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ConversionScripts

Go Model to LAMMPS:

To make a Go Model in LAMMPS, we first use the MMTSB Go Model Web Server. You provide the MMTSB server with a PDB file, and your email and it will send an email containing the Go model for that protein in charmm format. The charmm files are combined into a single tar file. To extract, run the command:

• $ tar -zxvf name_of_tarfile

To convert the files to a lammps format we have made a python script: GOLammpsConverter.py. This script requires the following files: GOLammpsReader.py GOLammpsWriter.py GOLammpsInfo.py. To get a copy of these scripts run the command:

• $ svn co svn+ssh:UserName@watt.et.byu.edu:~/What/Is/ThePath/go2lammps

You will need to change the variables in GOLammpsConverter.py so it they hold the names of the files you want to convert (the variables you have to change can be seen in the picture below). Once you have changed those variables, put the python files and the files from the MMTSB server in the same directory and run the command:python GOLammpsConverter.py.