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本帖最后由 ene 于 2019-6-9 16:21 编辑
genmem,genmixmem是sob老师开发的用于产生磷脂双分子层的程序。
原网址在这里:
genmem:http://sobereva.com/222;genmixmem:http://sobereva.com/245
这里上传了静态编译的genmem,genmixmem的64位linux版本,可直接运行。
genmixmem.Linux-x86_64-static.zip
(675.22 KB, 下载次数 Times of downloads: 26)
genmem.Linux-x86_64-static.zip
(660.5 KB, 下载次数 Times of downloads: 7)
需要注意的是linux版本与windows的输入文件不可混用,在linux下,genmixmem的input文件中的磷脂文件名需要双引号。示例如下
- mixmem.pdb ;The path of output file
- 5 ;The number of lipid types
- 64 ;The number of lipids in each layer, should be square of an integer
- 64 ;Box length (Angstrom)
- 0 ;0=Don't randomly rotate molecule, 1=randomly rotate molecule, -1/-2/-3=rotate 45/90/180 degree in the second layer
- 80.5,39.5 ;The Z position of the reference atom in layer 1 and layer 2
- #
- # Below is pdb file of each lipid type, its number in each layer and the index of reference atom
- #
- "pdbinput/DGDG343z.pdb",20,27
- "pdbinput/LysoPGz.pdb",10,5
- "pdbinput/MGDG366z.pdb",14,26
- "pdbinput/PA342z.pdb",15,21
- "pdbinput/PC364z.pdb",5,24
- NOTE: The geometry of the lipid provided in your pdb file should be aligned to Z axis, and the head group should be toward to the positive direction of Z axis. The lipid will be evenly placed in the box.
- Hint: Commonly a lipid occupies 65 Angstrom^2, you can correspondingly estimate box length.
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