CLI

TIES can be access via both command line and python interface.

In the smallest example one can carry out a superimposition employing only two ligands

ties --ligands l03.mol2 l02.mol2

Ideally these .mol2 files already have a pre-assigned charges in the last column for each atom. See for example MCL1 case.

In the case of this example, we are working on molecules that are negatively charges (-1e), and we need to specify it:

ties --ligands l03.mol2 l02.mol2 --ligand-net-charge -1

The order the of the ligands matters and more ligands can be passed. This command creates by default a ties-input directory with all output files. These include meta_*_*.json files which contain the details about how the ligands were superimposed, and what configuration was used. The general directory structure will look like this:

    ties
    ├── mol2
    │    ├── l02
    │    └── l03
    ├── prep
    │   ├── ligand_frcmods
    │   │   ├── l02
    │   │   └── l03
    │   └── morph_frcmods
    │       └── tests
    │           └── l02_l03
    └── ties-l02-l03
        └── lig
            └── build

Note that all the output generated by ambertools is stored, and can be investigated.

The full RBFE requires also the protein, as well as the net charge of the ligands used in the transformation:

ties -l l02.mol2 l03.mol2 -nc -1 --protein protein.pdb

Check all the options with

ties -h

Warning

This code is currently experimental and under active development. If you notice any problems, report them. *