explanation of QCLObot-modeler YAML File

QCLObot-modeler playbook is separated by following two parts:

vars section

definition of variables
tasks section

definition of task for general and for frame molecule

vars section

Declare the variable. The declared variables can be used with “with_items” and so on.

tasks section

The tasks section is consist of three parts:

protonate

protonate

Protonate the molecule.

src

Specify the PDB file.

- name: 2MGO
  protonate:
    src: 2mgo.pdb

neutralize

Add ions to neutralize. Ignore ions on the ion-pairs.

- name: 2MGO_optx
  neutralize:
    reference: 2MGO_opt
    dest: 2MGO_optx.pdb

opt

Do energy minimization simulation.

reference

Specify the task to be the input structure.

belly_mask:

(option)

Use the belly method. The force of a specified molecule is considered to be zero.

- name: 2MGO_optx_mdwatx_optwatx
  opt:
    reference: 2MGO_optx_mdwatx
    belly_mask:
      - water
      - ions
    dest: 2MGO_optx_mdwatx.pdb

md

Run molecular dynamics simulation.

name

(mandatory) Give this task a name. A directory of this name is created. The task is executed in this directory.

reference

Specify the task to be the input structure.

solvation:

(option) Specify the solvation model.

belly_mask:

(option)

Use the belly method. The force of a specified molecule is considered to be zero.

- name: 2MGO_optx_mdwatx
  md:
    reference: 2MGO_optx
    solvation:
      method: cap
      model: TIP3PBOX
    belly_mask:
      - water
      - ions