Re: namdplot: command not found

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Thu Oct 13 2005 - 16:09:03 CDT

The problem might be the location (name) of the awk command that is being
invoked
from within namdplot.

type: which awk or which gawk or which nawk

and see where the awk command is sitting.

Regards
Brian

On Thu, 13 Oct 2005, bo baker wrote:

> Hello,
>
> Thanks for your suggestions. But I am still stucked. The commands
> didn't work. Here is how I did:
>
> [mriv209-01:~] bo% cd desktop
> [mriv209-01:~/desktop] bo% chmod a+x namdplot
> [mriv209-01:~/desktop] bo% /Users/bo/Desktop/namdplot TEMP pbr1.log
> tcsh: /Users/bo/Desktop/namdplot: Command not found.
>
>
> Then I try 'chmod 755':
>
> [mriv209-01:~/desktop] bo% chmod 755 namdplot
> [mriv209-01:~/desktop] bo% /Users/bo/Desktop/namdplot TEMP pbr1.log
> tcsh: /Users/bo/Desktop/namdplot: Command not found.
>
> The computer just can't find the command. Is this problem related to
> my computer? or it is a general problem for nay operation systems?
> NAMD tutorial should specify how these commands would work on the
> other computers, ie Mac. And it would be much easier for people like
> me as a new user of NAMD.
>
> All the best
>
> Bo
>
>
> On 10/12/05, Robert Brunner <rbrunner_at_uiuc.edu> wrote:
> > You need to make namdplot executable before it will run. Type this
> > once in the namdplot directory:
> >
> > chmod a+x namdplot
> >
> > then you should be able to run ./namdplot
> >
> > Robert
> >
> > On Oct 12, 2005, at 3:27 PM, bo baker wrote:
> >
> > > Hi, Thanks for your suggestion.
> > >
> > > I try the command from my account as well as the 'adm' account. But I
> > > got the message saying that 'namplot: permission denied'. Here is how
> > > I did:
> > >
> > > ----
> > > [mriv209-01:~/desktop] bo% cd desktop
> > > [mriv209-01:~/desktop] bo% ./namdplot
> > > tcsh: ./namdplot: Permission denied.
> > > ----
> > >
> > > Then I try the admister account:
> > > ----
> > > adm% /Applications/NAMD_2.6b1_MacOSX-PPC/namdplot TEMP pbr1.log
> > > tcsh: /Applications/NAMD_2.6b1_MacOSX-PPC/namdplot: Permission denied.
> > > ----
> > >
> > > Do I do something wrong? Thank you for your advice.
> > >
> > > Bo
> > >
> > > On 10/11/05, Robert Brunner <rbrunner_at_uiuc.edu> wrote:
> > >
> > >> You need to tell the OS where namdplot is, since its not it one of
> > >> the directories it normally searches. Use "./namdplot" instead of
> > >> "namdplot" so that it know to find namdplot in the current directory.
> > >>
> > >> Robert
> > >>
> > >> On Oct 11, 2005, at 6:56 PM, bo baker wrote:
> > >>
> > >>
> > >>> Hello:
> > >>>
> > >>> Thank you very much for your suggestions. Yes, I use Mac OS X. I
> > >>> downloaded the 'namdplot' script from the NAMD/utilities. And I have
> > >>> the .log file in the same directory. Then I try to call 'namdplot
> > >>> TEMP pbr1.log' as the tutorial suggested. But the computer can't
> > >>> recognize 'namdplot' command. I guess that some commands need to be
> > >>> added before 'namdplot'. Here is how I did:
> > >>>
> > >>> [mriv209-01:~/desktop] bo% namdplot
> > >>> tcsh: namdplot: Command not found.
> > >>> [mriv209-01:~/desktop] bo% namdplot TEMP pdr1.log
> > >>> tcsh: namdplot: Command not found.
> > >>>
> > >>> I don't have experience to wrtie a program in unix. Can anyone
> > >>> suggest
> > >>> me how to modify the 'namdplot' script , so I can use it for the
> > >>> Mac?
> > >>> I don't have 'xmgrace' in the computer. I would like to write it
> > >>> into
> > >>> text file. So I can convert the data with other graph program later.
> > >>>
> > >>> I have included the 'namdplot' script as an attachment. Your help
> > >>> will
> > >>> be very appreciated.
> > >>>
> > >>> Bo
> > >>>
> > >>>
> > >
> >
> >
> >
> >
>

************************************************
  Brian Bennion, Ph.D.
  Bioscience Directorate
  Lawrence Livermore National Laboratory
  P.O. Box 808, L-448 bennion1_at_llnl.gov
  7000 East Avenue phone: (925) 422-5722
  Livermore, CA 94550 fax: (925) 424-6605
************************************************

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