VMD-L Mailing List

From: Hyundeok Song (songhk_at_email.uc.edu)
Date: Tue Jun 02 2009 - 08:49:20 CDT

Dear VMD users

I have a question about the result from VMD HOLE script.

I calculated the coordinate vs channel radius of Gramicidin by two methods (HOLE program and VMD-HOLE script)
But two results are not same. ( very different )

I prefer to use VMD HOLE script than HOLE program because I need it through many time frames.

If someone has already done this by VMD HOLE script, could you explain this? Do I miss something?
Any comments and suggestions are welcome.
Thanks.

hyun.

1) by HOLE program (used example file of HOLE)
input: 01_1grm_single.pdb,01_example.inp,
$ hole2 < 01_example.inp > 01_example.log

output: 01_example.log, example.qpt, example.sph
And then plot from 01_example.log

2) by VMD - HOLE script
input: hole.tcl, run_hole.vmd
$ vmd -dispdev text -e run_hole.vmd > run_hole.log

output: run_hole.log, tmpholeinputfiles.pdb
And then plot from run_hole.log

--- run_hole.vmd ---
source hole.tcl
mol load pdb 01_1grm_single.pdb
set sel [atomselect top all]
Hole::runhole $sel

exit
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