[Chimera-users] H-bond analysis in case of TIP4P water model ?

Eric Pettersen pett at cgl.ucsf.edu
Tue Sep 4 14:02:58 PDT 2012

On Sep 3, 2012, at 6:28 AM, Marek Maly wrote:

> Hello,
> it seem to me that Chimera is not able to do H-bond analysis between
> water molecules when TIP4P water model is used. Am I right or I overlooked something ?

Upon further review, I can reproduce the problem you're having.  The "extra point" of the TIP4P water (atom "EPW") is screwing up Chimera's H-bond finding.  You need to delete that "atom" ("del @epw" in the command line), then Chimera will be able to find the inter-water H bonds.


                        Eric Pettersen
                        UCSF Computer Graphics Lab

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