[ENH]: Support for QM/MM simulations with QUICK

[marioernestovaldes]

In which tool?

gmx_MMPBSA

New Feature

The sander program has the capability to run QM/MM simulations with the quantum chemical code QUICK (QUantum Interaction Computational Kernel) shipped along with AmberTools.

Page 182, https://ambermd.org/doc12/Amber23.pdf

Notes: -It does not support GB, thus define igb=0 in the input file -Specify the QUICK_BASIS environment variable before running the calculations with

export QUICK_BASIS=$AMBERHOME/AmberTools/src/quick/basis

Input file for sander:

&cntrl
ntb=0, nsnb=99999, cut=999.0, imin=5, 
ncyc=0, igb=0, saltcon=0.15, 
surften=0.0072, ifqnt=1, 
dec_verbose=0, 
/
&qmmm
qmmask = ':40-41',
qm_theory = 'quick',
qmmm_int = 1,
qm_ewald = 0,
/
&quick
method = 'B3LYP',
basis = 'def2-svp'
/

Description

From issue https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/454#issuecomment-1925850215

Provide more flexibility to select qm_residues. With this new option, it might be possible to select residues from one entity (i.e. receptor or ligand only)

Relevance

low

Difficulty to implement

medium