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asymmetric_bilayer
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| asymmetric_bilayer [2022/08/24 09:50] – [Step 1: generate monolayers] edit | asymmetric_bilayer [2026/03/04 00:09] (current) – [Package and operation] edit | ||
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| Contact email: mkhsieh1027@gmail.com \\ | Contact email: mkhsieh1027@gmail.com \\ | ||
| - | (The package was constructed based on bacterial inner membrane models with phospholipids; the system with steroid | + | **Update |
| + | The update (asym_memb_builder_v5.tgz) reflects the corresponding modification of ion residue names in IONS, replacing the POT and CAL resnames. In Step 6, phosphorus atoms are constrained in step5_input.ref following CHARMM minimization. Using the helper file (./ | ||
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| + | **Update (08.24.2022): | ||
| + | The package | ||
| + | The packages may not be able to apply to system with glycolipids. | ||
| + | The system with proteins should use a limited version asym_memb_builder_v4_prot | ||
| + | Please provide comments and feedbacks to improve this package. Thanks.\\ | ||
| + | In step5.2, one should be able to create input for several MD simulation packages by Force Field Converter at CHARMM-GUI page (https:// | ||
| + | where takes the step5_assembly.psf and step5_assembly.crd file generated from step5.1 with step5_assembly.str information. | ||
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| The **asym_memb_builder** is used to generate an asymmetric lipid bilayer from two symmetric bilayers by manipulating the smaller monolayer to match the size of the larger monolayer if the size if very different (more than 5%). The package is adapted from the scripts of CHRAMM Membrane Builder, having 5 sequential steps to build a simulation box of asymmetric membrane with explicit water and ions. Briefly, after checking the input symmetric bilayer information (Step1.0) and isolating lipid, water, and ion of each leaflet (Step1.1), the script provides the potential enlarged monolayers (Step1.2) for user’s selection and recreate a half simulation box with lateral waters and ions from original molecular structure in the input symmetric membrane system (Step1.3). The asymmetric bilayer is generated at Step2 using the original input molecular structures. The simulation box size is checked at Step3 and the concentration of KCl could be modified by editing step3_size.str if user would like to update it. The asymmetric bilayer will be rechecked and isolated by individual segment (lipid, water, and ion) at Step4.1; the water box is directly adapted from the original input without change (inactive the Step4.2); and the number of ions for neutralizing system or matching the updated KCl concentration is processed at Step4.3. Then, all the updated segments (lipid, water, and ion) are assembled at Step5.1, and the input files of the asymmetric bilayer is prepared for NAMD at Step5.2. As usual CHARMM-GUI practice, the simulation is followed by step6 equilibrium and step7 production runs. \\ | The **asym_memb_builder** is used to generate an asymmetric lipid bilayer from two symmetric bilayers by manipulating the smaller monolayer to match the size of the larger monolayer if the size if very different (more than 5%). The package is adapted from the scripts of CHRAMM Membrane Builder, having 5 sequential steps to build a simulation box of asymmetric membrane with explicit water and ions. Briefly, after checking the input symmetric bilayer information (Step1.0) and isolating lipid, water, and ion of each leaflet (Step1.1), the script provides the potential enlarged monolayers (Step1.2) for user’s selection and recreate a half simulation box with lateral waters and ions from original molecular structure in the input symmetric membrane system (Step1.3). The asymmetric bilayer is generated at Step2 using the original input molecular structures. The simulation box size is checked at Step3 and the concentration of KCl could be modified by editing step3_size.str if user would like to update it. The asymmetric bilayer will be rechecked and isolated by individual segment (lipid, water, and ion) at Step4.1; the water box is directly adapted from the original input without change (inactive the Step4.2); and the number of ions for neutralizing system or matching the updated KCl concentration is processed at Step4.3. Then, all the updated segments (lipid, water, and ion) are assembled at Step5.1, and the input files of the asymmetric bilayer is prepared for NAMD at Step5.2. As usual CHARMM-GUI practice, the simulation is followed by step6 equilibrium and step7 production runs. \\ | ||
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| ====== Package and operation ====== | ====== Package and operation ====== | ||
| For DT2, the package at / | For DT2, the package at / | ||
| - | or download the package through the link {{ : | + | / |
| + | / | ||
| + | or download the package through the link {{ : | ||
| Authors: Min-Kang Hsieh and Jeffery B. Klauda \\ | Authors: Min-Kang Hsieh and Jeffery B. Klauda \\ | ||
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| Output files: | Output files: | ||
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| - | In step 1.2, the small monolayer would be enlarged with a random centering point to equal the size of the other leaflet by adding lipids. First, the program checks the size of two imported monolayers. If more than a 5 % difference in the size (X length), the program executes the adding lipids process to the small monolayer. The operation of adding lipids is that (1) randomly selects the center point of the small monolayer and clones it to a n x n repeating cell in the x-y plane; (2) the surface is cut in the desired size (equals to the x length of the large monolayer); (3) the lipids outside the cutting area are deleted to form a new monolayer. In the current version, users could decide how many monolayers they would like to generate for selection by changing the parameter Bulidmax in max_options.str (default is 5 for both top and bottom leaflets of the small bilayer). A list of options for new generated monolayer is stored in step1.2_adding_lipid_info.txt, | + | In step 1.2, the small monolayer would be enlarged with a random centering point to equal the size of the other leaflet by adding lipids. First, the program checks the size of two imported monolayers. If more than a 5 % difference in the size (X length), the program executes the adding lipids process to the small monolayer. The operation of adding lipids is that (1) randomly selects the center point of the small monolayer and clones it to a n x n repeating cell in the x-y plane; (2) the surface is cut in the desired size (equals to the x length of the large monolayer); (3) the lipids outside the cutting area (v4: the phosphate of lipids; v5: the COM of lipids as referring for each lipid) |
| {{: | {{: | ||
| where xi is the mole fraction of the lipid i in the new and original monolayer. The score is the reverse of a sum of absolute relative deviation of the fraction, that is, the higher of the value, the higher similarity in the new and original monolayer in the lipid composition. \\ | where xi is the mole fraction of the lipid i in the new and original monolayer. The score is the reverse of a sum of absolute relative deviation of the fraction, that is, the higher of the value, the higher similarity in the new and original monolayer in the lipid composition. \\ | ||
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| 2. **step2_gen_bilayer.str**: | 2. **step2_gen_bilayer.str**: | ||
| \\ | \\ | ||
| - | In step 2, the two monolayers listing in the input file (**step2_opt_a.str** or **step2_opt_b.str**) are combined to form a bilayer. If there is no adding | + | In step 2, the two monolayers listing in the input file (**step2_opt_a.str** or **step2_opt_b.str**) are combined to form a bilayer. If adding |
| \\ | \\ | ||
| ==== Step 3: | ==== Step 3: | ||
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| **Step5.2: Generate NAMD input** \\ | **Step5.2: Generate NAMD input** \\ | ||
| + | **Update: | ||
| + | One should be able to create input for several MD simulation packages by **Force Field Converter** at CHARMM-GUI page (https:// | ||
| + | where takes the step5_assembly.psf and step5_assembly.crd file generated from step5.1 with step5_assembly.str information. | ||
| + | |||
| CHARMM configuration file: **step5.2_input.inp** \\ | CHARMM configuration file: **step5.2_input.inp** \\ | ||
| Output files: ./namd directory \\ | Output files: ./namd directory \\ | ||
asymmetric_bilayer.1661349033.txt.gz · Last modified: 2022/08/24 09:50 by edit