Converting ext2 filesystem to ext3

ext 2 stands for second extended file system. You may have installed your linux with an ext2 . If you wish to convert it to ext3, fire the command below

tune2fs -c 0 -i 30 -j /dev/hda1

Before doing this try checking your file system by using the command df -T. After rebooting, running the command df -T again should confirm that you've been successful.

www.linux.org

Essential gromacs commands!

Hey ,

Many of you might want to use gromacs or are using it now. Gromacs is used the most by the bio-community to perform molecular dynamic simulations on bio molecules. I have compiled a list of commands which would help you from the start to the end.

1) pdb2gmx -f pdbid.pdb -o pdbid_processed.gro -water spce

2) editconf -f pdbid_processed.gro -o pdbid_box.gro -c -d 1.0 -bt cubic

3) genbox -cp pdbid_box.gro -cs spc216.gro -o pdbid_solvated.gro -p topol.top

4) grompp -f minimization.mdp -c pdbid_solvated.gro -p topol.top -o minpdbid.tpr

5) mdrun -v -deffnm minpdbid

6) grompp -f nvt.mdp -c minpdbid.gro -p topol.top -o nvtpdbid.tpr

7) mdrun -v -deffnm nvtpdbid

8) grompp -f npt.mdp -c nvtpdbid.gro -t nvtpdbid.trr -p topol.top -o nptpdbid.tpr

9) mdrun -v -deffnm nptpdbid

10) grompp -f mdrun.mdp -c nptpdbid.gro -t nptpdbid.trr -e nptpdbid.edr -p topol.top -o mdpdbid.tpr

11) mdrun -v -deffnm mdpdbid

Note that all .mdp files contain all the configurations. You can have your own file saved in the folder. I have not attached those files.

Gzip,Gunzip and Tar

A simple tip. If you need to quickly create a tar.gz archive of a folder named abc, then try the following command

tar -cvzpf desired_file_name.tar.gz /path/to/folder/abc

and if you need to get the folder back from the archive

tar -xvzpf filename.tar.gz

This is better and quick compared to the two step procedure of first using unzip and then tar.

More on File Mainpulations

Hey,

Sometimes its tedious to get the file as u want it to be. One such case is obtaining ATOM records from a PDB file. For those of you who dont know about pdb files (http://www.wwpdb.org/documentation/format32/v3.2.html) the link is a good place to start.

But in short it contains various sections like HEADERS,ATOM,HETATM,CONECT etc. ATOM records always begin with the word 'ATOM' , HETATM records with 'HETATM' and so on.

At times you would want to extract just the atom record. Instead going through the routine procedure of opening it in a text editor and then deleting all the lines that does not being with ATOM, heres a short,easy and a single line command.

grep 'ATOM  ' pdbid.pdb>| atom.pdb

Thats it .. You have the atom records saved in atom.pdb

Export, Set and Setenv commands

While installing many bioinformatics softwares you are required to set the environmental variable. Some of the softwares instructs you to set the variable using export and some using setenv but at times these commands do not work.

Ideally we would like to define a variable and it should be accessed in all the shells or processes invoked by the original shell. This can be achieved by the export command in ksh/sh as shown below.

export PATH="/root/satish/"

To check if the path has been set you could use the following command

echo $PATH and it should give you /root/satish/ has the output.

set and setenv are the c-shell (csh/tcsh) alternatives for setting a local variable and environment variable respectively. The set command is used for setting local variable, setenv is uesd for setting an environment variable:

To know what shell you are using type

echo $SHELL

the output will be /bin/bash or /bin/csh and so on. Depending on your shell use the above commands.

Configuring Ctrl+alt+del on your

On your Windows machine one of the most used keys are ctrl+alt+del :P . On a Linux machine there is something called as top which gives you the processes that are running and you can terminate them (same as end task). But if you would like to configure ctrl+alt+delete then you can do that too.

Go to "System > Preferences > Keyboard Shortcuts

Enter the new Ctrl-Alt-Del: At the bottom of the "Keyboard Shortcuts" window, click on "Add", to add a new "Custom Shortcut" combination. (remove the old ctrl-alt-del if it is already assigned)

Name: Ctrl-Alt-Del (name it whatever you want)

Command: gnome-system-monitor

Click "Apply" and you're done!
Test it out by pressing "Ctrl-Alt-Del"!

If you still want to stick to the linux style which is awesome just start your terminal and type "top" and hit enter.

You will be shown the name of the process and its id (PID).. just note down that id (example :- PID=5277)

Then on the terminal type kill 5277 thats it...

The tale of the tail

If you guys have been using linux then you must have surely come across a command known as "tail" .It is used to display the last few lines of a text file. It is one the best and standard ways of watching or tracking your log files.

When you start a docking or simulation in text mode or in command mode, most of the time the screen goes blank and the cursor does not allow you to enter a new command which essentially means that your job is going on. Now the question is how do you know how much has it progressed. Most of the this program creates a output file or a log file. You could open a new terminal window and cd into that folder and then type the following command :

tail -f logfile.log or tail -f outputfile.out

-f tells the tail to follow the update and hence the latest update gets printed on the screen. By defaul tail prints out the last ten lines but with -f the entire file is monitored as and when the file gets updated.

Pretty useful command...

Anti Virus for Linux

This could have been the shortest blog having just 2 words " Not Required".

There are many companies which sell linux based antivirus but most of the times
the threat that they detect are windows specific.

If you want to provide protection to the windows users connected to you in a network then may be u could install clam anti virus. I also dont say that a linux box is 100 % secure.

Linux also has SELinux (Security Enhanced Linux) which controls over processes, filesystems, sockets, network interfaces etc. Enabling SELinux (default : Enabled)
helps a lot. All in all Antivirus is not required in a linux system.

Auto remove repeats from a file

Say if you have a file with multiple peptides in a file and you want
to keep only one instance of each peptide.

This script would be of great use.

You could save it as removeduplicates.pl and run it as you run a
normal perl script.

open(FILE,"FILENAME");
@peptides=;
%seen=();
@unique=grep{! $seen{$_} ++} @peptides;
print @unique;

If you want to print the output to a file , do the following

perl removeduplicates.pl > Outputfilename

Remove a line having a particular word

Hi,

Its a sed script rather a sed one liner.

Many a times you might have to remove lines that contain particular word from a file.
eg) In your pdb file you might want to remove all the HETATM records or all lines containing ANISOU , you could easily do it by the following line in your terminal

sed '/ANISOU/d' filename>outputfilename

The above code opens the file "filename" and deletes everyline that has ANISOU and saves it to "outputfilename"

Convert your RHEL to CentOS

Hi guys,

Of late i had a few problems with Red hat enterprise Linux. I had used CentOS earlier and i liked it a lot. So i decided to get CentOS installed instead of the RHEL. But then i did not want to format my computer . I tried out a method which atleast worked pretty well for me. You dont have to format your box. Just do the following steps and convert your RHEL to CentOS.

Start by issuing this command at your terminal

cat /etc/redhat-release

The output would be redhat enterprise linux blah blah .....

now

rpm -e --nodeps redhat-release

rpm -e --nodeps yum-rhn-plugin

wget http://mirror.centos.org/centos/RPM-GPG-KEY-CentOS-5

rpm --import RPM-GPG-KEY-CentOS-5

rpm -Uvh http://mirror.centos.org/centos/5/os/x86_64/CentOS/centos-release-notes-5.3-3.x86_64.rpm

rpm -Uvh http://mirror.centos.org/centos/5/os/x86_64/CentOS/centos-release-5-3.el5.centos.1.x86_64.rpm

wget http://mirror.centos.org/centos/5/os/x86_64/CentOS/yum-3.2.19-18.el5.centos.noarch.rpm

You could also download the files from mirrors.centos.org and then do a rpm -ivh file.rpm

Once you do this just fire the following command from your terminal

cat /etc/redhat-release

and it should say that your OS is CentOS..

Happy CentOSing niggas :-)