I set the "watnam" according to the .gro naming, which is TIP3, and it worked.
Thank you.
________________________________
From: Patricio Barletta via AMBER <amber.ambermd.org>
Sent: 06 September 2026 18:33
To: amber.ambermd.org <amber.ambermd.org>
Subject: Re: [AMBER] Exiting due to the presence of inconsistent SHAKEH hydrogen clusters
Amber's indices are 0-based, VMD uses 1-based indexing, maybe that's why you couldn't find them?
In any case, given that the numbers are consecutive, it sounds like the hydrogens come from water molecules, which are the only hydrogens that can have 2 partners. pmemd knows this and doesn't use shake when a molecule and its atoms are recognized as water, and uses the rattle routine instead. I'm guessing that the conversion tool kept the gromacs names (they use SOL for water), instead of using amber's (WAT).
You can rename your solvent in your mdin (check flag 'watnam' in the manual, along with the other atom renaming flags), but if I'm correct, and the problem comes from the water naming, I'd suggest to look into the conversion tool manual, there must be a way to rename the solvent during the conversion.
Let me know if this was the case. I couldn't download the files, so I can't see your system.
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Subject: AMBER Digest, Vol 5022, Issue 1
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AMBER Mailing List Digest
Today's Topics:
1. Exiting due to the presence of inconsistent SHAKEH hydrogen
clusters (Suvajit Das)
----------------------------------------------------------------------
Message: 1
Date: Sat, 5 Sep 2026 04:44:59 +0000
From: Suvajit Das <suvajit.das.jcbose.ac.in>
To: "ElBagoury, Abdulrahman Walid Attia Ibrahim via AMBER"
<amber.ambermd.org>
Subject: [AMBER] Exiting due to the presence of inconsistent SHAKEH
hydrogen clusters
Message-ID:
<PN2PR01MB897990DF12637F5D74DDD963D3B42.PN2PR01MB8979.INDPRD01.PROD.OUTLOOK.COM>
Content-Type: text/plain; charset="iso-8859-1"
Dear Experts,
I am simply trying to run an MD simulation of a few amino acids in water in Amber. For a specific reason, I converted the .gro and topol.top from GROMACS output to Amber extensions using ParmEd -
gromber topol.top npt.gro topdir toppar
outparm npt.parm7 npt.rst7
However, it shows an error after the MD command:
110: 231 - 232 and 112: 232 - 233
Hydrogen atom 232 appears to have multiple bonds to atoms 231 and 233 which is illegal for SHAKEH.
Exiting due to the presence of inconsistent SHAKEH hydrogen clusters.
I tried to look up the atom indices in VMD, but no such things are seen. I tried a whole-protein system using GROMACS and Amber and received the same error.
Kindly provide a solution.
I'm attaching the folder with the files.
Thank you and regards,
Sincerely,
Suvajit
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Received on Wed Sep 09 2026 - 01:00:02 PDT
