Dear AMBER Community,
MCPB is not recognizing the bond between the Zn ion and the nearest O of an aspartate sidechain in my system. Instead, it is trying to define a bond with the farthest O, but finding it to be 2.96 Å long and of 0 kcal/(mol*Å^2) strength. I’ve highlighted the bond MCPB “sees”. I don’t understand why it doesn’t see the bond to the closer oxygen. What can I do to fix this situation? Below is a Dropbox link to a directory with all the needed files to reproduce the issue.
Dropbox link: https://www.dropbox.com/s/jn7b34m0mvjb05q/ProblemWithBondDefinition.zip?dl=0 <https://www.dropbox.com/s/jn7b34m0mvjb05q/ProblemWithBondDefinition.zip?dl=0>
Best,
Matthew
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Received on Sat Oct 15 2022 - 09:00:02 PDT
