None of the hydrogens in my protein is bound to more than one atom.
My system is unusual in that it has extra atoms in an "alchemical"
scheme to grow an extra residue.
Pietro
Quoting David A Case <david.case.rutgers.edu>:
> 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 - 19:30:03 PDT
