VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 02 2009 - 09:53:26 CDT

Hi,
  Read the top of the hole.tcl script, it contains various comments
about the parameters that the user must customize for their run.
Most likely, you're doing something different when you run HOLE by
hand than when you run it via the hole.tcl script. You'll want to
make sure that you're getting the same parameters in both cases before
you do your trajectory analysis.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jun 02, 2009 at 09:49:20AM -0400, Hyundeok Song wrote:
> 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
> --------------------- 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078