Re: [AMBER] intra-residue water bridge with cpptraj

From: Daniel Roe <>
Date: Fri, 5 May 2017 09:00:04 -0400


On Fri, May 5, 2017 at 4:17 AM, Joanna Sarzynska <> wrote:
> I understand that water molecule was hydrogen bonded simultaneously to
> three atoms: OP2_34 OP2_67 (protonoacceptors) and HN1_81 atom
> (protonodonor) over 2822 frames.

This is correct. The way that cpptraj detects a water bridge is that
during the solute-solvent hydrogen bond calculation, for each water
involved in a hydrogen bond the atoms (or residues) that it is bonded
to are recorded. So for 2822 frames there was a single water that was
simultaneously hydrogen bonded to OP2_24, OP2_67, and HN1_81. Note
that this does not necessarily need to be the same water for each

> But it is not clear for me why water molecule made hydrogen bond between
> OP2_34 and HN1_81 atoms only over 2032 frames. Does it mean that water
> molecule was hydrogen bonded to OP2_34 and HN1_81 over 2822+2032 frames?

Exactly. The same is true for OP2_67 and HN1_81 (2822+1670).
Technically it is possible that while all three are bound, HN1_81 and
OP2_34 are also bound to a second water. However, it is highly
unlikely that this occurs since this would be extremely crowded. So I
think your interpretation is correct.


PS - At some point I plan on added time series data for bridges which
would make this more apparent. It's on my to-do list.

> Joanna S.
> W dniu 28.04.2017 o 12:22, Joanna Sarzynska pisze:
>> Dear Dan,
>> Thank you very much for your replay.
>> I have installed the GitHub version of cpptraj (V18.00b) and with the
>> 'bridgebyatom' keyword I got what I wanted.
>> Best,
>> Joanna Sarzynska
>> W dniu 26.04.2017 o 17:25, Daniel Roe pisze:
>>> Hi,
>>> You'll have to use the GitHub version of cpptraj:
>>> I recently introduced a bunch of enhancements and features for the
>>> 'hbond' command, one of which is the introduction of the
>>> 'bridgebyatom' keyword, which will give you the results you want. The
>>> 'hbond' command now also benefits from OpenMP (i.e. cpptraj.OMP,
>>> cpptraj.OMP.MPI, etc). See
>>> for full details.
>>> Hope this helps,
>>> -Dan
>>> On Wed, Apr 26, 2017 at 10:27 AM, Joanna Sarzynska
>>> <> wrote:
>>>> Dear Amber users,
>>>> I want to analyze a water bridge within the same residue.
>>>> As I know, cpptraj was able to identify only the water bridge between
>>>> two different residues. I have seen that currently hbond module in
>>>> cpptraj is updated but still I can not figure out how to analyze the
>>>> water bridge within the same molecule. I use CPPTRAJ: V16.16.
>>>> Is there any version of cpptraj that can handle with intra-residue
>>>> water
>>>> bridge?
>>>> Best,
>>>> Joanna Sarzynska, Poznan
>>>> _______________________________________________
>>>> AMBER mailing list
> --
> Joanna Sarzynska
> Institute of Bioorganic Chemistry
> Polish Academy of Sciences
> Z. Noskowskiego 12/14
> 61-704 PoznaƄ, Poland
> _______________________________________________
> AMBER mailing list

Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Fri May 05 2017 - 06:30:03 PDT
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