准备hole.inp 文件
! example input file run on Arseniev's gramicidin structure
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! 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
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
sos_triangle -s < solid_surface.sos > solid_surface.vmd_plot
sph_process -sos -dotden 15 -color hole_out.sph solid_surface.sos