To recap it turns out that the element symbol does supersede the atom and residue name which seems to provide a sneaky workaround to the unrecognized ligand issue in PISA.
However this information does come with the disclaimer that it does not replace electrostatic calculations such as CHARMM or AMBER. To quote Eugene Krissinel "be wary about specific energy values given by PISA, especially for protein-ligand interactions. They are quite approximate. PISA does simplified calculations which are very sensitive to the quality of interface, which differs from structure to structure." Once again thank you all for the quick responses. Katherine On Wed, Feb 23, 2011 at 10:51 AM, Katherine Sippel < katherine.sip...@gmail.com> wrote: > Hi all, > > I have sort of an oddball question regarding how PISA reads the ligand file > into the program for calculations. Does the element symbol of the PDB file > take precedence over the atom name or residue name? > > Specifically, if a ligand contains either atom names or residue names that > are inconsistent with those in the CCP4 monomer library will the resulting > energetic calculation be valid? > > Thanks, > > Katherine >
