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):
Note: 1abe.mol2 was generated from 1abe.pdb (PDB database)
using
SYBYL, which assigns aromatic types to bonds in Asp, Glu and Arg
sidechains.
These types are converted to localized single / double bonds by the
modify bond type command. This step may fail, if the geometry
(bond
lengths, bond angles) of the input structure deviates significantly
from
expected, 'ideal' geometry.
- 3 - Manually move the ligand into the binding site of the protein:
move the ligand to position between LYS 10 and ARG 151, when happy, do
Wit!P> freeze /arabinose
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.
- 6 - Define atom sets mobile , chiral , comparison , and mols:
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.
Note: The .mol2 file contains Macromodel atom types, and
is probably
useless for programs like SYBYL.
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.
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.