Dear AMBER Community,
I am conducting research on a CYP450 enzymatic reaction and have built a model of the key Compound I intermediate, which features an Fe(IV)=O species in the Heme center.
The force field parameters for the metal center were developed using MCPB.py with the bonded model, based on quantum mechanics (QM) calculations. This approach worked perfectly for system building in tleap and for running stable production MD simulations in explicit solvent with AmberTools 24.
Now, I am attempting to perform a binding free energy analysis using MMPBSA.py. The calculation fails at the beginning of the GB step with the classic "bad atom type" error. I have confirmed from my prmtop file that the atom type for the Fe(IV) ion is M1.
My AmberTools 24 was install by Conda, and I didn’t find F90 files to add them into it.
I understand that MCPB.py does not generate the GB radii required by sander, which is the source of this error. My question is about the best practice for this specific, advanced use case.
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Wenbo Xu
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xwb7533.163.com
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Received on Sat Aug 30 2025 - 06:30:02 PDT
