VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jun 17 2005 - 17:39:48 CDT

Hi,
  Did you make sure to load the prmtop and mdcrd files into the same
molecule, or did they get loaded into separate molecules? What platform
are you running VMD on?

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jun 17, 2005 at 01:30:29PM +0200, Claire Zerafa wrote:
> Dear all,
>
> I am trying to load some trajectories from amber8 into vmd. I was trying to
> first load a .prmtop file, and then a .mdcrd file.
>
> So when i loaded the .prmtop file (parm7) under the section for Atoms I
> could see 25201, which is the total number of atoms in the .prmtop file.
> Under the sections for frames and Vol, the integer 0 was listed.
>
> Then i tried to load .mdcrd files which i produced during a dynamics run
> from amber 8. I loaded these as crdbox, because they were produced during a
> solvated dynamic run.
>
> When the mdcrd files loaded there was a 0 integer listed beneath Atoms,
> Frames, and Vol, and an accomanpying message came up in the console which
> said:
>
> "some frames from file X could not be loaded because the number of atoms
> could not be determined. Load a structure file first, then try loading this
> file again.
>
> Then I started again an read in a .pdb file first. This read correctly, but
> then I still had the same results with the .prmtop and .mdcrd files.
>
> I am working on an Octane SGI.
>
> Thanks
>
> claire 

-- 
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