Re: [AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3 water model

From: Sadegh Faramarzi Ganjabad <>
Date: Wed, 23 May 2018 15:36:30 -0400


I'm not using top_all27_na.rtf or top_all27_prot_na.rtf. Here is the syntax
I use on parmed

chamber -top top_all36_lipid.rtf -param par_all36_lipid.prm -param
par_all36m_prot.prm -param par_all36_cgenff.prm -param par_all36_na.prm
-param ddm2.prm -param par_all36_carb.prm -param par_all36_prot_mod.prm
-str toppar_all36_lipid_detergent.str -str ../retinal-depro.str -toppar
toppar_water_ions_fixed.str -psf all-ion.psf -crd all-ion_new.pdb -nocmap
-box 75.4,75.13,83.8

I checked the files above, they don't have the error that top_all27_na.rtf
has. Interestingly. I have tested the same param/topology files for another
system for which the water molecules are generated with VMD. They work
well. But for the system generated with CHARM-GUI website I get that SHAKEH
error for water molecules.

I'm using AmberTools 18. I'm sending you all the files I use. I looked at
the pdb file, atoms with indices 23639, 23638, 23640 are the first water
molecule that appears on pdb file after the bilayer atoms.

Date: Tue, 22 May 2018 15:53:54 -0400
From: David A Case <>
Subject: Re: [AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3
        water model
To: AMBER Mailing List <>
Content-Type: text/plain; charset=us-ascii

> On Mon, May 21, 2018, Sadegh Faramarzi Ganjabad wrote:
> >
> > I have converted CHARMM inputs to AMBER inputs. Not sure why but there
> > extra bonds between two hydrogen atoms in the water molecules in the
> > original CHARMM files. When I try to run the AMBER inputs it complains
> > about those extra bonds. Here is the error I get
> >
> > Hydrogen atom 23639 appears to have multiple bonds to atoms 23638 and
> > 23640 which is illegal for SHAKEH.
Please see the recent mailing list entry about a similar problem. Are
you using top_all27_na.rtf or top_all27_prot_na.rtf? If, so that post might
have help for you.

If the hydrogens above are really in water, can you say exactly how you
convert CHARMM to AMBER inputs? Which version of AmberTools do you


Sadegh Faramarzi,
Research Assistant
West Virginia University, Department of Chemistry
AMBER mailing list
Received on Wed May 23 2018 - 13:00:03 PDT
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