doc box formatting

docs/src/documentation.md

@@ -337,11 +337,14 @@ Currently atom classes are not supported, only atom types.
 Residue patches, virtual sites, file includes and any force types other than `HarmonicBondForce`/`HarmonicAngleForce`/`PeriodicTorsionForce`/`NonbondedForce` are currently ignored.
 
 !!! tip "Obtaining compatible structure files"
+
     Future work will increase the features and robustness when reading in structure files. In the mean time, the following tips may help you to read in a file correctly and without errors:
+
         - Make sure there are no missing residues or heavy atoms. Tools such as [MODELLER](https://salilab.org/modeller) and [SCWRL4](http://dunbrack.fccc.edu/lab/scwrl) can fix these issues.
         - Remove the hydrogen atoms and add them back [using OpenMM](http://docs.openmm.org/latest/userguide/application/03_model_building_editing.html#adding-hydrogens), which will ensure they have atom names compatible with the OpenMM force field files.
         - Make sure that all residue names match the corresponding residue template name and that all atom names match the appropriate atom in the residue template.
         - Non-standard residues also require `CONECT` records for Chemfiles to assign bonds correctly, see for example [a compatible alanine dipeptide file](https://github.com/noeblassel/SINEQSummerSchool2023/blob/main/notebooks/dipeptide_nowater.pdb).
+
     Some PDB files that read in fine can be found [here](https://github.com/greener-group/GB99dms/tree/main/structures/training/conf_1).
 
 To run on the GPU, set `gpu=true`.