VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 12 2011 - 13:08:13 CDT

Hi,
  Based on my reading of the HOLE page, you may need to write the intended
input for qpt_conv to a file first, and then run qpt_conf with input redirected
from the file. I think that you may want to do it that way so you can
get the proper carriage return characters into the input stream for qpt_conv.
Without the carriage returns, I don't know what it would do. I just read
the man page here and haven't tried it personally:
  http://d2o.bioch.ox.ac.uk:38080/doc/hole_d04.html

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jul 07, 2011 at 12:21:00PM +0200, maria goranovic wrote:
> Sorry for spamming, but this is what i am trying to do to automate
> qpt_conv:
> echo D temp.qpt temp.vmd_plot 1 | qpt_conv
> Although qpt_conv takes in the first argument (D), it does not take the
> rest and exits. I have no idea what I am doing wrong. In its interactive
> form, qpt_conv does need the user to press a return key after each entry,
>
> any suggestions?
> On Tue, Jul 5, 2011 at 5:05 PM, maria goranovic <mariagoranovic_at_gmail.com>
> wrote:
>
> I am trying to use Hole to find and display cavities in a protein. Hole
> uses the executable qpt_conv to convert sph output to a format readable
> by vmd. However, qpt_conv seems to be interactive. It requires entering
> "D" and a few return strokes to produce the vmd_plot file format. How
> can one get around this without recompiling the hole code?
> Additionally, how does one display an entire trajectory alongwith a
> series of hole-produced vmd_plot files which hold the dotted
> representation of the cavity? I am hoping some one has done this before,
> and will be kind enough to share the experience?
> Thank you in advance,
> -Maria-
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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