AMBER Archive (2002)

Subject: Re: your mail

From: darden (darden_at_gamera.niehs.nih.gov)
Date: Sun Nov 24 2002 - 16:46:35 CST

The message "-o command not found" looks to me like its coming from the
command shell and not sander. Are you running sander from some kind of
script?? A way your error maybe could happen is if there is a
carriage return inserted somewhere in the usual sander command line
inside a script. In any case I can't think of any place in the sander
program where such a message can be generated.
Here's a suggestion. Change the name of your coordinate input file to
inpcrd and the name of your topology file to prmtop. Call the file of
input commands mdin and finally copy or link the sander executable to the
directory containing these files (ideally no other files but the above 3
data files and the sander executable). Then type
sander -i mdin &
this should work unless you have restraints needing a file or some other
more complex setup. If you need to use more names of files
(e.g. sander -i mdin -o mdout -p parm ...) you can
alsways start simply as above and then experiment. If the command is too
long for one line don't put a carraige return in; just keep typing

Hope this works for you
Tom Darden
 On Sat, 23 Nov 2002, Narang Manpreet Kaur wrote:

>
> Dear Amber users,
> I am having a peculiar problem while running tjhe
> program it gives following and gets interrupted.
> -o command not found. I have also changed my output file name to mdinfo
> but still it does not work.
>
> Please Help.
> Thanks in Advance
> Manpreet Kaur Narang
> Research Scholar
> Deptt.Biotechnology
> Indian Institute of Technology Roorkee (IITR)
> Roorkee, 247 667 India
>