VMD-L Mailing List

From: Vineet Pande (pande_vineet_at_yahoo.com)
Date: Thu Jan 26 2006 - 01:33:19 CST

Thanks John-
I am running on Windows XP, trajectory is a merged and
recentered CHARMM output with 2000 frames which i
think is making the problem; because when I load the
same trajectory but with less frames (i.e. around 20
frames by jumping more picoseconds of trajectory per
frame), it works fine. So its either the "file size
problem" or as you mention the "platform problem". Do
we expect to load very many frames with solvent for a
large system like mine in any other platform like
Linux etc.? I am dealing with a system of total 107295
ATOMS and the trajectory is a .cor (binary) CHARMM
file, which is read correctly as a "CHARMM; NAMD;
XPLOR, DCD" type in VMD.

Regards..
Vineet Pande
Karolinska Institute, Stockholm

--- John Stone <johns_at_ks.uiuc.edu> wrote:

>
> 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:
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>

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