Subsections
4.3 Usage
4.3.1 Command Line Interface
Executing molcharge with no arguments will result in:
prompt> molcharge
No argument specified on the command line
Required parameters:
-in : Input filename
-out : Output filename
For more help type:
molcharge --help'
For a complete listing of parameters, use the argument ``-help all''
4.3.1.1 Command-Line Options
Molcharge has several flags that are used to determine which type of partial
charges to utilize. In addition, there is a single flag to control whether
structural optimization should be carried out for models which use an AM1
calculation.
- -am1
- Assign AM1 partial charges to each atom.
- -am1bcc
- Assign AM1-BCC partial charges to each atom.
- -clear,-none
- Set the partial charges to zero.
- -formal
- Set the partial charges of each atom to it's
formal charge. Unlike the
-none command line option, this at least
preserves the net charge on the molecule.
- -gasteiger
- Assign Marsili-Gasteiger partial charges to each
atom.
- -in
- This is the input file. This file can contain molecules in a
wide-variety of molecular formats. For further details please see the
chapter discussing them below. Some of the partial charging models, such
as AM1 and AM1BCC require coordinates in order to calculate charges. While
the input file is required, the ``-in'' flag is optional. If no ``-in''
flag is specified, the first unflagged parameter is used as the input file.
- -initial
- Set the charges to the Gasteiger seed charges.
- -mmff
- Assign MMFF94 partial charges to each atom.
- -noh
- Specified a united-atom charge model. First, charges are
calculated with explicit hydrogens. Then, each explicit hydrogen is
converted to an implicit hydrogen and it's partial charge is added to the
partial charge of it's parent heavy-atom.
- -opls
- Assign OPLS partial charges to recognized protein
atoms. Atoms that don't have a residue name and atom name matching a
dictionary entry are assigned the value zero.
- -out
- This is the output file and it is a required parameter. Since
this object of molcharge is to generate partial charges, it will only write
to formats that can specify a partial charge. These formats currently
include only
.mol2, .mol2H and .oeb. For further
information on molecular formats please see the chapter discussing them
below. While the output file is required, the ``-out'' flag is optional.
If no ``-out'' flag is specified, the second unflagged parameter is used as
the output file.
- -param
- This can be used to name an input parameter file of molcharge settings, especially useful for running the program with similar flags as a previous run. Flags coming after -param override parameters set by the parameter file.
- -paramfile
- The filename for the output parameter file can be set with this flag.
- -prefix
- Similar to -paramfile, the parameter file will be written to what follows this flag plus the extension `.param'.
- -singlePoint
- Do not optimize the coordinates under the AM1 potential
before calculating the charges. [default = optimize]
4.3.2 Example executions
An example run of the molcharge program is given below.
prompt> molcharge drugs.sdf drugs.mol2
This executes molcharge with the default parameters, to sprout explicit
hydrogens and assign MMFF94 partial charges. The file drugs.sdf
is opened in SD format for input, and the output is written to the file
drugs.mol2 in Sybyl .mol2 format.
