Re: [AMBER] SHAKEH hydrogen clusters

From: <>
Date: Sat, 12 Sep 2020 05:30:55 +0000

Here is a small example. It is a prmtop based alchemical scheme where
the system is simulated with progressively different prmtops to alter
the geometry of the system. In this case, the intended outcome is to
"grow" a glycine right after the alanine. The system fails with pmemd,
but it works perfectly fine with sander. The attached prmtop and
inpcrd represent the first step of the simulation.

Quoting David A Case <>:

> 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?
> ...thx...dac
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Received on Fri Sep 11 2020 - 23:00:02 PDT
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