sdf2tinkerxyz



sdf2tinkerxyz is able to automatically convert a SDF file into one or more TINKER XYZ files with automatic assignment of MMFF94 atom types, bond types and charges. The SDF file is read from standard input; therefore, if conversion from a format different from SDF is desired, such format can be conveniently piped through OpenBabel into sdf2tinkerxyz, as shown in the examples below.
A KEY file is also created with charge and bond information. XYZ and KEY files by default are written in the current working directory, but a different directory (which must already exist) can be chosen with the -p command line option. If an existing KEY file is indicated through the -k command line option, charge and bond information will be appended to the chosen KEY file. XYZ and KEY filenames are generated out of the molecule names read from the SDF file; if duplicate names exist, a numeric suffix will be appended to distinguish them (e.g., _01, _02, etc.). This behaviour may be modified through the -n command line option: if present, this option will force addition of a progressive numeric suffix to all filenames.


EXAMPLES

# the following command reads structures from the structures.sdf file
and outputs XYZ and KEY files in the current working directory
sdf2tinkerxyz < structures.sdf

# the following command reads structures from the structures.sdf file
and outputs XYZ and KEY files in the xyz_structures directory,
appending charge/bond keywowrds to the minimize.key KEY file
sdf2tinkerxyz -p xyz_structures -k minimize.key < structures.sdf

# the following command reads structures from the ligands.mol2 file
and outputs XYZ and KEY files in the xyz_structures directory,
appending charge/bond keywowrds to the minimize.key KEY file; a
progressive numeric suffix is assigned to all XYZ/KEY files
babel -imol2 ligands.mol2 -osdf \
    | sdf2tinkerxyz -p xyz_structures -k minimize.key -n

# the following command reads coordinates from the protein.pdb file
and outputs XYZ and KEY files in the current directory, appending
charge/bond keywowrds to the minimize.key KEY file
babel -ipdb protein.pdb -osdf | sdf2tinkerxyz -k minimize.key

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Last update:
June 21. 2014 20:28:23

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