Step 2: Preparation and Submission of Input Files for the QM
Procedure
For MFCC, after generating fragments and conjugating caps, all fragments
(–ligand), caps (–ligand), and ligand molecules are evaluated by QM
calculations (if N fragments have been generated for a protein, the
number of QM input files will be 4N – 1). Because the first (last)
fragment and conjugated cap(s) share the same structure, they are not
calculated, and the number of input files is 4N − 9 (large, even for a
moderately sized protein). Therefore, automated preparation of QM input
files is desirable. In the implementation of GridMol version 2.0, users
can select one QM package (e.g., Gaussian) and provide parameters to
allow automatic generation of the input files.
For FMO, because the process of generating a GAMESS input file is not
straightforward, users must create a complex input file while consulting
a manual. In the implementation described here, we analyze each
fragment’s characteristics and perform an automated generation of the
input file. Bonds are fractioned electrostatically, and bond-specific
electron pairs remain intact. Each atom in a molecule is grouped into a
unique fragment, with the charge of each fragment assigned according to
its electrons, which are assigned heterolytically during molecule
fragmentation. In FMO, the sp2 or
sp3 hybrid orbitals are used for bond detachment. In
this study, we created orbitals for sp3 C,
sp3 N, and sp2 C for frequently used
Gaussian-based functions [STO-3G, 6-31G, 6-31G (d), and 6-31G (d,
p)] and inserted them into the database. After selecting the basis
set, the hybrid molecular orbitals block for a specific basis set can be
automatically written into the $FMOHYB group of the input file.
Once generated, the QM input files for MFCC, or GAMESS for FMO, can be
submitted to the grid environment, where a ‘best’ destination node
(according to the scheduling policy) is selected to finish the job. The
input files can be processed concurrently, with each activity
accelerated by parallel computing.