lec3

Steps and commands
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1. Cleaning can be done using grep. For example if HOH is the only hetero atom, this can be done using:

					$ grep -v HOH 1aki.pdb > cleaned1aki.pdb

The option '-v' tells grep to find every line that doesn't contain the keyword "HOH" in the file 1aki.pdb. These findings are then redirected to a new file:
cleaned1aki.pdb.


2. Applying forcefiled can be done using the command:

	            $ gmx pdb2gmx -f cleaned1aki.pdb -o protein.gro

   The 'gmx' command calls Gromacs. 'pdb2gmx' is a subroutine in the Gromacs package that applies the forcefield. The '-f' option names the input file, which's
   "cleaned1aki.pdb" and the '-o' options names the file where to send the output.

2a. There are several force field models standardized for different situation. While executing this command Gromacs will provide 15 inbuilt forcefield and ask
    the user to choose one. After choosing an appropriate force field, one will also need to specify proper water model. There are 7 water models inbuilt inside
	Gromacs. However it is completely possible to add external force field and water model, but that will be discussed later.

3. The next step is defining the box - aka the region where we'll concentrate our effort. This can be done using the command:

				$ gmx editconf -f protein.gro -o box.gro -c -d 1.0 -bt cubic

Here, 'editconf' is another gmx module than reconfigures the position of the protein. The '-f' and '-o' options again specifies respectively the input and the
output file name as their argument. Rest of the options and argument are:

   				'-c'	Specifies that the protein must be at the center of the box.
				'-bt'	Stands for "Box Type". As per the argument, a cubic box is chosen here. But any uniform platonic solid is possible.
				'-d'	Option specifies periodic boundary. A 1.0nm of periodic boundary is specified here.

The exact box size here is determined by Gromacs.


4. Next, the solvation is done using the command:

				$ gmx solvate -cp box.gro -cs spc216.gro -o solve.gro -p topol.top

   'solvate' is the Gromacs module that does this step. Here:
   				
				'-cp' specifies the input file 'box.gro'
				'-cs' specifies the water model for the solvents
				'-o' specifies the output file as usual
				'-p' specifies the file that recoreds the topology. Any previous 'topol.top' file will be renamed by adding '#' at both end and adding a version
				     number. For example the previous topology file from force field generation proceude is renamed to "#topol.top.1#".
   
As like the previous step, the exact amount of water is determined by Gromacs. However, this time these molecules are specified with 'SOL' keyword.