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Top Forums Shell Programming and Scripting For loop to run external program Post 302557615 by cfajohnson on Wednesday 21st of September 2011 05:12:46 PM
Old 09-21-2011
Quote:
Originally Posted by oldmanwinter
Thank you, except now it says "line 5: vina: command not found" if I change the code to
Code:
#!/bin/bash
FILES=/home/afalk/Desktop/battest/*.pdbqt
for f in $FILES 
do
$vina --config /home/afalk/Desktop/A.txt --ligand "$f".pdbqt
done

it returns "line 5: --config: command not found" config is an internal command for vina.

It is trying to run the command, --config, because $vina is empty.
 

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config(8)						      System Manager's Manual							 config(8)

NAME
config - Builds system configuration files SYNOPSIS
/sys/conf/config [-k] [-p] [-q] system_name FLAGS
Creates a define variable 'KDEBUG' that can be used to conditionally compile source code for kernel debugging. Configure the system for profiling. You must have sources to use this flag. Concatenates and displays all the system configuration files, including any configura- tion files described in the /sys/conf/NAME.list file. DESCRIPTION
The doconfig command calls the config command to build a set of system configuration files from a file that describes the sort of system that is being configured. The config command also takes as input another file that tells it what files are needed to generate a system. This other file can be augmented by a configuration-specific set of files that name alternate files for a specific machine. Normally, you should run the doconfig program and not the config command. If you need to issue the config command, be sure to change your directory to the /sys/conf directory. As an argument to the config command, specify the name of a system configuration file containing device specifications, configuration options and other system parameters for that specific system configuration. The config command places all its output files in the directory The output of config consists of a number of files; each machine type has its own specific set of files. All machine types have a makefile which is used by make during the system build. Typically, there are also a set of header files which contain definitions of the number of various devices that will be compiled into the system, and a set of swap configuration files contain definitions for the disk areas to be used for swapping, the root file system, argument processing, and system dumps. After running config, you run make depend in the directory where the new makefile was created. If any other error messages are produced by config, the problems in the configuration file should be corrected and config should be run again. Attempts to compile a system that had configuration errors are likely to be unsuccessful. NOTES
The line numbers reported in error messages are usually off by one. FILES
List of common files used to build the system List of files specific to NAME, where NAME is the value specified for the ident option in the system configuration file Machine-independent portion of the makefile template used for building kernels from binaries Machine-independent portion of the makefile template used for building kernels from sources Machine-dependent portion of the makefile template List of machine- specific files Machine-specific name to major device mapping file RELATED INFORMATION
Commands: make(1), doconfig(8) System Administration delim off config(8)
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