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

From: Joanna Sarzynska <>
Date: Fri, 5 May 2017 10:17:20 +0200

Dear Dan,
I use GitHub version of cpptraj (V18.00b) and with the 'bridgebyatom'
keyword to calculate water bridges.
Could you explain me how I can interpret this result:

Bridge Atm OP2_34 OP2_67 HN1_81, 2822 frames.
Bridge Atm OP2_34 HN1_81, 2032 frames.
Bridge Atm OP2_67 HN1_81, 1670 frames.

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.

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?

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
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Received on Fri May 05 2017 - 01:30:02 PDT
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