Docking tutorial

Protein-ligand docking and virtual screening tutorial

Necessary hardware:

• any computer with Internet connection

Necessary software (all free except PyMol):

• Putty
• VMD or UCSF Chimera or 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