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.
--
*Thanks and Regards*,
*K. Gayathri*
Research Scholar
Department of Physics
Anna University
Chennai-25
