Embedded Files
Charmm-gui is a web-based graphical user interface for CHARMM which is used for biomolecular modeling and simulation.
Charmm-gui is a web-based graphical user interface for CHARMM which is used for biomolecular modeling and simulation.
Go charmm-gui webpage, click "Input Generator", select “Membrane Builder -> Bilayer Builder” on the side bar of the web page.
Upload the best model pdb file generated by Modeller and select PDB format . Click “Next Step”.
Check PDB info including the sequence information. Click “Next Step”.
Don't include the missing residues.
Step0: We do not mute the PDB file, click “Next Step”.
Step1: We use PDB orientation. Click “Next Step”.
Step2: Might take a little bit of time
Length of X and Y: 150 (depends on protein, cftr open-state model: 150, 3eml model: 100)
PC(phosphatidylcholine) Lipids: POPC 100 100 68.3
Click system info and record it.
Step3:
Include Ions, 0.15 M NaCL
Step4: Click "Next Step".
Step5: We use Gromacs and Desmond.
Visually check the step5_assembly.pdb.
Input generation: GRAOMCS, Desmond,
Temperature: 310 K
Click “Next Step”.
Step6: Click "Next Step".
Download tar ball file at the top right corner of the web page, and rename it as proteinCharmm-gui.tgz (for example, 3emlCharmm-gui.tgz).
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