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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