Issue with Handling Topology Files with Three Columns in ligand_alchemy.py

[h28363231]

Dear Developer Team,

I am currently working with the develop branch of pmx and encountered an issue in the file pmx/src/pmx/ligand_alchemy.py, specifically within the method _get_ff_entry. The issue arises when handling topology files that contain only three columns, such as the example below:

[ bonds ]
; ai aj funct b0 Kb
1 2 1
1 26 1
1 27 1
1 28 1

In this method, there is a line of code: out = cp.deepcopy(b), and later, the code attempts to access out[3:][0]. This results in a problem because there are only three columns in the topology file, hence, accessing out[3:][0] does not exist and causes an error.

Could you please advise on how to modify the script to handle this scenario appropriately or consider updating the code to handle such cases in the develop branch?

Thank you for your assistance and looking forward to your guidance.

Best regards,

Jack Liu

[vgapsys]

This function is used when constructing hybrid topologies. For that it is necessary to have parameters explicitly defined in the input topology files. In this case, bond length and force constant are missing