HOLE 快速执行 （生物）

原文在这：
http://www.holeprogram.org/doc/
准备hole.inp 文件
需要将 coord B-water.pdb
改为 coord 你的.pdb

! example input file run on Arseniev's gramicidin structure

点击查看代码

! example input file run on Arseniev's gramicidin structure
! note everything preceded by a "!" is a comment and will be ignored by HOLE
!
! follow instructions in doc/index.html to run this job
!
! first cards which must be  included for HOLE to work
! note that HOLE input is case insensitive (except file names)
coord B-water.pdb           ! Co-ordinates in pdb format
radius /home/ubuntu/hole/rad/simple.rad   ! Use simple AMBER vdw radii
                                ! n.b. can use ~ in hole
!
! now optional cards
sphpdb hole_out.sph             ! pdb format output of hole sphere centre info
                                ! (for use in sph_process program)
endrad 5.                       ! This is the pore radius that is taken
                                ! as where channel ends. 5.0 Angstroms is good
                                ! for a narrow channel

一路执行以下命令

hole < hole.inp > hole_out.txt
egrep "mid-|sampled" hole_out.txt > hole_out.tsv
sph_process -dotden 15 -color hole_out.sph dotsurface.qpt
qpt_conv

输入 D 然后一直回车
sph_process -sos -dotden 15 -color hole_out.sph solid_surface.sos
sos_triangle -s < solid_surface.sos > solid_surface.vmd_plot

最后会有这些文件