Previous: Requirements
In the following example, a protein and ligand are considered. The molecular structure of the the protein and the ligand have to be generated as outlined in Sections 3.7 and 3.13. The ligand requires the definition of the topology, e.g.,
topology
autogenerate angles=true dihedrals=false end
residue LIGA
atom A type=C end
atom B type=C end
atom C type=C end
atom D type=O end
bond A B
bond B C
bond C D
improper A B C D
end
end
segment
name=LIGA
molecule number=1 name=LIGA end
end
Note that mass statements may be required if the
atom types of the ligand are non-standard.
The protein parameters can be obtained from one of X-PLOR's protein parameter files. In general, the ligand parameters will be unknown. Suppose that the ligand coordinates are known from an appropriate crystal structure. We can learn the unknown ligand parameters from the known Cartesian coordinates. For purposes of structure determination, it is usually sufficient to set the energy constants to a uniform value.
The following statements define the unknown ligand parameters. They should be inserted in all X-PLOR protocols at any place after the molecular structure and coordinate files have been read and before the first energy evaluation is performed. These statements must also be inserted just before the hbuild statement in the molecular structure generation protocol (Section 3.13).
{*Learn bond, bond angle, and improper angle parameters.*}
flags exclude * include bonds angles impropers end
parameters
learn initiate sele=(segid LIGA) mode=nostatistics end
learn accumulate end
learn terminate end
end
{*Set the energy constants.*}
parameters
BOND (segid LIGA) (segid LIGA) 400. TOKEN
ANGLE (segid LIGA) (segid LIGA) (segid LIGA) 60. TOKEN
IMPR (segid LIGA) (segid LIGA) (segid LIGA) (segid LIGA) 50. TOKEN TOKEN
{*Set the nonbonded parameters (only if required).*}
NBON ( (name A or name B or name C) and segid "LIGA" ) 0.1 3.5 0.1 3.5
NBON ( name D and segid "LIGA" ) 0.1 3.4 0.1 3.4
end
{* activate other energy terms *}
flags include vdw elec pvdw pele end.
Note that the learn statement automatically sets the periodicity of
all learned dihedral and improper angles to zero. Also note that
the user has to specify improper and dihedral angles in the topology
definition of the ligand (see above) in order to maintain planarity
and chirality in certain parts of the ligand. Nonbonded
parameters may have to be set by appropriate parameter statements unless
they are already defined through type-based parameters.
Finally, one has to activate the nonbonded energy terms and any
other energy terms that might be needed, using the flags statement.