Structures

Supported inputs and structure preparation

PyMACS can start from local structural files or fetch structures from the PDB. The important beginner skill is knowing what the selected input contains.

Supported starts

  • Local PDB files.
  • Local CIF or mmCIF files.
  • Fetched PDB entries using a PDB ID.
  • Curated example inputs under Example_Choices/.

Common commands

Copy command 
python 1_AutomateGromacs.py --pdb model.pdb
python 1_AutomateGromacs.py --pdb model.mmcif
python 1_AutomateGromacs.py --fetch-pdb 9UWJ
python 1_AutomateGromacs.py --fetch-pdb 9UWJ --fetch-format pdb

Chain and cleanup controls

Flag Use
--keep-chains A,B Keep only selected polymer chains.
--drop-chains B Remove selected polymer chains.
--chain-names Rap1B,Rap1GAP Apply readable chain names in chain order.
--chain-map A:Rap1B,B:Rap1GAP Apply explicit chain ID to name mapping.
--remove-input-waters Remove crystallographic waters before setup.
--remove-input-ions Remove ordinary ions before setup.
--strict-pdb-validation Stop early when selected structure warnings should be treated as fatal.

Beginner checks

  • Confirm the ligand or cofactor residue name in the input structure.
  • Do not drop chains unless you know those chains are irrelevant.
  • Use CIF or mmCIF when PDB formatting loses important structure details.
  • View the selected structure before trusting a long simulation.