Re: [AMBER] SHAKEH hydrogen clusters

From: David A Case <>
Date: Fri, 11 Sep 2020 11:27:15 -0400

On Fri, Sep 11, 2020, wrote:

>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.

Can you make a small example that illustrates the problem? I think we
need prmtop/inpcrd/mdin files that fail in order to track down the
problem. Is there anything you can see that might lead pmemd to think
atom 19 is a hydrogen? If you remove the "extra atoms" does the problem
go away?


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Received on Fri Sep 11 2020 - 08:30:02 PDT
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