VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 16 2006 - 14:17:03 CST
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Lily,
If you loaded the DCD by itself (i.e. no PSF, or PDB file), then
this is exactly the behavior one would expect, since DCD files only
contain atom coordinates and no other information, not enough to draw
a proper molecular structure in any case.. You'll need to additionally
load in a PDB, PSF, or some other structure file in order to see your
trajectory properly in VMD.
John Stone
vmd_at_ks.uiuc.edu
On Thu, Feb 16, 2006 at 12:05:24PM -0800, lily jin wrote:
> No, I didn't get any error message there. It says:
>
> info> Using plugin dcd for coordinates from file...
> info> Finished with coordinate file...
>
> Also I can see the file information in the VMD Main window, but nothing in the OpenGL window.
>
> John Stone <johns_at_ks.uiuc.edu> wrote:
> Hi,
> Did you get any error messages in the VMD text console when loading
> the DCD file on Windows?
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Feb 16, 2006 at 11:24:16AM -0800, lily jin wrote:
> > I generated a new dcd file from the original one by using catdcd.LINUX on the Cluster. However, while I transfer it to my pc, and I tried to open it by VMD, I could see nothing on the VMD screen even there is not any error information. I don't have experiences on NAMD, can you tell me if this is caused by the original dcd file or anything else? Thank you very much!
> >
> >
> > Lily
> >
> > ---------------------------------
> > Yahoo! Mail
> > Use Photomail to share photos without annoying attachments.
> --
> 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
>
>
>
> Lily
>
> ---------------------------------
>
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-- 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
- Next message: Ana Celia Araujo Vila Verde: "RE: problem with script to get RMSD"
- Previous message: John Stone: "Re: How can i use the catdcd plugin with the VMD windows version?"
- Maybe in reply to: John Stone: "Re: catdcd.LINUX"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]