AMBER Archive (2006)

Subject: AMBER: RE: about the fix_numbering_pdb.csh in Amber Tutorial_eight

From: Ross Walker (
Date: Tue Apr 18 2006 - 10:42:41 CDT

Dear Shulin,
The ?'s are correct in this script they act as wildcards that match exactly
1 character each. So
ls -l *.pdb.????
will match blah.pdb.1987 but not blah.pdb.198
Anyway, I have attached the correct version of the script. This works on my
Redhat AS4 linux box. What system are you using and what is the error you
see? There is nothing 'illegal' about having 4 ?'s in a row so I suspect
there is an issue with your operating system or shell. What OS and shell are
you using?
Also, make sure you have set the script to be executable:
chmod +x fix_numbering_pdb.csh
And that you use the ./ infront of it to execute it.
If it still doesn't work can you send me some more details, I.e. what system
you are using etc and exactly what the error message is and I can try to
help further.
All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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From: Shulin Zhuang []
Sent: Tuesday, April 18, 2006 01:47
Subject: about the fix_numbering_pdb.csh in Amber Tutorial_eight

Dear Prof. Ross Walker,
These two days, I am doing the MMTB cluster excese about section 6 of your
amber tutorial"All Atom Structure Prediction and Folding Simulations of a
Stable Protein". However, I can not execute the script file
fix_numbering_pdb.csh . In this file, there are too many signs of "?", suche
as set numfil = `ls -1 *.pdb.???? | wc -l` I guess, the place occupied by
thes "?" in this flie may be any signals which are not correctly displayed
in the web. Is this right? Woul you like to give me the correct
fix_numbering_pdb.csh ? Great thanks. Take you time.
Best regard

   Shulin Zhuang
Chemistry Department 
Zhejiang University PRC 

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