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Micelle Builder
The Micelle Builder helps the user generate a series of CHARMM inputs necessary to build a pure/mixed micelle system or a protein/micelle complex for molecular dynamics simulations. A brief description of each step is given below.

Please note that

  • NAMD inputs (v2.7b3 or after) are provided for equilibration and production (see STEP6). Input files can be found in "namd" directory when you download tar archive ("charmm-gui.tgz") after all the input file generation.
  • GROMACS inputs (v5.0 or after) are provided for minimization, equilibration and production (see STEP6). Input files can be found in "gromacs" directory when you download tar archive ("charmm-gui.tgz") after all the input file generation. See gromacs/README.
  • AMBER inputs (v16 or after) are provided for minimization, equilibration and production (see STEP6). Input files can be found in "amber" directory when you download tar archive ("charmm-gui.tgz") after all the input file generation. See amber/README.
  • GENESIS inputs (v1.1.0 or after) are provided for minimization, equilibration and production (see STEP6). Input files can be found in "genesis" directory when you download tar archive ("charmm-gui.tgz") after all the input file generation.
  • OpenMM inputs (v6.2 or after) and running scripts are provided for equilibration and production (see STEP6). Input files can be found in "openmm" directory when you download tar archive ("charmm-gui.tgz") after all the input file generation. See openmm/README.
  • CHARMM/OpenMM inputs (c39b1 or after) are provided for equilibration and production (see STEP6). Input files can be found in "charmm_openmm" directory when you download tar archive ("charmm-gui.tgz") after all the input file generation.
  • The protein must be oriented with respect to a micelle whose center is located at (0, 0, 0)
  • RCSB PDB structures are NOT pre-oriented, but can be oriented in step 2 (see below)
  • OPM (http://opm.phar.umich.edu) provides pre-oriented protein coordinates with respect to the membrane normal
  • A homogenous/heterogenous micelle can be built with SDS, LMPG, DHPC, DPC, TPC, ADDG, BDDG, ADG, BDG, ADDM, BDDM, ADM, and BDM
  • Rectangular geometries is supported for a system shape
  • If you are not familiar with the first PDB reading step, please first watch these video demos.
  • The OPM PDB does not contain "TER" between ATOM and HETATM, so that CHARMM-GUI often fails to recognize ligand molecules. In such case, the user should manually insert "TER" in appropriate places.
References for Micelle Builder:

S. Jo, T. Kim, V.G. Iyer, and W. Im (2008)
CHARMM-GUI: A Web-based Graphical User Interface for CHARMM. J. Comput. Chem. 29:1859-1865


X. Cheng, S. Jo, H.S. Lee, J.B. Klauda and W. Im (2013)
CHARMM-GUI Micelle Builder for Pure/Mixed Micelle and Protein/Micelle Complex Systems. J. Chem. Inf. Model. 53:2171-2180


J. Lee, X. Cheng, J.M. Swails, M.S. Yeom, P.K. Eastman, J.A. Lemkul, S. Wei, J. Buckner, J.C. Jeong, Y. Qi, S. Jo, V.S. Pande, D.A. Case, C.L. Brooks III, A.D. MacKerell Jr, J.B. Klauda, and W. Im (2016)
CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations using the CHARMM36 Additive Force Field. J. Chem. Theory Comput. 12:405-413


Protein/Micelle System

Download PDB File: Download Source:

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PDB Format: PDB PDBx/mmCIF CHARMM

Micelle Only System

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A brief explanation of each step:
  • STEP1: Read protein coordinates
    The user can download the coordinates from RCSB (PDB website) or OPM (http://opm.phar.umich.edu). OPM provides pre-oriented protein coordiantes with respect to the membrane normal. The user can upload the PDB (or CHARMM) format coordinates from the user's local machine, once you properly orient the protein in membranes.

  • STEP2: Orient the protein
    If the PDB coordinates are from RCSB, it is necessary to properly orient the protein and have its hydrophobic region within the micelle.

  • STEP3: Determine the system size
    The system size is determined by the water extent from the surface of the protein/micelle complex. The complex size depends on protein size and detergent type. For now, four types of detergents (DHPC, DPC, SDS, and TPC) are available. The system size is equivalent along any of X, Y and Z-axis.

  • STEP4: Build the components
    Based on the system size determined in the previous step, this step builds individual pieces such as (1) the detergents around the protein, (2) additional water molecules to fully solvate the protein, and (3) ions (with Monte Carlo sampling) for a given concentration.

  • STEP5: Assemble the components
    All the pieces (protein, detergents, water, and ions) are assembled together in this step.

  • STEP6: Equilibrate the system
    Due to the their computation time, only the input files for six "suggested" equilibration steps are provided.

    NAMD inputs are provided for equilibration (step6.1 through step6.6) and production
    • namd/step6.[1-6]_equilibration.inp: use generated coordinates of a micelle/protein complex (or micelle only system) to perform equilibration. Equilibration inputs use collective variable restraints to slowly release the system to facilitate stable simulation.
    • namd/step7.1_production.inp: use the restart file from NAMD equilibration and continue production runs.

    GROMACS inputs are provided for minimization (step6.0), equilibration (step6.1 through step6.6) and production
    • gromacs/step6.0_minimization.mdp: use generated coordinates of a micelle/protein complex (or micelle only system) to perform minimization.
    • gromacs/step6.[1-6]_equilibration.mdp: use minimized coordinates from GROMACS to perform equilibration.
    • gromacs/step7_production.mdp: use equilibrated coordinates from GROMACS and continue production runs.

    AMBER inputs are provided for minimization (step6.0), equilibration (step6.1 through step6.6) and production
    • amber/step6.0_minimization.mdin: use generated coordinates of a micelle/protein complex (or micelle only system) to perform minimization.
    • amber/step6.[1-6]_equilibration.mdin: use minimized coordinates from AMBER to perform equilibration.
    • amber/step7_production.mdin: use equilibrated coordinates from AMBER and continue production runs.

    GENESIS inputs are provided for minimization (step6.0), equilibration (step6.1 through step6.6) and production
    • genesis/step6.0_minimization.inp: use generated coordinates of a micelle/protein complex (or micelle only system) to perform minimization.
    • genesis/step6.[1-6]_equilibration.inp: use minimized coordinates from GENESIS to perform equilibration.
    • genesis/step7_production.inp: use equilibrated coordinates from GENESIS and continue production runs.

    OpenMM inputs and running scripts are provided for equilibration (step6.1 through step6.6) and production
    • openmm/openmm_run.py: OpenMM running scripts written in python.
    • openmm/step6.[1-6]_equilibration.inp: use generated coordinates of a micelle/protein complex (or micelle only system) to perform equilibration.
    • openmm/step7_production.inp: use the restart file from OpenMM and continue production runs.

    CHARMM/OpenMM inputs are provided for equilibration (step6.1 through step6.6) and production
    • charmm_openmm/step6.[1-6]_equilibration.inp: use generated coordinates of a micelle/protein complex (or micelle only system) to perform equilibration.
    • charmm_openmm/step7_production.inp: use the restart file from CHARMM/OpenMM and continue production runs.