[gmx-users] Re: make_ndx

[Nuno R. L. Ferreira]

If I understood well your question, you want to select atoms around a {x y z}.
Under VMD, play with the commands:

within, same and exwithin.

An example: 

set number_frames [molinfo top get numframes]
set selection [atomselect top "exwithin 3 of protein"]
for {set i 0} {$i < $number_frames} {incr i} {
   $selection frame i
   $selection update
  set frame_index($i) [$selection get index]
}

This will give the index of the atoms around 3 angst. from protein, excluding protein atoms, for each frame in the loaded traj., and will save index values of those select atoms to the array frame_index(). 

Though vmd-list is more suitable to answer this question, just to show you that vmd is really very flexible ;-)

Regards
N.
  ----- Original Message ----- 
  From: VISWANADHA SRIDHARA 
  To: Discussion list for GROMACS users 
  Sent: Saturday, July 02, 2005 1:29 AM
  Subject: Re: [gmx-users] Re: make_ndx


  Hi Tsjerk,

  Thanks for the advice. Actually I knew how to do using VMD, but I need to get the index file on a fly( say a trajectory), so its kind of difficult to get index no.s out in a fly using VMD too. Anyways I will try to use Pymol too.

  Thanks. 

  "T.A.Wassenaar" <T.A.Wassenaar at rug.nl>
  Sent by: gmx-users-bounces at gromacs.org
  07/01/2005 09:29 PM ZE2Please respond toDiscussion list for GROMACS users 

  To   Discussion list for GROMACS users <gmx-users at gromacs.org>
  cc   
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  Subject   Re: [gmx-users] Re: make_ndx
   



  Hi Sri,

  It is not possible to do this in gromacs. Pymol can make
  such selections, but then you need a script to write an
  index file from a Pymol selection. If you know a bit of
  python that shouldn't be too hard.

  Hope it helps,

  Tsjerk

  On Fri, 1 Jul 2005 09:33:36 -0400
  VISWANADHA SRIDHARA <vsrid001 at odu.edu> wrote:
  > Hi GMX users,
  >
  > I was wondering whether there is any option in make_ndx
  >to get the index of
  > the atoms(or molecules) as a function of the box
  >vectors.
  > In other words, can I get the index of the molecules
  >separately which are
  > 1nm spherical radius in a 3nm cube as an example.(say
  >cube's center is the
  > sphere's center too).
  >
  > Thanks in advance,
  > Sri
  >
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