lec9

Cleaning the protein
--------------------
1. Cleaning step this time involves, cleaning the protein of any heteromatom like before, but additionally the ligand also have to be cleaned from everything 
else. First the ligand is extracted:

   			$ grep JZ4 3htb.pdb > JZ4.pdb

JZ4 here mark the ligand atoms. The protein then is extracted like before:

   			$ grep -v HETATM 3htb.pdb > cln_3htb.pdb

This can be done in any sequence, since grep doesn't alter the original file.


Applying the forcefield
-----------------------
1. Forcefield is applied to the cleaned protien molecule like before:

			$ gmx pdb2gmx -f cln_3htb.pdb -o protein.gro

As can be seen, the pdb2gmx is taking in the cln_3htb.pdb file which is specified as input by the '-f' option and spitting out the protein.gro file following
the '-o' option. The forcefield applied this time is "CHARMM36 all-atom force field (July 2020)", an external forcefield. The water model is "SPC/E" - extended 
simple point charge.


2. Now, polar hydrogen is to be added to the ligand moleucle using Avogadro 2.0. This is done by opening the JZ4.pdb file in Avogadro 2.0 and:

			Build -> Hydrogen -> Add Hydrogens

After adding hydrogen, the file is to be saved in .mol2 format:

			Molecule -> [enter the name JZ4.mol2] -> [select all files as save format] -> save

Note that, Avogadro 2.0 installed by standard installation command lacks MOL2 writer. So, other Avogadro 2.0 modules have to be installed for this step. In the
current system, its done using the Synaptic package manager GUI. However, a detail study of the Avogadro 2.0 will reveal the detail and a way to install the
modules using command line.

3. The JZ4.mol2 file generated in this way have to be edited. The second line containing asterics have to be replaced with the file name JZ4.

4. This JZ4.mol2 file now needs to be modified using the perl script "sort_mol2_bonds.pl". The command:

			$ perl sort_mol2_bonds.pl JZ4.mol2 JZ4_new.mol2

5. The output file "JZ4_new.mol2" is now ready for processing by CGenFF server. To submit any molecule, the CGenFF website requires registration as a user and
log in as that user. After that the JZ4_new.mol2 file have to be uploaded, which will be processed and the output file will appear as the webpage updates. The
output file, which is a text file, have to be saved in the proper directory.