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Optmaven-2.0 16 June 2018 Written by Matthew F. Allan and Ratul Chowdhury with contributions from Tong Li and Robert J. Pantazes Costas Maranas Laboratory, Department of Chemical Engineering The Pennsylvania State University University Park, PA 16802

DEPENDENCIES

Python 2.7: https://www.python.org/ NumPy 1.13+: http://www.numpy.org/ SciPy 0.19+: https://www.scipy.org/ Biopython 1.7+: https://biopython.org/ VMD 1.9+: http://www.ks.uiuc.edu/Research/vmd/ NAMD 2.12+: http://www.ks.uiuc.edu/Research/namd/ CHARMM 34+: https://www.charmm.org/ CPLEX - Python API: https://www.ibm.com/support/knowledgecenter/SSSA5P_12.7.1/ilog.odms.cplex.help/CPLEX/GettingStarted/topics/set_up/setup_overview.html DGSOL (only if running embedder module): http://www.mcs.anl.gov/~more/dgsol/

INSTALLATION

OptMAVEn-2.0 needs no installation. Merely unzip and/or untar the compressed directory and move it to the location of choice. However, you must edit the file src/standards.py by specifying the following environment variables:

PythonCommand: the path to the Python executable CharmmCommand: the path to the CHARMM executable CplexDirectory: the directory in which the CPLEX modules are located VmdCommand: the path to the VMD executable NamdCommand: the path to the NAMD executable PbsQueue: the name of the PBS queue to which to submit jobs

For example, change the line PythonCommand = "" to PythonCommand = "/usr/bin/python"

DIRECTORY STRUCTURE

The OptMAVEN-2.0 directory contains the following subdirectories:

src: source modules in Python and TCL data: data files needed for OptMAVEn-2.0 to run. Subdirectories: antibodies: MAPs database and framework antibody structures input_files: CHARMM topology, parameter, and solvation files pdbs: structures of the input antigens experiments: contains all experiment directories

The OptMAVEn-2.0 directory also contains the following executables:

OptMAVEN-2.0: start an OptMAVEn-2.0 experiment find_contacts: find the residues that make contacts between two molecules interaction_energy: compute the interaction energy between two molecules check_status: check the status of the experiments remove_experiment: remove an experiment permanently

RUNNING OPTMAVEN-2.0

Navigate to the main directory of OptMAVEn-2.0 and type ./OptMAVEn-2.0 to start OptMAVEn-2.0. You will be prompted for the following information:

Name of the experiment Whether or not to use benchmarking The gap penalty to use during clustering Whether or not to customize the following settings: Antigen positioning grid Antigen positioning clash cutoff CHARMM topology files CHARMM parameter files CHARMM solvation files CHARMM energy terms CHARMM iteration limit Queue walltime Queue batch size File or PDB id of the antigen Whether or not to exclude heteroatoms from each chain The chain(s) that constitute(s) the antigen The residue(s) that constitute(s) the epitope to target

The following command-line arguments may be specified for OptMAVEn-2.0: --keeptemp: keep temporary files. Useful for debugging but requires more space --exclude_hetero: 'ask' (default), 'yes', or 'no' 'ask': ask if heteroatoms should be excluded 'yes': automatically exclude all heteroatoms 'no': do not exclude any heteroatoms

CHECKING THE STATUS

The status may be checked by running ./check_status from the main directory. Supplying a command-line argument returns only the experiments whose names contain the argument. For example: ./check_status exp would report the status of experiments named 'exp', 'exp2', and 'my_experiment' but not 'myExperiment'.

VIEWING THE RESULTS

The results of an experiment 'EXP_NAME' are saved in the file experiments/EXP_NAME/Results.csv. Additionally, a summary of the inputs is given in experiments/EXP_NAME/Summary.txt.

TROUBLESHOOTING

If an experiment 'EXP_NAME' fails, an error message will be written to the file experiments/EXP_NAME/errors.txt. Please review the error message to diagnose the problem. In the case that no error message is generated, the problem likely arose from the PBS queueing system. Please ensure that the queue is set up correctly and verify all environment settings (e.g. the path to the Python executable defined in src/standards.py).