From: Stéphane Teletchéa (steletch_at_biomedicale.univ-paris5.fr)
Date: Fri Sep 20 2002 - 04:24:12 CDT

I think the answer is like you describe.
To test it, use the command tr (under linux), you'll be able to easily
convert your windows text file under linux text files.
I don't have the syntax in mind, but i know that it's the tool your looking
for.

Stef

Le Jeudi 19 Septembre 2002 22:16, John Stone a écrit :
> Hi Surjit,
>
> On Thu, Sep 19, 2002 at 03:35:46PM -0400, Surjit Dixit wrote:
> > Hi,
> > I have a CD with a trajectory and parameter topology file (AMBER format)
> > burnt on a Windows machine.
> > I am able to view this trajectory with VMD on Windows machines but VMD
> > on linux crashes when I
> > try to read these files. ptraj, another program in Amber suite also has
> > problems reading these files, so something
> > is surely wrong with the file.
>
> If VMD can read the file correctly on Windows, then it must be some
> other problem. Since I assume you're running Linux on the same machine,
> then its not an endianism problem, it might be some other strange issue.
> What type of machine was the original AMBER simulation run on?
> Was it on a Windows machine or on Unix? This makes a difference.
>
> > Both of these are text files.
>
> I suspected that this is a problem with CR/LF handling in
> both VMD and ptraj, even before I read this comment, now its
> almost assuredly the cause.
>
> > If I copy(ftp) these same files from the linux machine to another
> > windows machine, VMD reads the files neatly
> > on windows. I am able to read this files with vi editor on the linux
> > machine and both of them look normal. I thought it might be
> > something to do with the end of line problem because of the dos->unix
> > movement but but viewing it in vi, I am not able
> > to detect anything abnormal about these files.
>
> Yes, I believe this is exactly the problem.
>
> > I know this is not a VMD problem, but thought somebody on the list might
> > have some ideas about the source of such
> > a problem. I am running out of ideas and would appreciate any help.
>
> How big is the file?
> If you can provide us with a copy of the file (or one like it) I bet
> we can fix VMD so it is immune to the CR/LF problems. We've run into
> similar issues with text files on Windows, Mac, and Unix, as all three
> platforms use a different CR/LF end of line convention.
> If you've got a small example that exhibits the problem, I can give you
> an FTP area to upload it and we can try to do something about this in
> the VMD file reader plugins for the old revs of AMBER.
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu