CWL Classical Molecular Interaction Potentials
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CMIP tutorial using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of computing classical molecular interaction potentials from protein structures, step by step, using the BioExcel Building Blocks library (biobb). Examples shown are Molecular Interaction Potentials (MIPs) grids, protein-protein/ligand interaction potentials, and protein titration. The particular structures used are the Lysozyme protein (PDB code 1AKI), and a MD simulation of the complex formed by the SARS-CoV-2 Receptor Binding Domain and the human Angiotensin Converting Enzyme 2 (PDB code 6VW1).

The code wrapped is the Classical Molecular Interaction Potentials (CMIP) code:

Classical molecular interaction potentials: Improved setup procedure in molecular dynamics simulations of proteins. Gelpí, J.L., Kalko, S.G., Barril, X., Cirera, J., de la Cruz, X., Luque, F.J. and Orozco, M. (2001) Proteins, 45: 428-437. https://doi.org/10.1002/prot.1159

Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU H2020 823830, EU H2020 675728).

Licensed under the Apache License 2.0, see the file LICENSE for details.

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SEEK ID: https://workflowhub.eu/workflows/2156?version=1

DOI: 10.48546/workflowhub.workflow.2156.1

Inputs

ID Name Description Type
step0_cmip_prepare_pdb_input_pdb_path Input file Input PDB file path.
  • File
step0_cmip_prepare_pdb_output_cmip_pdb_path Output file Output PDB file path.
  • string
step1_cmip_titration_output_pdb_path Output file Path to the output PDB file.
  • string
step1_cmip_titration_config Config file Configuration file for biobb_cmip.cmip_titration tool.
  • string
step2_cat_pdb_output_structure_path Output file Output protein file path.
  • string
step3_cmip_run_pos_output_log_path Output file Path to the output CMIP log file LOG.
  • string
step3_cmip_run_pos_output_cube_path Output file Path to the output grid file in cube format.
  • string
step3_cmip_run_pos_config Config file Configuration file for biobb_cmip.cmip_run tool.
  • string
step4_cmip_run_neg_output_log_path Output file Path to the output CMIP log file LOG.
  • string
step4_cmip_run_neg_output_cube_path Output file Path to the output grid file in cube format.
  • string
step4_cmip_run_neg_config Config file Configuration file for biobb_cmip.cmip_run tool.
  • string
step5_cmip_run_neu_output_log_path Output file Path to the output CMIP log file LOG.
  • string
step5_cmip_run_neu_output_cube_path Output file Path to the output grid file in cube format.
  • string
step5_cmip_run_neu_config Config file Configuration file for biobb_cmip.cmip_run tool.
  • string
step6_remove_pdb_water_input_pdb_path Input file Input PDB file path.
  • File
step6_remove_pdb_water_output_pdb_path Output file Output PDB file path.
  • string
step7_extract_heteroatoms_output_heteroatom_path Output file Output heteroatom file path.
  • string
step7_extract_heteroatoms_config Config file Configuration file for biobb_structure_utils.extract_heteroatoms tool.
  • string
step8_reduce_add_hydrogens_output_path Output file Path to the output file.
  • string
step9_acpype_params_ac_output_path_inpcrd Output file Path to the INPCRD output file.
  • string
step9_acpype_params_ac_output_path_frcmod Output file Path to the FRCMOD output file.
  • string
step9_acpype_params_ac_output_path_lib Output file Path to the LIB output file.
  • string
step9_acpype_params_ac_output_path_prmtop Output file Path to the PRMTOP output file.
  • string
step9_acpype_params_ac_config Config file Configuration file for biobb_chemistry.acpype_params_ac tool.
  • string
step10_leap_gen_top_output_pdb_path Output file Output 3D structure PDB file matching the topology file.
  • string
step10_leap_gen_top_output_top_path Output file Output topology file (AMBER ParmTop).
  • string
step10_leap_gen_top_output_crd_path Output file Output coordinates file (AMBER crd).
  • string
step10_leap_gen_top_config Config file Configuration file for biobb_amber.leap_gen_top tool.
  • string
step11_sander_mdrun_output_traj_path Output file Output trajectory file.
  • string
step11_sander_mdrun_output_rst_path Output file Output restart file.
  • string
step11_sander_mdrun_output_log_path Output file Output log file.
  • string
step11_sander_mdrun_config Config file Configuration file for biobb_amber.sander_mdrun tool.
  • string
step12_amber_to_pdb_output_pdb_path Output file Structure PDB file.
  • string
step13_cmip_prepare_structure_output_cmip_pdb_path Output file Path to the output PDB file.
  • string
step14_remove_ligand_output_structure_path Output file Output structure file path.
  • string
step14_remove_ligand_config Config file Configuration file for biobb_structure_utils.remove_ligand tool.
  • string
step15_cmip_ignore_residues_output_cmip_pdb_path Output file Output PDB file path.
  • string
step15_cmip_ignore_residues_config Config file Configuration file for biobb_cmip.cmip_ignore_residues tool.
  • string
step16_cmip_run_int_en_output_log_path Output file Path to the output CMIP log file LOG.
  • string
step16_cmip_run_int_en_output_byat_path Output file Path to the output atom by atom energy file.
  • string
step16_cmip_run_int_en_config Config file Configuration file for biobb_cmip.cmip_run tool.
  • string
step17_cmip_prepare_structure_input_pdb_path Input file Path to the input PDB file.
  • File
step17_cmip_prepare_structure_input_topology_path Input file Path to the input topology path.
  • File
step17_cmip_prepare_structure_output_cmip_pdb_path Output file Path to the output PDB file.
  • string
step18_extract_chain_a_output_structure_path Output file Output structure file path.
  • string
step18_extract_chain_a_config Config file Configuration file for biobb_structure_utils.extract_chain tool.
  • string
step19_extract_chain_b_output_structure_path Output file Output structure file path.
  • string
step19_extract_chain_b_config Config file Configuration file for biobb_structure_utils.extract_chain tool.
  • string
step20_cmip_run_rbd_output_log_path Output file Path to the output CMIP log file LOG.
  • string
step20_cmip_run_rbd_output_json_box_path Output file Path to the output CMIP box in JSON format.
  • string
step20_cmip_run_rbd_config Config file Configuration file for biobb_cmip.cmip_run tool.
  • string
step21_cmip_run_hace2_output_log_path Output file Path to the output CMIP log file LOG.
  • string
step21_cmip_run_hace2_output_json_box_path Output file Path to the output CMIP box in JSON format.
  • string
step21_cmip_run_hace2_config Config file Configuration file for biobb_cmip.cmip_run tool.
  • string
step22_cmip_run_rbd_hace2_output_log_path Output file Path to the output CMIP log file LOG.
  • string
step22_cmip_run_rbd_hace2_output_json_box_path Output file Path to the output CMIP box in JSON format.
  • string
step22_cmip_run_rbd_hace2_config Config file Configuration file for biobb_cmip.cmip_run tool.
  • string
step23_cmip_ignore_residues_rbd_output_cmip_pdb_path Output file Output PDB file path.
  • string
step23_cmip_ignore_residues_rbd_config Config file Configuration file for biobb_cmip.cmip_ignore_residues tool.
  • string
step24_cmip_run_prot_prot_output_json_box_path Output file Path to the output CMIP box in JSON format.
  • string
step24_cmip_run_prot_prot_output_json_external_box_path Output file Path to the output external CMIP box in JSON format.
  • string
step24_cmip_run_prot_prot_output_log_path Output file Path to the output CMIP log file LOG.
  • string
step24_cmip_run_prot_prot_output_byat_path Output file Path to the output atom by atom energy file.
  • string
step24_cmip_run_prot_prot_config Config file Configuration file for biobb_cmip.cmip_run tool.
  • string
step25_cmip_ignore_residues_hace2_output_cmip_pdb_path Output file Output PDB file path.
  • string
step25_cmip_ignore_residues_hace2_config Config file Configuration file for biobb_cmip.cmip_ignore_residues tool.
  • string
step26_cmip_run_complex_output_json_box_path Output file Path to the output CMIP box in JSON format.
  • string
step26_cmip_run_complex_output_json_external_box_path Output file Path to the output external CMIP box in JSON format.
  • string
step26_cmip_run_complex_output_log_path Output file Path to the output CMIP log file LOG.
  • string
step26_cmip_run_complex_output_byat_path Output file Path to the output atom by atom energy file.
  • string
step26_cmip_run_complex_config Config file Configuration file for biobb_cmip.cmip_run tool.
  • string

Steps

ID Name Description
step0_cmip_prepare_pdb cmip_prepare_pdb Creates a CMIP suitable PDB from an standar PDB file
step1_cmip_titration cmip_titration CMIP cmip module compute classical molecular interaction potentials.
step2_cat_pdb cat_pdb Class to concat two PDB structures in a single PDB file.
step3_cmip_run_pos cmip_run CMIP cmip module compute classical molecular interaction potentials.
step4_cmip_run_neg cmip_run CMIP cmip module compute classical molecular interaction potentials.
step5_cmip_run_neu cmip_run CMIP cmip module compute classical molecular interaction potentials.
step6_remove_pdb_water remove_pdb_water This class is a wrapper of the Structure Checking tool to remove water molecules from PDB 3D structures.
step7_extract_heteroatoms extract_heteroatoms Class to extract hetero-atoms from a 3D structure.
step8_reduce_add_hydrogens reduce_add_hydrogens Adds hydrogen atoms to small molecules.
step9_acpype_params_ac acpype_params_ac Small molecule parameterization for AMBER MD package.
step10_leap_gen_top leap_gen_top Generates a MD topology from a molecule structure using tLeap tool from the AmberTools MD package
step11_sander_mdrun sander_mdrun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step12_amber_to_pdb amber_to_pdb Generates a PDB structure from AMBER topology (parmtop) and coordinates (crd) files, using the ambpdb tool from the AmberTools MD package
step13_cmip_prepare_structure cmip_prepare_structure Creates a CMIP suitable PDB from an standar structure file
step14_remove_ligand remove_ligand Class to remove the selected ligand atoms from a 3D structure.
step15_cmip_ignore_residues cmip_ignore_residues Mark residues which charges will be ignored in the CMIP potential calculations.
step16_cmip_run_int_en cmip_run CMIP cmip module compute classical molecular interaction potentials.
step17_cmip_prepare_structure cmip_prepare_structure Creates a CMIP suitable PDB from an standar structure file
step18_extract_chain_a extract_chain This class is a wrapper of the Structure Checking tool to extract a chain from a 3D structure.
step19_extract_chain_b extract_chain This class is a wrapper of the Structure Checking tool to extract a chain from a 3D structure.
step20_cmip_run_rbd cmip_run CMIP cmip module compute classical molecular interaction potentials.
step21_cmip_run_hace2 cmip_run CMIP cmip module compute classical molecular interaction potentials.
step22_cmip_run_rbd_hace2 cmip_run CMIP cmip module compute classical molecular interaction potentials.
step23_cmip_ignore_residues_rbd cmip_ignore_residues Mark residues which charges will be ignored in the CMIP potential calculations.
step24_cmip_run_prot_prot cmip_run CMIP cmip module compute classical molecular interaction potentials.
step25_cmip_ignore_residues_hace2 cmip_ignore_residues Mark residues which charges will be ignored in the CMIP potential calculations.
step26_cmip_run_complex cmip_run CMIP cmip module compute classical molecular interaction potentials.

Outputs

ID Name Description Type
step0_cmip_prepare_pdb_out1 output_cmip_pdb_path Output PDB file path.
  • File
step1_cmip_titration_out1 output_pdb_path Path to the output PDB file.
  • File
step2_cat_pdb_out1 output_structure_path Output protein file path.
  • File
step3_cmip_run_pos_out1 output_log_path Path to the output CMIP log file LOG.
  • File
step3_cmip_run_pos_out2 output_cube_path Path to the output grid file in cube format.
  • File
step4_cmip_run_neg_out1 output_log_path Path to the output CMIP log file LOG.
  • File
step4_cmip_run_neg_out2 output_cube_path Path to the output grid file in cube format.
  • File
step5_cmip_run_neu_out1 output_log_path Path to the output CMIP log file LOG.
  • File
step5_cmip_run_neu_out2 output_cube_path Path to the output grid file in cube format.
  • File
step6_remove_pdb_water_out1 output_pdb_path Output PDB file path.
  • File
step7_extract_heteroatoms_out1 output_heteroatom_path Output heteroatom file path.
  • File
step8_reduce_add_hydrogens_out1 output_path Path to the output file.
  • File
step9_acpype_params_ac_out1 output_path_inpcrd Path to the INPCRD output file.
  • File
step9_acpype_params_ac_out2 output_path_frcmod Path to the FRCMOD output file.
  • File
step9_acpype_params_ac_out3 output_path_lib Path to the LIB output file.
  • File
step9_acpype_params_ac_out4 output_path_prmtop Path to the PRMTOP output file.
  • File
step10_leap_gen_top_out1 output_pdb_path Output 3D structure PDB file matching the topology file.
  • File
step10_leap_gen_top_out2 output_top_path Output topology file (AMBER ParmTop).
  • File
step10_leap_gen_top_out3 output_crd_path Output coordinates file (AMBER crd).
  • File
step11_sander_mdrun_out1 output_traj_path Output trajectory file.
  • File
step11_sander_mdrun_out2 output_rst_path Output restart file.
  • File
step11_sander_mdrun_out3 output_log_path Output log file.
  • File
step12_amber_to_pdb_out1 output_pdb_path Structure PDB file.
  • File
step13_cmip_prepare_structure_out1 output_cmip_pdb_path Path to the output PDB file.
  • File
step14_remove_ligand_out1 output_structure_path Output structure file path.
  • File
step15_cmip_ignore_residues_out1 output_cmip_pdb_path Output PDB file path.
  • File
step16_cmip_run_int_en_out1 output_log_path Path to the output CMIP log file LOG.
  • File
step16_cmip_run_int_en_out2 output_byat_path Path to the output atom by atom energy file.
  • File
step17_cmip_prepare_structure_out1 output_cmip_pdb_path Path to the output PDB file.
  • File
step18_extract_chain_a_out1 output_structure_path Output structure file path.
  • File
step19_extract_chain_b_out1 output_structure_path Output structure file path.
  • File
step20_cmip_run_rbd_out1 output_log_path Path to the output CMIP log file LOG.
  • File
step20_cmip_run_rbd_out2 output_json_box_path Path to the output CMIP box in JSON format.
  • File
step21_cmip_run_hace2_out1 output_log_path Path to the output CMIP log file LOG.
  • File
step21_cmip_run_hace2_out2 output_json_box_path Path to the output CMIP box in JSON format.
  • File
step22_cmip_run_rbd_hace2_out1 output_log_path Path to the output CMIP log file LOG.
  • File
step22_cmip_run_rbd_hace2_out2 output_json_box_path Path to the output CMIP box in JSON format.
  • File
step23_cmip_ignore_residues_rbd_out1 output_cmip_pdb_path Output PDB file path.
  • File
step24_cmip_run_prot_prot_out1 output_json_box_path Path to the output CMIP box in JSON format.
  • File
step24_cmip_run_prot_prot_out2 output_json_external_box_path Path to the output external CMIP box in JSON format.
  • File
step24_cmip_run_prot_prot_out3 output_log_path Path to the output CMIP log file LOG.
  • File
step24_cmip_run_prot_prot_out4 output_byat_path Path to the output atom by atom energy file.
  • File
step25_cmip_ignore_residues_hace2_out1 output_cmip_pdb_path Output PDB file path.
  • File
step26_cmip_run_complex_out1 output_json_box_path Path to the output CMIP box in JSON format.
  • File
step26_cmip_run_complex_out2 output_json_external_box_path Path to the output external CMIP box in JSON format.
  • File
step26_cmip_run_complex_out3 output_log_path Path to the output CMIP log file LOG.
  • File
step26_cmip_run_complex_out4 output_byat_path Path to the output atom by atom energy file.
  • File

Version History

Version 1 (earliest) Created 1st Apr 2026 at 09:17 by Genís Bayarri

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Citation
Bayarri, G., & Hospital, A. (2026). CWL Classical Molecular Interaction Potentials. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.2156.1
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Created: 1st Apr 2026 at 09:17

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