On Thu, Sep 10, 2020, Pietro Aronica wrote:
>
>I have an unusual system that I am trying to simulate with
>pmemd.cuda_SPFP. The simulation fails at the start with the following error:
>
>0: 19 - 20 and 4: 19 - 21
>Hydrogen atom 19 appears to have multiple bonds to atoms 20 and 21 which
>is illegal for SHAKEH.
>Exiting due to the presence of inconsistent SHAKEH hydrogen clusters.
>
>The thing is, 19 isn't a hydrogen: it's carbon, bound to hydrogens 20
>and 21.
Check atom 20 (numbering starting from 1): is that a hydrogen with more
than one bond? What is it that is "unusual" about your system?
....dac
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Received on Thu Sep 10 2020 - 10:30:02 PDT
