Keeping track of H-bonds in trajectories
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
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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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 _______________________________________________ ChimeraX-users mailing list -- <mailto:chimerax-users@cgl.ucsf.edu> chimerax-users@cgl.ucsf.edu To unsubscribe send an email to <mailto:chimerax-users-leave@cgl.ucsf.edu> chimerax-users-leave@cgl.ucsf.edu Archives: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/> https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (2)
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Alexandra Zahradnikova -
Eric Pettersen