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Docking tutorial

Protein-ligand docking and virtual screening tutorial

Necessary hardware:

  • any computer with Internet connection

Necessary software (all free except PyMol):

Small Linux tutorial

Linux - usual directory structure

root directiory /

  • /bin = system commands

  • /boot = startup programs

  • /dev = devices (disks and otehrs)

  • /etc = settings

  • /home = users' home directories

  • /home/vojtech = home directory of the user vojtech

  • /lib = libraries

  • /lost+found = ?

  • /media or /mnt = access to CD/DVD or USB drives

  • /opt = other programs

  • /proc = processes

  • /root = superuser's home directory

  • /sbin = additional programs

  • /sys = system

  • /temp or /tmp = temporary data

  • /usr = main user programs

  • /var = others

names of files: case-sensitive, avoid space, or @$%^&*()+=/

Linux help

man man - command man with parameter man - the manual for the manual program

man -h - command man with modifier -h - the manual's help

Main Linux commands for file manipulation

  • ls - prints files/dirs in the current dir

  • ls *.txt - prints files with name ending .txt in the current dir

  • ls -l - same as ls but in a long format

  • ls -a - same as ls but including hidden files

  • ls -t - same as ls but in the order of file creation

  • ls -rt - same as ls -t but reverse

  • cd dirname - go to the subdir called dirname

  • cd .. - go to the upper directory

  • mkdir dirname - make directory called dirname

  • pwd - print current dir

  • ls ~ - prints files/dirs in the home dir

  • cp file1.txt file2.txt - copy file1.txt to file2.txt

  • mv file1.txt file2.txt - move file1.txt to file2.txt

  • cp ../file1.txt . - copy file1.txt from upper directory here

  • rm file1.txt - delete file1.txt

  • mc - Midnight Commander

Main Linux commands for text manipulation

  • cat file1.txt - prints the text content

  • head file1.txt - prints the first 10 lines of the text content

  • head -100 file1.txt - prints the first 1000 lines of the text content

  • tail file1.txt - prints the last 10 line of the text content

  • more file1.txt - prints the text content page by page (can be contorled by Enter, Space or q, similar to less)

  • grep 00033 file1.txt - prints lines containing 00033

  • grep -v 00033 file1.txt - prints lines not containing 00033

  • grep -i BB file1.txt - prints lines containing BB, bb, Bb or bB

  • grep "00 33" file1.txt - prints lines containing "00 33"

  • wc file1.txt - counts words and lines

  • diff file1.txt file2.txt - prints differences in files

Redirections and pipes

  • cat file1.txt file2.txt > file12.txt - joints two files into file12.txt

  • grep 000 file1.txt > file2.txt - prints lines from file1.txt containing 000 to file2.txt

  • creation of a file by cat

cat > file3.txt
Write something
here
Ctrl+D

  • echo "Write something here" > file1.txt - creation of a file by echo

  • cat file1.txt >> file2.txt - appends file1.txt at the end of file2.txt

  • egrep 000 file1.txt | wc = counts lines containing 000 in file1.txt

Access rights

-rw-r--r--   1 spiwokv spiwokv  2116502 Jun 18  2012 adaptive.avi
-rw-r--r--   1 spiwokv spiwokv    12288 Jan 23 20:46 BI_Spiwok2_A.doc
-rw-r--r--   1 spiwokv spiwokv    98816 Jan 23 20:47 BI_Spiwok2_C.doc
drwxrwxr-x 103 spiwokv spiwokv     4096 Mar 27 20:40 byrokracy
  • chmod a+r adaptive.avi - gives all users a right to read the file

Linux processes

  • ps - print running processes

  • top - interactive version of ps

  • kill 10695 - kills the process number 10695