Sarath Chandra wrote: > Now the scripts are working. Log files are being generated successfully. > > I am trying to use complete_pdb.py to add missing atoms to my pdbfile. > > Here is the command i am using > > mod9v5 complete_pdb.py (ChainA.pdb)
Is that really exactly what you're typing, complete with the "(ChainA.pdb)" ? I can't tell if that will work without seeing your complete_pdb.py script, but my suspicion is that it won't if you are putting literal parentheses in there.
> The following log file is being generated ...
OK, that log file shows that Modeller is successfully running. But maybe you didn't tell it to do anything?
> I have been using the following link > http://salilab.org/modeller/manual/node403.html
That describes how to use the complete_pdb() function, but you still have to write a little script to actually use it. If all you want to do is read in an input PDB, fill in missing atoms, and write out the completed PDB, something like the following should work:
from modeller import * from modeller.scripts import complete_pdb
env = environ() env.libs.topology.read('${LIB}/top_heav.lib') env.libs.parameters.read('${LIB}/par.lib')
m = complete_pdb(env, "input.pdb") m.write(file="output.pdb")
Ben Webb, Modeller Caretaker