VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Nov 21 2006 - 11:21:20 CST

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