From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Oct 12 2005 - 15:41:43 CDT
Sounds like the permissions need to be changed.
Try typing: chmod 755 namdplot (to make it executable)
Then use ./namdplot to run it.
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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