -done

    Wit!P> define set /complex/mols
    atoms: /complex/L -atom seqnr 1 -done

    Note:  mobile is the set of all atoms that are allowed to move during the LMOD search, chiral is the set of atoms that need to be checked  against inversion of stereochemical configuration, comparison is the set of atoms to be used when comparing conformations to determine their uniqueness, and mols is a set containing exactly one atom from each molecule to be independently rotated / translated during the LMOD search.  The definition of the chiral is sufficient for this example, but of course too simplistic for the application of general organic molecules.
     

- 7 - Generate  .mol2 (Tripos MOL2) and .dat (Macromodel) for complex.
    Wit!P> write mol2 complex.mol2 /complex
    Wit!P> write mmod complex.dat  /complex
    Wit!P> exit yes

    Note: The .mol2 file contains Macromodel atom types, and is probably useless for programs like SYBYL.
     

- 8 - Generate Macromodel .com and .sbc files, using the LMOD template.com file:
    AW on luna 23> preLMOD -c template.com complex
    4669 atoms

    Note: preLMOD is a Perl script which reads a .mol2 file, and generates the Macromodel .com and .sbc files needed by LMOD. The .com file is generated from the template specified by the -c option, by replacing COMP, CHIG and MOLS Macromodel commands in the template by new commands generated from the set definitions in the .mol2 file. In addition,  the first to lines of the template will be replaced by the file names of the input and output structures. Al l other commands are simply copied from the template to the new .com file. If the -c option is not used, the new .com file will be created from scratch.
     

- 9 - Run the LMOD calculation:
    AW on luna 24> $SCHRODINGER/bmin complex
- 10 - Convert .out file from LMOD search to Wit!P .cnf file:
    AW on luna 25> mae2cnf complex.out > complex.cnf

    Note: mae2cnf is a Perl script which generates a Wit!P .cnf file from a new-style (m2io) formatted compressed multi-conformer file. If the LMOD output is an old-style (mmio) file, the -o flag must be set in mae2cnf, or the conversion will fail silently. Energies will be converted from kJ/mol to kcal/mol.
     

- 11 - View results in Wit!P/Confa:
    AWI on luna 26> witnotp &
    Wit!P> read mol2 complex.mol2
    Wit!P> confa
    Confa> template /complex
    Confa> read complex.cnf
    Confa> browse
    ...




A.Widmer, NIBR/CPC/CSG-SB