[gmx-users] pdb_to_xvzr not working

Justin A. Lemkul jalemkul at vt.edu
Sat Sep 13 16:46:04 CEST 2008

Morteza Khabiri wrote:
> Dear
> I want make hole in my system. Because of this I oblige to use MSMS programm
> to calculate the surface of my protein. Before using MSMS we should change
> pdb file format to xyzr  file format. I should use pdb_to_xvzr to produce
> xvzr file. Unfortunately I couldn't run  pdb_to_xvzr. After running i
> faced with the following error:
> ./pdb_to_xyzr: line 102: nawk: command not found
> thats very nice of you if someone could help me how to active pdb_to_xyzr.
> I use chmod but it did not work.

"nawk" is a Unix/Linux utility.  It looks like the program requires this tool to 
work, so you need to install it.  If it is installed, you will need to add its 
location to your $PATH.


> Thanks alot
> Morteza
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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