i want to do protein-ligand docking, i got my ligand from pubchem and calculated its energy using avogadro(435.61 kj/mol) and using prodrg i did ligand minimization and found its energy from avogadro(1731.5 kj/mol), and if i use different force filed the energy is changing, so which one i use for my docking purpose? Plz help
Use SwissPDB viewer or Vegaz software or Chemdraw program. Swiss pdb viewer would provide energy minimization value for the ligands. then
thank you Anum for ur guidance.
But when i m trying to know the energy from swissPDB viewer, it showing Topology error, even i tired using output got from Swiss param( tool for topology ), then also getting same error...
Plz help,,,
DG-AMMOS is a new tool try this
http://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::rpbs.DG-AMMOS
Other tools are also available, you can check them here
http://www.mti.univ-paris-diderot.fr/fr/downloads.html
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology