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

From: David A Case <>
Date: Tue, 22 May 2018 15:53:54 -0400

> On Mon, May 21, 2018, Sadegh Faramarzi Ganjabad wrote:
> >
> > I have converted CHARMM inputs to AMBER inputs. Not sure why but there are
> > 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


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Received on Tue May 22 2018 - 13:00:02 PDT
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