-
Notifications
You must be signed in to change notification settings - Fork 66
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Problem with visualizing the ligand with gromacs file #152
Comments
Hi, It's a bit hard to tell without more info. What is the selection command that you are using to create |
Hi, |
Great, thank you for posting the solution here! |
If you run By default the plot aggregates interactions from all frames and filters the less frequent ones with a threshold. You can also switch to plotting a single frame (kind="frame") and specify which frame to display (frame=frame number). |
thanks a lot :) |
Hi,
I am using the Gromacs file (xtc and tpr file) for prolif. once I selected the ligand, it detect correctly the ligand and its whole atom. however when I want to visualize using this command"# create a molecule from the MDAnalysis selection
ligand_mol = plf.Molecule.from_mda(ligand_selection)
display
plf.display_residues(ligand_mol, size=(400, 200))".
I am giving this error: AttributeError: No hydrogen atom could be found in the topology, but the converter requires all hydrogens to be explicit. You can use the parameter
NoImplicit=False
when using the converter to allow implicit hydrogens and disable inferring bond orders and charges. You can also useforce=True
to ignore this error.could you please help how to fix the issue?
The text was updated successfully, but these errors were encountered: