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

From: David A Case <>
Date: Tue, 22 May 2018 20:32:17 -0400

On Tue, May 22, 2018, Sadegh Faramarzi Ganjabad wrote:
> Thanks for replying. Those atoms are actually parts of a water molecule.
> That's why I'm surprised, if AMBER allows an H-H bond why it gives that
> error? Can't it be because in the original psf file those extra bonds
> already exist?

We need more information, as I mentioned earlier: how exactly did you
convert CHARMM to Amber format, and what version of AmberTools are you
using? (Problems with waters in earlier versions have been fixed.)


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Received on Tue May 22 2018 - 18:00:02 PDT
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