Reference
Summary
- The perm-pdb.py script in the input directory is copied from $HOME/softwarewales/SCRIPTS/make_perm.allow/
- The old_mol.pdb input file was obtained earlier using tleap in AMBER while creating initial topology and coordinates file
- Run the following from the command line
module load anaconda/python2/5.3.0
perm-pdb.py old_mol.pdb AMBER
- The output file perm.allow is given in the expected_output directory.
- The perm.allow is required for running OPTIM and PATHSAMPLE.