VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Oct 26 2012 - 10:34:23 CDT

Hi,
  You should be able to use VMD atom selections to write out frames
as NAMD binary restart files. Here's an example:
  set sel [atomselect top all]
  $sel writenamdbin molecule.coor

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Oct 24, 2012 at 03:13:37PM -0400, Jose Borreguero wrote:
> Dear VMD users,
>
> I want to extract and save one particular frame from a DCD trajectory, and
> pass it to NAMD as the .coor file (binary coordinate restart file). I
> don't know what is the format of the .coor file so I don't know which
> format should I choose when extracting and saving the frame with VMD.
>
> The frames of my dcd trajectory also contain the unit cell dimension info.
> Will this info be preserved when I extract the frame? I want to use this
> instead of having to generate an .xsc file by looking in the .xst file.
>
> Finally, What is the TCL command like? Is it something like 'write coor
> init.coor beg $frame end $frame'? Sorry for this silly question but I'm a
> newbie.
>
> Any help is immensely appreciated!
> Jose M. Borreguero 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
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