[ENH]: qm atom mask selection

[camattelaer]

In which tool?

gmx_MMPBSA

New Feature

Currently qmmask selection is based on full residues, either directly via residue number or within specific distance of the ligand.

Additional option to set qmmask directly for selected atoms would be beneficial to prevent SCF issues if the MD was run using only an MM forcefield.

Description

It would be nice if there was an option to set the QM atom mask other than only based on residue numbers.

Currently creating QM-MM boundary through residues numbers 'cuts' through amide bonds, which is a poor choice of QM-MM boundary.

With MMPBSA.py this is currently only possible using -make-mdins and -use-mdins flags:

1. generate inputs by running MMPBSA.py with -mdins-flag
2. the user modifies the qmmask in the respective input files to not include amide backbone atoms, eg 'cutting' through Calpha-Cbeta bond
3. run MMGBSA.py using modified input files using -use-mdins flag

Currently running some tests and a simulation where gmx_MMPBSA was having troubles with SCF convergence had much better results using the MMPBSA.py approach removing the backbone atoms

I do not expect this to be quickly implemented, but I do believe it would be an added value to gmx_MMPBSA

(relevance: in my opinion low since only applies to people interested in QM-MMGBSA approach, unfortunately i am one of those people) (difficulty: in my opinion medium, perhaps even high, because it does require some additional intermediary file manipulation to run MMPBSA)

Relevance

low

Difficulty to implement

medium