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4.0 Tips on using HOLE, Sample input file

4.1 Tips on using HOLE

• You need to produce a Brookhaven protein databank (.pdb) format file containing the coordinates of the ion channel you are interested in.
• Normally it is a good idea to remove from consideration any ions or water molecules which are present in the centre of channel of interest. This can easily be achieved by using a IGNORE card followed by the relevant residue types in the input file.
• You must identify a point which lies within the pore of interest (for CPOINT card)
• lot more to be added***!

4.2 Sample input file

! This is an example of how to run hole
! example input file run on Arseniev's gramicidin structure
! note everything preceeded by a "!" is a comment and will be ignored by HOLE
!
! This example run by line:
! hole < example.inp > example.out &
!
! first cards which must be quoted 
! note that HOLE is case insensitive (except file names)
coord 1grm_single.pdb           ! Co-ordinates in pdb format
radius ~/hole2/rad/simple.rad	! Use simple AMBER vdw radii
				! n.b. can use ~ in hole
cvect  0 1 0                    ! channel runs approx up Y axis
cpoint 0 0 3 		 	! a point in pore
!
! now optional cards
sample 0.25                     ! distance between planes
pltout example.qpt              ! quanta plot file output
sphpdb example.sph              ! pdb format output of hole sphere centre 
				! (for use in sphqpt program)
endrad 5.			! to avoid having enormous ends

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