Parametrizer Commandline Usage

Setup

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

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

Parametrizer.py

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

Output files

Outputs of Parametrizer are documented in the WaNo documentation .