VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Nov 29 2006 - 15:04:27 CST

Hi,
  If running "unix2dos" has an affect on whether or not the trajectory loads,
then the source of the problem is file conversion between your Linux and
Windows host, and has nothing to do with VMD at all. Most likely something
different occured when you copied the trajectory to the machines with the
other versions of VMD which did not result in corruption. When copying
binary file formats (such as DCD) you have to be very careful that no
carriage return or line feed translation is done at any step, otherwise
the file will be corrupted. Tools like unix2dos and dos2unix are meant
for text files only. If applying them to a DCD fixed your problem, then
the file had been corrupted to begin with and running the translator
on it just returned the binary values to what they should have been.
(even a non-text binary file like a DCD will contain CR/LF chars, by
 coincidence, so text processing tools will sometimes operate on them,
 but this is absolutely to be avoided as there are typically other
 side effects that are not necessarily reversible.)

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Nov 28, 2006 at 02:41:53PM +0800, Shaojie Ma wrote:
> Dear Sir:
> Thank you for so quick reponse!
> I have loaded the dcd file into vmd1.8.5 on windows correctly now. I just execute the following command to convert the dcd file:
> unix2dos mydcd.dcd
> and then load the dcd file. I also find that the unix fomat dcd do not need to be converted for previous vmd on windows, however, this is needed for vmd1.8.5 on windows!
>
>
> ----- Original Message -----
> From: "John Stone" <johns_at_ks.uiuc.edu>
> To: "Shaojie Ma" <mashaojie_at_nuaa.edu.cn>
> Cc: "vmd" <vmd-l_at_ks.uiuc.edu>
> Sent: Tuesday, November 28, 2006 12:21 PM
> Subject: Re: vmd-l: Read dcd file error using vmd1.8.5 for windows
>
>
> >
> > Hi,
> > How large is the trajectory file you're loading?
> > Did you load the file locally, or was this over a Samba mount,
> > or something of that sort? If you haven't copied the file locally,
> > I'd recommend doing that prior to trying to load it, as there are
> > various bugs with old versions of Samba and large files. (>= 2GB)
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Tue, Nov 28, 2006 at 11:49:46AM +0800, Shaojie Ma wrote:
> >> Dear Sir:
> >> I load a dcd file which was created by namd 2.5 for Linux using vmd1.8.5 for windows. It can not load the dcd file correctly, the error is following:
> >> dcdplugin) read_dcdheader: premature end of file
> >> ERROR) Could not read file ../analys.dcd
> >> I try loading the dcd file using vmd1.8.4 or vmd1.8.3 on windows. They can load the dcd file correctly! What should I do?
> >> **************************************************
> >> Shaojie Ma
> >> Institute of Nano Science
> >> Nanjing University of Aeronautics and Astronautics
> >> mashaojie_at_nuaa.edu.cn
> >> Nanjing 210016, China
> >> **************************************************
> >
> > --
> > 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