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

From: David A Case <>
Date: Tue, 22 May 2018 08:15:20 -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.

I'm guessing(?) that the atoms listed above are in fact not part of a
water molecule: is that the case. (Amber expects rigid waters to have three
bonds--the H--H bond is used to keep the molecule rigid.)

We are working on a fix, as described in other recent posts on this
mailing list. But for right now, I don't have anything to propose. I
hope we can track this down soon.


AMBER mailing list
Received on Tue May 22 2018 - 05:30:02 PDT
Custom Search