AMBER: RE: Tutorial#1 ptraj/sander problem

From: Ross Walker <>
Date: Tue, 17 May 2005 15:56:59 -0700

Dear Dani,

> Thanks so much for your e-mail.
> I am unable to e-mail those files so I am making them available at :
> em348_S05/kohen.tar.gz
> (gz file with my mdcrd file )
> as well as my sander output
> em348_S05/polyAT_vac_md1_12Acut.out
> (the names are the same as those in your tutorial)

I have downloaded your mdcrd files and can confirm that I get the same
behaviour with ptraj on my machine. The first step has a RMS of 0 while the
second step has an rms of over 200 angstroms even though in VMD things look
fine. I have tracked this down to the fact that your mdcrd file is DOS
formatted, has ASCII Carriage return and line feed at the end of each line
while mine is UNIX format, has just a line feed at the end of each line. Did
you run this calculation on a windows machine? Under Cygwin maybe? It seems
strange that you would get a DOS formatted mdcrd file. There is a simple
fix, however, on most Linux machines there is a command called dos2unix that
will convert a dos format file to a unix formatted one. If you do this and
then re-run the ptraj script you get the correct answer.

So, it seems that ptraj is misreading mdcrd files when they are in DOS
format. Indeed I suspect that there is nothing in the code to handle DOS
formatted files. At some point I will try and take a look and issue a bug
fix. For the moment, however, you will need to convert your mdcrd files to
UNIX format.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Wed May 18 2005 - 00:53:00 PDT
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