Parametrizer Commandline Usage
To allow for commandline execution export the Nanomatch directory and source the parameterizer config file:
export NANOMATCH=/path/to/your/nanomatch export NANOVER=V2 source $NANOMATCH/$NANOVER/configs/parametrizer.config
As a side note it is very much advised to export the NANOMATCH directory and the current version in your .bashrc file and source the config file during the batch job.
General options of the software and what they mean are explained in the WaNo documentation .
Starting a parametrizer simulation
To start parametrizer, first generate an example settings file by invoking
and open it with an editor. Change all settings accordingly. Most importantly set a DFT engine and choose whether geometrical optimization should be run. Also give the molecule a three letter identifier.
Adding dihedral angles
To add dihedral angle definitions (these are required in case you also want to parametrize the dihedral forcefield), call
add_dihedral_angles.sh output_molecule.mol2 molecule.spf
Outputs of Parametrizer are documented in the WaNo documentation .
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