Follow-up:
I’d like to update my post with some details for future reference.
During QM minimization, the oxygen of the aspartate sidechain coordinated to Zn in my system switched from OD1 to OD2 so that OD1 could realize a H-bonding interaction with a nearby His. As a result, the Zn-O bond MCPB defined in the first step ended up with a force constant of 0, and no other Zn-O bond was defined.
I realized I could correct this issue by going into the fingerprint file generated by MCPB. There, I saw:
83-ASP-OD1 1208 O2 -> Y8
83-ASP-OD2 1209 O2 -> O2
where Y8 indicates the 8th ligand (2 Zn ions, each tetra-coordinated). So I simply flipped the mapping to O2 and Y8 for these two oxygens. I also needed to change the below line to indicate the correct bond:
LINK 2188-ZN 1208-OD1
After doing these minor changes, everything worked. I’ve run a few ns of MD and everything looks stable.
Best,
Matthew
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Received on Mon Oct 17 2022 - 04:30:02 PDT
