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Force field calculation of heme

In this application, you can create inputs for MCPB.py and Gaussian for the calculation of forcefield parameters of heme.

Flow of Input-File Creation:
  • Step1. Select a PDB entry (on the right side of this page)
  • Step2. Choose a heme chain.
  • Step3. Select a protein coordinate file (if a modeled structure is available).
  • Step4. Choose small-molecule axial ligands (water, CO, O2, ...) to include, and their net charges (if the heme has such ligands).
  • Step5. Set the parameters for MCPB.py: charge of Fe, spin multiplicity and cutoff.
MCPB.py is a tool to construct force filed parameters for metal ions [1].
See the tutorial on how to create force field parameters.

[1] P. LiKenneth and M. Merz, Jr, Journal of Chemical Information and Modeling 56(4), 599-604, 2016, https://pubs.acs.org/doi/10.1021/acs.jcim.5b00674

Step 1.

Select entry by PDB ID.
hemejiro