Re: namdplot: command not found

From: Sterling Paramore (paramore_at_hec.utah.edu)
Date: Thu Oct 13 2005 - 14:59:36 CDT

Try:

[mriv209-01:~] bo% cd desktop
[mriv209-01:~/desktop] bo% chmod a+x namdplot
[mriv209-01:~/desktop] bo% ./namdplot TEMP pbr1.log

Directories are case-sensitive, ~/desktop and ~/Desktop are not the same
directory.

-Sterling

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
>>>>>
>>>>>
>>>>>
>>>>>
>>
>>
>>
>>

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