Problem with visualizing the ligand with gromacs file

[yousefymohammad]

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 use force=True to ignore this error. could you please help how to fix the issue?

[cbouy]

Hi,

It's a bit hard to tell without more info. What is the selection command that you are using to create ligand_selection? And what is the output of ligand_selection.elements?

[yousefymohammad]

Hi, thanks for your reply. the problem was fixed. I just share what I did. regarding the selection command I am using "ligand_selection = u.select_atoms("resname G13". in beginning I thought that my be the hydrogen is implicit and it can not detect, I check it and it is explicit. it shows all of the hydrogens with this command "ligand_selection.names". however in the next step it can not visualize the ligand. I used this two line to guess the the element and add it to the topology attribute: gess_elements = guess_types(u.atoms.names) u.add_TopologyAttr('elements', gess_elements)

[cbouy]

Great, thank you for posting the solution here!

[cbouy]

If you run fp.plot_lignetwork? it should display some help on that: there are 2 parameters that are of interest for you here: kind and threshold.

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).

[yousefymohammad]

thanks a lot :)