Re: [AMBER] Cpptraj HBond salt bridge output question

From: Daniel Roe <>
Date: Wed, 25 Oct 2017 11:39:56 -0400


You'll have to use the GitHub version of cpptraj
(, which has the new
'bridgebyatom' keyword for 'hbond'; I think this will give you the
output you want.

Hope this helps,


On Wed, Oct 25, 2017 at 11:22 AM, Amy Rice <> wrote:
> Hi all,
> I have a membrane system with a large number of ions and am interested in
> seeing which functional groups these ions are bridging. The use of
> solventdonor, solventacceptor, and bridgeout keywords gives information on
> which residues the ions are coordinating, but since I have very large
> residue definitions this output does not provide the level of detail that I
> am interested in. Is there any way to have hbond output which specific
> atoms are involved in the interactions, rather than just which residues?
> For example, the bridge output looks like this:
> Bridge Res 227:HEP5 233:HEP5, 62502 frames.
> Is there any way to make it something like this instead:
> Bridge Res 227:HEP5.atoms_involved 233:HEP5.atoms_involved, 62502 frames.
> Thank you for your help,
> - Amy
> --
> Amy Rice
> Ph.D. Student
> Physics Department
> Illinois Institute of Technology
> _______________________________________________
> 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 Wed Oct 25 2017 - 09:00:03 PDT
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