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?
Cross-posted here: https://www.researchgate.net/post/How_do_you_calculate_the_free_binding_energy_of_a_protein-protein_interaction_from_a_molecular_dynamics_simulation
Galaxy resources:
Tools
- Search with keywords or review under the
ChemicalToolboxtool group at usegalaxy.* servers - Or, use the domain-specific server ChemicalToolbox - Galaxy Community Hub
Tutorials
Help
Each tool form has a help section at the bottom. Upstream tools or example inputs are usually referenced, and that is true for the MMPBSA/MMGBSA tool.