Quickstart
QMrebind needs an existing AMBER .parm7 with parameters defined for the entire system. QMrebind will replace the partial charges for the relevant atoms (typically of the ligand) based on the QMMM calculation, but keep all other parameters the same.
Make sure you have a .parm7 and .pdb file ready to reparametrize, if you don’t have any handy at this moment, then feel free to download these two:
Input PDB file Requirements
QMrebind accepts the PDB input file with the following requirements:
PDB file typically should have the box vector information.
Ligand and the receptor must be assigned a residue name with the ligand following the receptor.
Run QMrebind
Make sure that the correct conda env is activated:
conda activate QMMM
Assuming that one downloaded the files at the top of this page, QMrebind can be run with the following command:
python ~/qmrebind/qmrebind/run_qmrebind_amber.py hostguest.pdb hostguest.parm7 -L APN
As one can see, the PDB file and the PARM7 file must be provided, in that order, then the resname defining the ligand is provided with the ‘-L’ argument. Alternatively, one may provide the exact atom indices of the ligand:
python ~/qmrebind/qmrebind/run_qmrebind_amber.py hostguest.pdb hostguest.parm7 -l "147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161"
Many options exist as inputs to the run_qmrebind_amber.py. One can see
more of these options by visiting the
Program Options page or by running the
run_qmrebind_amber.py program with the ‘-h’ argument.