Molecular Coordinate File Format Notes
There a many different types of Molecular Coordinate File Formats. These
notes describe how to convert from one format to another.
To convert PC-MODEL files to PDB files:
- Download the pcm2pdb.pl script.
- Type chmod 744 pcm2pdb.pl to make the script an executable.
- Type pcm2pdb.pl input_file.pcm output_file.pdb
The resulting output_file.pdb file is a PDB file.
- Start InsightII
- Click on Molecule/Get, and get the output_file.pdb file
- Your molecule may not have correct bond orders or atom potentials. See the
InsightII Builder Notes for instructions
describing how to fix these problems.
- Each substructure in the PC-MODEL file will be defined as a separate residue
in InsightII. In practice, most PC-MODEL files are composed of just one substructure,
so the entire molecule will be one residue. This is usually not a problem.
However, since the CUTOFF parameter must be twice as large as the longest distance of the largest residue,
the CUTOFF parameter may have to be very large to accommodate a molecule composed of a single residue.
Again, this is not a problem if your molecule is not large. See the
Discover Notes for a description of the CUTOFF parameter.
To convert the IUMSC's crt files to PDB files:
- Download the crt2pdb.pl script.
- Type chmod 744 crt2pdb.pl to make the script an executable.
- Type crt2pdb.pl filename > output_file where filename is the
name of the crt file and output_file is the name of the pdb file.
The resulting output_file.pdb file is a PDB file.
- Start InsightII
- Click on Molecule/Get, and get the output_file.pdb file
- Your molecule may not have correct bond orders or atom potentials. See the
InsightII Builder Notes for instructions
describing how to fix these problems.
- The entire molecule will be defined as 1 residue in InsightII.
This is usually not a problem.
However, since the CUTOFF parameter must be twice as large as the longest distance of the largest residue,
the CUTOFF parameter may have to be very large to accommodate a molecule composed of a single residue.
Again, this is not a problem if your molecule is not large. See the
Discover Notes for a description of the CUTOFF parameter.
The following instructions use BABEL to interconvert MacroModel and MM3 files.
To convert a MacroModel (mmod) file to MM3 format and run a MM3 calculation:
- Download the mmod_to_mm3.csh script.
- Type chmod 744 mmod_to_mm3.csh to make the script an executable.
- Type mmod_to_mm3.csh filename.mmod
If you don't supply filename.mmod in this command, you will be promted for
the filename during execution of the script.
- Results of the MM3 calculation are stored in a file named TAPE9.MM3
To convert a MM3 file to MacroModel (mmod) file format:
- Download the mm3_to_mmod.csh script.
- Type chmod 744 mm3_to_mmod.csh to make the script an executable.
- Type mm3_to_mmod.csh filename
If you don't supply filename in this command, you will be promted for
the filename during execution of the script, or you may choose to use the default
TAPE9.MM3 filename produced by a MM3 calculation.
BABEL
See the Babel Notes.
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Last updated: 6/6/2001