VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Nov 21 2006 - 13:22:11 CST

Jennie,
  Hmm, can you show me the exact commands you're using when you
write the CRD? It worked for me when I did this simple test:
mol new 1e79
molinfo top get { a b c }
 (output is "267.200012 107.199997 135.899994")

# write the CRD file with box info
set sel [atomselect top all]
$sel writecrdbox foo.crd

# last line of the CRD is the box size (for 1e79):
tail -1 foo.crd
  (output is " 267.200 107.200 135.900")

Let me know if this helps clarify things.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Nov 21, 2006 at 11:13:46AM -0800, Jennie Thomas wrote:
> Hello John,
>
> Thanks for your help with this. I'm using VMD for MACOSXX86, version
> 1.8.5 (August 25, 2006). I would be happy to send you an example
> script and also the trajectory I'm using if you would like to do a test.
>
> When I load the dcd trajectory in vmd, I can get the box information
> at every timestep by simply changing the frame and using:
>
> atomselect top get a
> atomselect top get b
> atomselect top get c
>
> So, there is no doubt that vmd has the box information at every
> timestep loaded correctly. However, the box information is missing
> when I write the .crd file. Instead of getting the actual box
> information I get 0.0 0.0 0.0 in place of the box dimensions. This
> is a cubic box, so I don't need alpha, beta, and gamma.
>
> Thanks!
> Jennie
>
>
>
>
> On Nov 21, 2006, at 9:21 AM, John Stone wrote:
>
> >Hi,
> > I just checked the current versions of VMD and the AMBER CRD plugin,
> >and they already support writing of box information. The CRD format
> >only stores the a/b/c side lengths however, and not the alpha/beta/
> >gamma
> >angles, so the conversion from DCD to CRD will lose that information.
> >Which version of VMD were you using for your tests?
> >
> >Thanks,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Mon, Nov 20, 2006 at 10:46:26PM -0600, John Stone wrote:
> >>
> >>Jennie,
> >> I'll have to take a look at the AMBER CRD plugin tomorrow and
> >>see if the
> >>problem is simply that it doesn't include code to write the box
> >>information. If so, it may be a simple matter to add and send you a
> >>new version of the AMBER CRD plugin to try out.
> >>
> >> John Stone
> >> vmd_at_ks.uiuc.edu
> >>
> >>On Mon, Nov 20, 2006 at 08:09:12PM -0800, Jennie Thomas wrote:
> >>>Hi VMD experts,
> >>>
> >>>I have an analysis code (separate from VMD) that reads in AMBER
> >>>coordinate files. Someone has asked if I can use this code to
> >>>analyze a dcd trajectory, so I decided to try and use vmd to convert
> >>>from dcd to crdbox format. However, the box information is not
> >>>preserved when doing this. Because this is a constant pressure
> >>>simulation I need to use the box information at every step. Do you
> >>>know how to force vmd to write box information?
> >>>
> >>>I have a simple tcl script I am using:
> >>>
> >>># Load the system and the trajectory
> >>>mol new "box.cor" type cor
> >>>
> >>>mol addfile "00.trj" type dcd waitfor all
> >>>mol addfile "01.trj" type dcd waitfor all
> >>>
> >>>animate write crdbox traj.crd
> >>>
> >>>Do I need to be doing something more complicated to get box
> >>>information? Or does anyone have another suggestion for a file
> >>>format conversion tool?
> >>>
> >>>Thanks,
> >>>Jennie Thomas
> >>
> >>--
> >>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
> >
> >--
> >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
> > 

-- 
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