Protocols

High Throughput

To run in HT mode use the flag -HT that will perform: 3 growing steps of 3 pelesteps and a final exploration of 20 pele steps

python frag_pele/main.py -cp core.pdb -sef serie_file.conf -HT

Standard Precision

To run in SP mode use the default values that will perform: 6 growing steps of 6 pelesteps and a final exploration of 20 pele steps

python frag_pele/main.py -cp core.pdb -sef serie_file.conf

Covalent growing

To run covalent growing you must specify which residue do you want to use. In this example, we will grow a fragment onto the residue 145 of the chain A. To evaluate this kind of simulations you also need to specify as criteria the “LocalNonBindingEnergy” metric. It is mandatory to use PELE 1.6.2 to get results with this argument.

python frag_pele/main.py -cp core.pdb -sef serie_file.conf -cov A:145 -cr LocalNonBindingEnergy

Explorative

To run in EX mode use the flag -EX that will perform an standar growing simulation with a sampling simulation of: 2 steering, 0.5/0.3 translation, 0.4/0.15 rotation and 25 of box radius. Select the number of steps in this sampling simulation with the flag -es.

python frag_pele/main.py -cp core.pdb -sef serie_file.conf -EX -es 200

Personalized Sampling Simulation

If you want to use a different templatized control file in the sampling simulation, use the flag -sc to set its path

python frag_pele/main.py -cp core.pdb -sef serie_file.conf -sc /path/to/control_personalized.conf

Only prepare

If for any reason you would need to prepare all PDB files, templates and configuration files but without growing you can use this mode setting the flag -op. FragPELE will generate one folder for each fragment-core connection specified in the serie_file.conf.

python frag_pele/main.py -cp core.pdb -sef serie_file.conf -op

Only grow

After using the previous mode, to only execute the growing part of the code set the flag -og. Take into account that you will use the configuration specified in the preparation step.

python frag_pele/main.py -cp core.pdb -sef serie_file.conf -og