Hello K Gayathri, PDB files don't include receptor-ligand hydrogen bond information. If you save a PDB file you would need to run "hbonds" or H-Bonds tool to find the H-bonds again. However, the atomic coordinates in the file(s) are the same as what you saved, as long as receptor and ligand were saved relative to each other. You can reassure yourself by reopening the file(s) in Chimera and seeing that they are in the correct positions (ligand docked into receptor), and try re-running hbonds to see that the same interactions are present, but the H-bonds won't be saved in the file. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On May 15, 2026, at 6:34 AM, k Gayathri via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Dear Sir/Madam, I am a research scholar from Anna University, Chennai, India, and I have been using UCSF Chimera for my research for the past two years. Recently, I encountered an issue during the visualization and saving of protein–ligand interactions, which I have been unable to resolve. I performed docking simulations using AutoDock Vina and obtained the output in PDBQT format. Initially, I used the ViewDock module to visualize the docking poses and hydrogen-bond interactions. However, since the output file contained multiple poses, I was unable to correctly save only the favorable protein–ligand complex for further analysis. To address this, I used the vina_split utility to separate the individual poses from the docking output file. After splitting, I was able to open the single ligand pose in PDBQT format along with the protein and successfully visualize the hydrogen bonds. However, when I saved this selected protein–ligand complex in PDB format and reopened it, the hydrogen bonds were no longer visible in Chimera. As I require the final protein–ligand complex in PDB format for further molecular dynamics simulations, I would like to clarify the correct procedure for saving the selected docked pose together with the protein structure from the docking results. I would also like to confirm whether the saved PDB complex remains structurally reliable for subsequent MD studies, even though the hydrogen bonds are not displayed after reopening. I would be grateful if you could kindly guide me on the correct workflow for saving the protein–ligand complex from docking results and ensuring that the structure is suitable for further simulation studies. Thank you in advance for your support and guidance.