QuanteMM

B       File Formats

Input Files

.car and .mdf Files

These are the cartesian coordinate and molecular data files, which store quantities such as atom positions, lattice vector, and symmetry information. Please consult the documentation for the Discover_3 or Insight programs for details on their formats. Note that the atomic coordinates in the .car file are always given in angstroms. QuanteMM will write .car and .mdf files for two systems: the QM system and the MM system into which the QM system is embedded. The files are generated by executing the Setup/QM_MM_Systems command.

.inp Files

The .inp suffix denotes Discover_3 input files. There is an .inp file for both the QM and MM system. Please consult the documentation for the Discover_3 program for details on their format.

The following is an example of an .inp file created for a hybrid QM/MM geometry optimization on a finite system. The essential entry in this input file is the energy command which is used to calculate both total energy and first derivatives.

#MSI dsl 3



begin



# Stage 1 forcefield nonbond \-separate_coulomb \ vdw \ summation_method = no_cutoff \ coulomb \ -distance_dependent_dielectric \ dielectric_
value = 1 



# Stage 2 forcefield \ parameters bond_automatic = 1 \ angle_automatic = 1 \ torsion_automatic = 1 \ oop_automatic = 1 \ print_automatic = 
1 \ bond_stop = 1 \ angle_stop = 1 \ torsion_stop = 1 \ oop_stop = 1 \ cross_stop = 0 



# Stage 3 energy print +energies +first_derivative 

The .dat file is a MOPAC input file. The first three lines contain keywords followed by comments. The coordinates are appended. Note that cartesian coordinate input is required.

.input Files

Both DMol and Turbomole deposit their input parameters in a file with the .input extension. Please refer to the DMol and/or Turbomole documentation on detailed information on the file format.

.ec_def Files

The .ec_def file contains the definition of the QM system as it is embedded into the MM system. The relationship between the two systems is established by the QM_MM_Systems command in the QuanteMM user interface.

First line

CLUSTER EMBEDDED IN CRYSTAL => embedding into a system periodic in three dimensions.

CLUSTER EMBEDDED IN MOLECULE => embedding into a finite system.

The following lines specify the QM system ::

ATOM x FROM y [(cell offset)] => defines mapping between QM (x) and MM (y) systems. Cell offsets are added if the MM system is periodic in three dimensions.

LINK ATOM a TYPE b FROM c REPLACES d [(cell offset)] : DISTANCE x => defines a capping atom by element type and the atom it is replacing. If DISTANCE is specified, the atom is placed on the bond axis c-d at a distance x from atom c.Cell offsets are added if the MM system is periodic in three dimensions.

SKIP CHARGE FROM x [(cell offset)] => the charge on atom x of the MM system is to be ignored.Cell offsets are added if the MM system is periodic in three dimensions.

MOVE CHARGE x TO y [(cell offset)] => add the charge x to the partial charge of the MM system atom y. Cell offsets are added if the MM system is periodic in three dimensions.

Last line

END

.csh Files

The .csh file is a UNIX C shell script that launches the QuanteMM background job. It is automatically generated by the Run/Run_QM_MM command of the QuanteMM interface, and the file prefix has the form bkgd_job_run_name, where run_name is the name of the background job. The prefix is modified by appending an integer number to make the file name unique. Old files are not overwritten.

Note that there are also .csh files for the DMol and Turbomole background jobs, which are generated by the Run/Run_DMol and Run/Run_Turbomole commands in the DMol and Turbomole interfaces, respectively. These files are created if DMol or Turbomole are selected as the quantum engine of the hybrid QM/MM calculation.

.csh_log Files

The .csh_log file collects any output generated during execution of the QuanteMM background job that are related to the setup of the job. The QuanteMM calculation results themselves are stored in a separate file with the .out suffix (see below).

Output Files

MOPAC, Discover_3 and QuanteMM deposit the calculation output in files with the .out extension. For QuanteMM, the prefix of the output .out file is given by the job name (specified by the Run_Name parameter in the Run/Run_QM_MM command).

.outmol Files

Turbomole and DMol deposit the calculation output in files with the .outmol extension. Please refer to the Turbomole and DMol documentation for more information on the format of this file.

.sum Files

Turbomole and DMol deposit the calculation output summary in files with the .sum extension. Please refer to the Turbomole and DMol documentation for more information on the format of this file

.turbo_archive Files

Turbomole stores the input options in control file format in a file with the .turbo_archive extension. This file contains all the data needed to do a properties calculation. Please refer to the Turbomole documentation for more information on the format of this file