On Fri, Jul 02, 2021, Swisher, Justin S wrote:
>
>when I do the checkValidity in parmed it tells me the inpcrd file is OK.
Use checkstructure in cpptraj. It is what checks for bad bonds and close
contacts, and you clearly have lots of both of them.
Once you see which atoms are on top of each other, and which bonds have
crazy bond lengths, you will probably get some good clues about what to fix
in your input structure.
....dac
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Received on Fri Jul 02 2021 - 19:30:02 PDT
