From Jacobson Lab Wiki
Running Plop - The suggested method for running Plop is through the use of a control file (often abbreviated .con). A control file contains a sequence of plop commands which will be performed by the plop executable. This is an example con file:
datadirectory /home/jane/plop/data file logfile janes_plop_job.log load pdb /home/jane/pdb_files/protein.pdb minimize residues all residues verbose yes write pdb protein_minimized.pdb
This con file tells plop to:
1) look in /home/jane/plop/data to find the necessary data files
2) log the output of the command to janes_plop_job.txt (in the current directory)
3) load /home/jane/pdb_files/protein.pdb into memory
4) minimize all residues using the default minimization options. With the exception of verbose, which is explicitly set to yes giving us more output
5) write the new minimized structure in pdb format to protein_minimized.pdb
Say the the con file is saved in minimize.con, then to run the file I would call:
And if plop is not in my path, I need to specify either a full (/home/jane/plop/plop) or relative path (./plop/plop) to the plop executable.
Another possibility is to put the path to the plop executable in the command file itself, make the command file executable and run the command file directly.
#!/home/jane/plop/plop datadirectory /home/jane/plop/data file logfile janes_plop_job.log load pdb /home/jane/pdb_files/protein.pdb minimize residues all residues verbose yes write pdb protein_minimized.pdb
Then Jane only needs to:
chmod +x minimize.con ./minimize.con
The two methods are equivalent, so use whichever you prefer.
It is also possible to run plop interactively on the command line. This is probably a bad idea.