VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 22 2007 - 21:06:20 CDT

Marcela,
  One of my colleagues here that works with NMR data had a suggestion
for you below.
  
  John Stone
  vmd_at_ks.uiuc.edu

> From: "Eric H. Lee" <ericlee_at_ks.uiuc.edu>
> Subject: Re: [mmadrid_at_psc.edu: vmd-l: visualizing NMR constrains]
>
> If the constraints were applied from a separate file as input to
> NAMD, then there is no automatic way. Its not impossible though. My
> suggestion would be to create a saved state where you manually draw
> the constraints into VMD by picking bonds or angles, and then load
> your trajectory into the psf with the initial pdb already loaded as
> the first frame (this would keep the lines you've drawn) - then as
> you animate through your trajectory, you can turn on and off the
> drawings for the bonds or angles you've restrained, in order to see
> how they are changing. The point of making the 1 frame savestate is
> that you can load the trajectory (or a longer version of it) anytime
> you want in the future without having to redo all the labeling and
> picking.
>
> -Eric
>

On Thu, Mar 22, 2007 at 06:14:37PM -0400, Marcela Madrid wrote:
> hi
> we just finished some restrained MD with NMR constrains, and were
> wondering whether there is
> a way to visualize NMR constrains? I am thinking for example loading the
> structures and the constrains, and seeing the constrains as hydrogen
> bonds between atoms?
>
> thanks, Marcela 

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