- http://www.charmm-gui.org
- Input Generator
- Membrane Builder
- Bilayer Builder
- Protein/Membrane system
- Download 4QTN from OPM database
- Select Chain A, B, and C, with residue ID 2-236. #Also add NNR if to make PnuC_3NR system.
- Use the PDB orientation.
- If NNR cannot be recognized by the system, that means atom numbering system is not the same as PDB record. You may need to download NNR from RCSB PDB and insert/replace the one in your own model.
- http://www.charmm-gui.org/?doc=input/membrane.bilayer&jobid=7604300295&project=membrane_bilayer
- http://www.charmm-gui.org/?doc=input/membrane.bilayer&jobid=7609535893&project=membrane_bilayer
#Calculate Cross-Sectional Area
#System Size Determination Options:
- Heterogeneous Lipid
- 1. Box Type: Rectangular
- 2. Length of Z based on: Water thickness (Minimum water height on top and bottom of the system)
- 3. Length of XY based on: Ratios of lipid components, POPE:POPG = 3:1
- Further optimize by check Numbers of lipid components, and change numbers of lipids to eliminate any errors
- POPE: 143 139 Upperleaflet Lowerleaflet
- POPG: 48 46 Upperleaflet Lowerleaflet
#Results:
- Box Type Rectangle
- Crystal Type TETRAGONAL
- System Size
A 120.581738 Dimension along the A (X) axis B 120.581738 Dimension along the B (Y) axis C 104.427824 Dimension along the C (Z) axis
-Crystal Angle
Alpha 90.0 Angle between the axis B and C Beta 90.0 Angle between the axis A and C Gamma 90.0 Angle between the axis A and B
#of Lipids
on Top 191 on Bottom 185 Z Center -2.77291175 Center of the system along the Z axis
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System Building Options:
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Replacement method Build system using replacement method Check lipid ring (and protein surface) penetration
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Component Building Options:
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Include Ions : 0.15 M NaCl (ion concentration)
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Ion Placing Method: Monte-Carlo