From Jacobson Lab Wiki
write is a top level plop command used to write output files.
The main command is
write pdb file
where file is a filename you specify for writing out the structure in Protein Data Bank format. This will output whatever structure is currently in PLOP’s memory. If you are writing a script with several commands in it, it is frequently useful to write out the structure after each step using “write pdb”.
There are several options that can be specified (default values are italic):
write pdb file & sym[metry] none/unit/sys[tem] & chg yes/no & type standard/delphi
The “symmetry” option can be useful when you have implemented crystallographic or biological symmetry (using the “sym” option under the “load pdb” statement). The option “symmetry unit” will write out either 1) the full crystallographic unit cell, if crystal symmetry is being used, or 2) the full biological unit, if biological symmetry is being used. The option “sym system” will instead write out one copy of the asymmetric unit plus all portions of surrounding copies (whether biological or crystal symmetry) within about 30 Å; this is what PLOP is actually simulating (i.e., it does not try to perform explicit lattice summations or anything like that).
The option “chg yes” will put the atomic partial charges in an “extra” column in the PDB file.
The option “type delphi” will modify the output PDB file to be readable by Delphi.