基本步骤：
- 用vmd的扩展工具新建膜（支持POPC/POPE），设置大小，然后输入膜的名称（membrane）。
- 把蛋白质文件（PDB）拉到vmd中，用vmd的psfgen工具生成protein.psf文件。我用的是VMD里面扩展工具自动生成。
- 把生成后的蛋白质和膜组合，移动到合适的位置。
- 保存膜coordinate和蛋白质的coordinate分别选择全部原子，分别命名为membrane.pdb 和protein_aligned.pdb。
- 退出vmd
- 在终端执行命令：vmd -dispdev text < combine.tcl | tee combine.log
- 然后会自动将蛋白质和膜组合，生成protein_mem.pdb 和protein_mem.psf
- 可以进行其他模拟了，比如能量最小化、粗粒化等。
- 注意：需要下载拓扑文件。
- 在vmd下完整命令是： membrane -l POPC -x 46.7 -y 46.7 -o membrane1 -top c27
- 以下是官方说明：
Plugin usage. The command syntax is simple and consistent with the solvate plugin syntax. Run the following commands in the VMD console:
package require membrane
Running membrane with no arguments gives a short overview of the syntax. For actual generating a membrane, run membrane as follows:
membrane -l <lipid_name> -x <size_in_X> -y <size_in_Y> {-o <output_prefix>}
Replace the contents of the angular brackets with the corresponding parameters:
- lipid_name can only be POPC or POPE at the moment. Other lipid structures will be generated too.
- size_in_X and size_in_Y are the required membrane dimensions in A. (The membrane is built in the XY plane).
-
output_prefix is an optional parameter, which is simple the output file name. By default, the generated files are named membrane.psf and membrane.pdb.
Embedding proteins in membrane. First, you need a coordinate file (protein.pdb) and a structure file (protein.psf) for the protein. The PSF file can be easily generated using the psfgen plugin. Load the both protein and membrane into VMD and align the protein to the proper position and orientation in the membrane. Aligning can be easily done using the VMD GUI front end (hit "9" key to switch VMD in the "move molecule" mode, see more details in the VMD manual) or the console (using commands "move", "moveby", "moveto"). Make sure to use all available experimental data to align the protein in the most accurate way possible. Then, save the protein coordinates in another PDB file (protein_aligned.pdb). The last step is merging the protein and the membrane and removing lipids that overlap with the protein groups. The Tcl script combine.tcl does that for you:
vmd -dispdev text < combine.tcl | tee combine.log
The protein-membrane complex coordinate and structure files are "protein-mem.psf/pdb". Note that the script requires the topology file top_all27_prot_lipid.inp (or a symbolic link to it) to be present in the working directory.
将几段肽插入膜怎么做呢？用vmd的extensions-modeling-merge structures可以了。
- 首先分别建立对于的psf文件
- 调整好彼此在膜中的位置
- 将他们两两合并，注意，每次都做一次psf
- 最终和上面单个植入膜中一样
- 进行动力学模拟,charmm-gui 选择CHARMM类型的蛋白质