VMD-L Mailing List

From: Surjit Dixit (sdixit_at_wesleyan.edu)
Date: Fri Sep 20 2002 - 07:29:47 CDT

Good Morning Stef
Thanks, that was useful. tr works like a charm!

tr -d '\r' < dos_file | tr -d '\032' > unixfile

Surjit

Stéphane Teletchéa wrote:

>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
>>
>>
>
>
>
>