Re: namdplot: command not found

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Oct 14 2005 - 14:44:14 CDT

What about just plain

./namdplot

Does it give you the usage line?

Brian

On Fri, 14 Oct 2005, bo baker wrote:

> Hello,
>
> Thank you very much for being spend your time to help me. I have try
> all your suggestions. Here are what I got:
>
> mriv209-01:~] bo% cd desktop
> [mriv209-01:~/desktop] bo% ./namdplot TEMP pbr1.log
> tcsh: ./namdplot: Command not found.
>
> Then I check 'ls -la' and ' head -30 namdplot'. Here are what I got:
>
> [mriv209-01:~/desktop] bo% ls -la
> total 28424
> drwxr--r-- 24 bo staff 816 12 Oct 13:20 .
> drwxrwxrwx 42 1703 244 1428 11 Oct 10:29 ..
> -rwx------ 1 bo staff 21508 12 Oct 13:41 .DS_Store
> -rw-r--r-- 1 bo staff 0 20 Jan 2004 .localized
> -rw-r--r-- 1 bo staff 1707 25 Sep 14:41 3Ddock-091920
> -rw-r--r-- 1 bo staff 1422 20 Sep 15:01 Amber-commands.txt
> drwxrwxrwx 27 bo staff 918 19 Sep 13:13 Documents
> drwxr-xr-x 22 bo staff 748 5 Sep 15:26 MD
> -rw-r--r-- 1 bo staff 235142 18 Jun 2004 N62-model1-2.pdb
> -rw-r--r-- 1 bo staff 235142 18 Jun 2004 N62.pdb
> -rw-r--r-- 1 bo staff 235142 13 Dec 2004 N62.txt
> drwxr-xr-x 16 bo staff 544 10 Oct 11:02 PBR
> -rw-r--r-- 1 bo staff 1945 12 Oct 13:20 PBR-namd-101005.txt
> drwxrwxrwx 21 bo staff 714 10 Oct 11:04 StAR
> -rw-r--r-- 1 bo staff 1423 2 Sep 15:26 VMD-commands.txt
> -rw-r--r-- 1 bo staff 17409 21 Sep 17:44 amber-092105
> drwxr-xr-x 20 bo staff 680 29 Sep 2004
> complete2.3_ppcDarwin7_acad_1-3alpha1
> -rwxr-xr-x 1 bo staff 3534 11 Oct 16:34 namdplot
> -rw-r--r-- 1 bo staff 8083 10 Oct 16:18 pbr-vmd-101005
> -rw-r--r-- 1 bo staff 910436 11 Oct 00:40 pbr1.log
> drwxr-xr-x 19 bo staff 646 13 Jul 17:04 pdbs
> -rw-r--r-- 1 bo staff 8501 3 Oct 11:34 sander-082505
> -rw-r--r-- 1 bo staff 2394 20 Sep 10:47 swiss-preference1
> -rw-r--r-- 1 bo staff 12835375 29 Apr 13:47 vmd183.dmg
> [mriv209-01:~/desktop] bo%
> [mriv209-01:~/desktop] bo%
> [mriv209-01:~/desktop] bo% head -30 namdplot
> echo "Usage: $0 [zero] [diff] [from <first>] [to <last>] [<yfield>
> [<yfield> . echo "Usage: $0 [zero] [diff] [from <first>] [to <last>]
> [<yfield> [<yfield> .[mriv209-01:~/desktop] bo% y $tmpfile &L" -pexec
> "YAXIS TICKLABEL PREC 0" \
>
>
> Then I search 'awk':
>
> [mriv209-01:~/desktop] bo% which awk
> /usr/bin/awk
> [mriv209-01:~/desktop] bo% which gawk
> gawk: Command not found.
> [mriv209-01:~/desktop] bo% which nawk
> nawk: Command not found.
> [mriv209-01:~/desktop] bo%
>
>
> Could you please help me to figure out what is wrong here with
> 'namdplot' command?
>
> Your advice have been very appreciated.
>
> Bo
>
> On 10/13/05, Robert Brunner <rbrunner_at_uiuc.edu> wrote:
> > From ~/desktop, try just running ./namdplot
> >
> > If that doesn't work, try running "ls -la" and send me the output.
> > Also type "head -30 namdplot" and send me that.
> >
> > As I mentioned in a previous message, the tutorials are actually
> > designed to be run on Macs, in particular, the PowerBooks the TCB
> > group uses to host workshops. However, as is mentioned on:
> > <http://www.ks.uiuc.edu/Training/Tutorials/>
> >
> > the tutorials assume that certain software (e.g. namdplot, xmgrace)
> > is already installed. Human resources being limited, the training
> > team has not had the opportunity to prepare installation instructions.
> >
> > Robert
> >
> > PS. I don't work on the tutorials, but I am (slightly) familiar with
> > them and Mac OS X.
> >
> > On Oct 13, 2005, at 2:26 PM, 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
> > >
> >
> >
> >
> >
>

************************************************
  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
************************************************

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:41:15 CST