Required parametersΒΆ

These parameters must always be present in the input.yaml. They define the basic settings that the Platform needs in order to run.

Any PELE simulation needs, at least:

  • system: the path to the PDB file that contains the initial structure for the simulation. It can also take several PDB files with the asterisk wildcard.

  • chain: the chain in the input PDB file that corresponds to the small molecule to perturb.

  • resname: the residue name in the input PDB file that corresponds to the small molecule to perturb.

To use a single input PDB file:

system: 'system.pdb'
chain: 'L'
resname: 'LIG'

To take all PDB files inside a folder:

system: 'PDBs/*.pdb'
chain: 'L'
resname: 'LIG'

Warning

Note that fragPELE uses different parameters than the rest of packages of PELE. Please, refer to fragPELE page to see the parameters that are required in this specific case.