Running the e-LBOW builder is not always a one-step procedure. On complicated it is advisable to check each step of the building and use some features of the builder to use previous results.
For example, the SMILES string for ATP from the distributed database:
elbow.builder --key atp
will result in a geometry that has been optimised using a simple force-field. A quick check of geometry using a molecule visualisation program such as PyMOL or MOLDEN can determine and remedy any geometric problems. An option will also display the final geometry:
elbow.builder --key atp --view molden
if molden is in the path.
Once you are pleased with the general geometry, e-LBOW can then be run:
elbow.builder --key atp --initial-geometry correct.pdb --opt
to provide a suitable starting geometry for the [AM1] optimisation specified via the --opt option.
A SMILES string does not contain atomic naming information so the atom names are simply numbered in order. If a file is available that contains the atomic naming desired, there can be introduced using the --template option. Using:
elbow.builder --key atp --final-geometry optimised.pdb --template naming.pdb
with use the geometry from optimised.pdb and the atomic and residue naming from naming.pdb. Note that the SMILES string is still supplied using the --key option as this is one of the better ways to specify topology information.
More information on output files is available.
For a complete list of builder options (expert options here).