I would like to calculate the free energy of binding of a protein-protein complex from a NAMD simulation. On Galaxy I can see an MMPBSA/MMGBSA tool, but this seems to require AMBER prmtop inputs. Are there any tools on Galaxy that can be used to calculate the free binding energy from a dcd trajectory?
- Search with keywords or review under the
ChemicalToolboxtool group at usegalaxy.* servers
- Or, use the domain-specific server ChemicalToolbox - Galaxy Community Hub
Each tool form has a help section at the bottom. Upstream tools or example inputs are usually referenced, and that is true for the