Dear Eric,

Thank you so much. It works perfectly.

Best

Sasha

From: Eric Pettersen [mailto:pett@cgl.ucsf.edu]
Sent: Tuesday, April 1, 2025 00:47
To: Alexandra Zahradnikova
Cc: chimerax-users@cgl.ucsf.edu
Subject: Re: [chimerax-users] Keeping track of H-bonds in trajectories

Hi Sasha,

By default, H-bonds will be computed for all frames of a trajectory (can be restricted to just the current frame with the “coordsets false” option).  You can also just compute the H-bonds between two residues, for example residues 13 and 17, and save the information (which will have all frames) to a file named “hbonds.txt” in your home directory with:

hbonds :13 restrict :17  save ~/hbonds.txt

--Eric

Eric Pettersen

UCSF Computer Graphics Lab

On Mar 28, 2025, at 8:07 AM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,

I am new in molecular simulation and not very much experienced with ChimeraX. Is there a way to keep track of H-bonds between two specific residues (they can form one or more H-bonds) during the course of the trajectories (in my case, .xtc files from gromacs)?

Thanks in advance

Sasha

________________________________________________________________________

Alexandra Zahradníková, PhD

Department of Cell Cardiology

Institute of Experimental Endocrinology

Biomedical Research Centre SAS

Dúbravská cesta 9

845 05 Bratislava

Slovakia

Mobile: +421 908 069 796

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