QMMM_generator
Since the majority of MD simulations is performed with the periodic boundary conditions (PBC), it is necessary to convert the PBC system to a cluster system for QM/MM calcluations. This utility generates snapshot structures for QM/MM calculations from MD data. Given the trajectory data (dcd, rst, pdb), the program carries out the following,
- Center the origin to the QM region (or any other specified region).
- Wrap all molecules to a simulation box.
- Remove unnecessary molecules if any.
and yields the PSF and coordinate files (in pdb and crd) for selected snapshots.
Generate a cluster system, where a protein is set to the center and solvent molecules are included around 20 Å of the protein.
[INPUT]
psffile = ../prot_solv.psf # protein structure file
reffile = ../prot_solv.pdb # PDB file
[OUTPUT]
qmmm_crdfile = snapshot{}.crd # CHARMM CARD file for QMMM calc.
qmmm_psffile = snapshot{}.psf # CHARMM PSF file for QMMM calc.
qmmm_pdbfile = snapshot{}.pdb # PDB file for reference of analysis
[TRAJECTORY]
trjfile1 = ../1_equil/nvt.dcd # MD trajectory file
md_step1 = 5000 # number of MD steps
mdout_period1 = 100 # MD output period
ana_period1 = 100 # analysis period
trj_type = COOR+BOX # (COOR/COOR+BOX)
trj_natom = 0 # (0:uses reference PDB atom count)
[SELECTION]
group1 = segid:PROA # Select protein
group2 = segid:PROA or \ # Select protein and molecules
(segid:PROA around_mol:20.0) # 20 Å around the protein.
group3 = segid:PROA and an:CA # Select Ca of the protein
[FITTING]
fitting_method = TR+ROT # NO/TR+ROT/TR/TR+ZROT/XYTR/XYTR+ZRO
fitting_atom = 3 # atom group used for fitting
mass_weight = NO # mass-weight is not applied
[OPTION]
check_only = NO # only checking input files (YES/NO)
coord_format = CHARMM # (CHARMM CARD)
qmmm_atom_index = 2 # atom groups for QM/MM systems
frame_number = 10:10:50 # begin:stride:end
reconcile_num_atoms = NO # (YES/NO)
origin_atom_index = 1 # atom groups for the origin of the system
[NOTES]
- The snapshot structures are fit to a reference structure,
reffile
in [INPUT]. frame_number
in [OPTION] can be specified in three ways:- Directly input frame numbers with comma or space, for example, 800, 1600, 2400.
- Input frame numbers in format of begin:stride:end, for example, 800:800:2400.
- The two expressions can be specified simultaneously separating with slash, for example, 1, 5, 9 / 13:4:30.
- The number of solvent molecules (20 Å around the protein) will be different among different frames. If
reconcile_num_atoms
in [OPTION is set to YES, the number of atoms are made as much similar as possible. origin_atom_index
in [OPTION] defines the origin of the system. When multiple atoms are specified, the center of mass of these atoms is set to the origin.
Written by Kiyoshi Yagi and Kenta Yamada @RIKEN Theoretical molecular science laboratory
Feb. 1, 2019