Re: [AMBER] problems with heating

From: David Case <>
Date: Wed, 22 Feb 2017 15:49:35 -0500

On Wed, Feb 22, 2017, Alicia Merlino wrote:
> 80: 177 - 178 and 81: 177 - 179
> Hydrogen atom 177 appears to have multiple bonds to atoms 178 and 179 which
> is illegal for SHAKEH.
> Exiting due to the presence of inconsistent SHAKEH hydrogen clusters.

As Hai suggested, use parmed to look at atoms 177 to 179 (which appear to
be CA, HA2 and HA3 in a glycine). I admit that this looks like a very
odd error. Is there any chance that the prmtop file has changed between the
minimization and heating steps? Does the error happen on the very first step
of heating (try to make a very short and simple test case, with ntpr=1,
to get the most information.) Did you have SHAKE turned on during the

Also, can you say what program you are running, and what version of Amber?
I'm having trouble finding the location in the code of the errors you
report above.


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Received on Wed Feb 22 2017 - 13:00:02 PST
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