Notes for PACE CG Bilayer Builder:
- Due to some implementation details of the force field, energy can only be calculated in NAMD currently. Input files can be found in "namd" directory when you download tar archive ("charmm-gui.tgz") after all the input file are generated.
- For lipid-only system, NAMD 2.10 or nightly build version is required to calculate the MARTINI Lennard-Jones switching energy correctly (NAMD 2.9 has a bug in the switching energy). The nightly build NAMD can be downloaded here.
- For protein-lipid system, a modified NAMD must be used. Please download the program here and compile it first.
- Rectangular geometries is supported for a system shape.
- The protein must be oriented with respect to a membrane bilayer whose normal is parallel to the Z-axis and whose center is located at Z=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.
- 15 lipids from the MARTINI force field are supported now: DLPC, DLPE, DPPC, DPPE, DSPC, DSPE, POPC, POPE, POPG, POPS, DOPC, DOPE, DOPG, DOPS, and DAPC
- 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.
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
Y. Qi, X. Cheng, W. Han, S. Jo, K. Schulten, and W. Im (2014)
CHARMM-GUI PACE CG Builder for Solution, Micelle, and Bilayer Coarse-Grained Simulations. J. Chem. Inf. Model. 54:1003–1009
W. Han and K. Schulten (2012)
Further Optimization of a Hybrid United-Atom and Coarse-Grained Force Field for Folding Simulations: Improved Backbone Hydration and Interactions between Charged Side Chains. J. Chem. Theory Comput. 8(11):4413–4424
C.K. Wan, W. Han, Y.D. Wu (2011)
Parameterization of PACE force field for membrane environment and simulation of helical peptides and helix–helix association. J. Chem. Theory Comput. 8(1):300-313
A brief explanation of each step:
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 from RCSB, it is necessary to properly orient the protein with respect to membranes. There are two options for doing this. It is the step in which the cross-section area of the protein along the Z-axis is calculated and displayed. The maximum top (10<Z<20) and bottom (-20<Z<-10) areas are used to determine the system size in XY.
- STEP3: Determine the system size
To determine the system size in XY, there are three options, in the case of homogeneous bilayer generation, based on (1) number of lipid layers around the protein, (2) specific number of lipid molecules in top and bottom, and (3) specific size of the system along X and Y. The system size along Z is determined by the water extent from the top and bottom of the protein. For now, six types of lipids (DMPC, DPPC, DOPC, POPC, DLPE, and POPE) and two types of system shapes in XY (rectangular and hexagonal) are available.
In the case of heterogeneous bilayer generation, there are two options to determine the system size: (1) ratio of lipid types to be used and initial (guess) size of the system along X and Y (2) specific number of lipid molecules and ratio of system size along X and Y The system size along Z is determined by the water extent from the top and bottom of the protein. If desired, hydration number (number of water molecules per one lipid molecule) can be used for this purpose.
- STEP4: Build the components
Based on the system size determined in the previous step, this step builds individual pieces such as (1) the lipid bilayer 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, lipid bilayer, additional 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. However, the user can find equilibrated coordinates for some membrnae proteins from the archive.
NAMD inputs are provided for equilibration (step6.1 through step6.6) and production
- namd/step6.[1-6]_equilibration.inp: use generated coordinates of a membrane/protein complex (or membrane 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 teh restart file from NAMD and continue production runs.
- STEP2: Orient the protein