Errors

Error #1:

AssertionError: The MOL2 file could not be imported in RDKit environment.

Possible causes and solutions:

Either the format of the file is wrong or there are errors in file itself. Check the guide on how to make MOL2 files for your ligand. Additionally, it is possible that RDKit does not recognise the atom types in your MOL2 file - this is very likely if you have prepared your MOL2 file through antechamber.

Example MOL2 file that gives an error:

      1 C1         23.2390   31.2210   19.4790 c3       202 LIG      0.111700

The c3 atom type record could be causing trouble. Try changing all atowmtypes to represent just the element with a capital letter:

      1 C1         23.2390   31.2210   19.4790 C        202 LIG      0.111700

That should solve the issue. Be careful with ions such as Cl.

Error #2:

Error: The MOL2 file does not match the selected ligand

or

AssertionError: The atomnames from MOL2 and topology files do not match.

This, of course, happens either if the ligand in MOL2 file does not match the ligand selected for LINTools analysis because they are different (i.e. pressed the wrong key for ligand selection) or there is mismatch in atoms, in this case, their number and/or names, e.g. protonated ligand would have extra hydrogen etc. Recommendation here would be to check the topology file against the MOL2 file and see that the atom numbers and names match.

This makes sure that the MOL2 file corresponds precisely to the ligand selection in topology file, avoiding issues and potential errors in the output.

Error #3:

AssertionError: Nothing to draw for this ligand ... (continued)

This error message comes with suggestions for action - read the full error message and act accordingly.

It can occur for one of 2 reasons - the ligand is either not in the binding site or spends little time there. In this case, having a look at the trajectory (or topology) is recommended to decide on further course of action - if the ligand escapes as soon as the simulation starts, there is no point in re-analysing it, however, if is stays and then leaves or moves, re-analysis can be very useful - either by reducing the [analysis cutoff] (https://github.com/ldomic/lintools/wiki/Description-of-available-options) (default at 0.3) or splitting the simulation either manually or using options available in LINTools.

Errors with SVG file or other errors that do not look like part of LINTools:

These are most likely bugs and the developers would like to encourage you to submit an issue report.