VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 25 2006 - 10:23:36 CST
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Hi,
What file format is your CHARMM trajectory written in?
Is it being loaded by VMD as a DCD file, or some other format (COOR?)?
If it is a DCD file, the next question is what platform you're
running VMD on? The specific error message you mention below
doesn't sound like anything in the DCD reader, thus my initial
question about which file format your trajectory was written in.
If the trajectory is written as a COOR file (read in VMD by corplugin),
then the problem could be one of several things. I just fixed a couple
of bugs in corplugin, specifically affecting the extended COOR format
for structures with more than 99,999 atoms. It could be that you've
just run into one of the problems I recently fixed. The next test version
I post on the web site will include the new corplugin, and may fix your
problem if it's an issue with file formatting. If your problem is due
to the file size, then the solution will depend on which platform you're
running VMD on.
John Stone
vmd_at_ks.uiuc.edu
On Wed, Jan 25, 2006 at 04:21:53AM -0800, Vineet Pande wrote:
> Hi,
> I am trying to load a CHARMM trajectory (after merging
> smaller chunks and recentering solvent), but VMD
> (version 1.8.4b6) gives an error message saying- Error
> opening file: improperly formatted line. The number of
> atoms in my system are 107295 and the size of the PBC
> trajectory is around 2GB. When I load similar file
> without solvent and PBCs, it works fine. Does it have
> anthing to do with size limits?
>
> Thanks in advance,
> Vineet Pande
> Karolinska Institute, Stockholm
>
>
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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
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