View source for Gromacs/C2/Creating-Input-Files/English


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|| '''Visual Cue'''
|| '''Narration'''

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|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the spoken tutorial on '''Creating Input Files'''.

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|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,
* Flow chart to setup a MD run for a protein in a solvent box
* Delete water molecules present in the starting '''pdb''' file
* '''pdb2gmx''' command and syntax
* Generate .'''gro''' and '''.top''' files

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|| '''Slide Number 3'''

'''Learning Objectives'''
||
* About selecting a force field 
* Specifiy the size and shape of bounding box for MD
* '''editconf''' command

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|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Firefox''' web browser v92
* '''gedit''' v3.36
* '''Gromacs''' v2021.2

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|| '''Slide Number 5'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial, 
* Learner must be familiar with basic computer skills.
* For pre-requisite tutorials, please visit this site.

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|| '''Slide Number 6'''

'''Code Files'''
|| * Files used in this tutorial are provided in the '''Code files''' link.
* Please download and extract the files.
* Make a copy and then use them while practising.

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|| Open a web browser and go to [https://manual.gromacs.org/archive/5.0/online/flow.html https://manual.gromacs.org/archive/5.0/online/flow.html] .
|| Open a web browser.
Go to the '''Gromacs''' manual link as seen here.

The flow chart here, shows the procedure for '''MD''' and data analysis.

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|| Cursor on the flow chart.
|| I will demonstrate parts of this procedure till the addition of a bounding box.

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|| 
|| Let’s consolidate all our input files into one folder.
From now on, I will not mention this separately.

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|| Press '''Ctrl''', '''Alt''' and '''T''' keys together.
|| Open a '''terminal''' by pressing '''Ctrl''', '''Alt''' and '''T''' keys together.

'''Windows''' users can open the '''Ubuntu''' 20.04 '''app'''.

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|| Type '''cd Documents''' and press '''Enter'''.
|| '''Linux''' users can change directory to '''Documents''' using the '''cd''' command as seen.

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|| Windows users may skip this step and remain in '''home''' directory.
|| Windows users must create this directory first. 
Hence, type '''mkdir''' space '''Documents''' before changing path.

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|| Type '''mkdir firstmd''' and press '''Enter'''.
|| I will create a new directory and name it '''firstmd'''.

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|| Type '''cd firstmd''' and press '''Enter'''.
|| Change directory to the newly created '''firstmd''' directory.

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|| '''Slide Number 7'''

'''File path for Windows Users'''
||
* '''Windows''' users must find the path of this directory in '''Windows'''.
* Detailed instructions are provided with the tutorial.
* Use this path when locating, opening or moving files, which are saved here.

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|| Open the '''File Manager'''. 
|| Open the '''File Manager'''.

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|| Copy '''1AKI.pdb''' to the '''firstmd''' directory.
|| Copy the '''1AKI.pdb''' input file to this directory.

For Windows users this path is likely to be in C drive and in the user system folder.

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|| Open the '''1AKI.pdb''' file in a text editor.
|| Then, open the '''pdb''' file in a text editor.

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|| Scroll to the end of the file.
|| Scroll to the bottom of the file.

In most files downloaded from the '''PDB''' website, water molecules will be present.

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|| Show water molecules '''HOH''' from '''1AKI.pdb''' file.
|| They are denoted as '''HOH''' and present at the end, before the model ends.

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|| Highlight the '''HOH''' from '''1AKI.pdb'''.
|| If so, be sure to delete them and save the file, before proceeding further.

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|| select all the '''HOH''' containing rows molecules and delete them.
|| Let’s select all the lines starting with '''HOH''' molecules and delete them.

Lysozyme is a stable, well studied model protein.

Hence we will also use it for learning the steps of protein '''MD''' for beginners.

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|| Show absence of '''H''' atom in the file.
|| Notice that hydrogens atoms are absent in this structure file.

We will not add them. 

The '''Gromacs''' commands will add the hydrogens for us.

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|| 
|| Structures determined by '''NMR''' methods may not contain the water molecules.

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|| Save the file and quit the text editor.
|| Now, save the file and quit the text editor.

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|| Annotation: '''Windows''' users use appropriate path in your system.
|| Let’s learn a few '''terminal''' commands to generate the input files for '''MD'''.

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|| Go to the '''terminal'''.
|| GO back to the '''terminal'''.

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|| Type '''gmx pdb2gmx -f 1AKI.pdb -o first.gro''' .
|| Enter the commands as seen and retain the syntax. 
All the commands start with the phrase '''gmx''' which calls '''Gromacs'''.

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|| Highlight '''pdb2gmx'''.
|| The second word tells '''Gromacs''', what command is to be performed. 

Here, it is '''pdb2gmx''', which will convert the '''pdb''' file to '''gro''' file format.

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|| Highlight '''-f 1AKI.pdb '''.
|| The '''hyphen f''' flag denotes the input file and it is '''1AKI.pdb'''.

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|| Press '''Enter'''.
|| The '''hyphen o''' flag refers to the output file and I will name it '''first.gro'''.

Press the '''Enter''' key and we will enter an interactive mode.

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|| Cursor on the force field and publication details selection.
|| Selection of '''force field''' and '''solvent''' addition is interactive in this command. 

First, several force fields are listed, for the user to pick from.

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|| Cursor on the details page.
|| The details of publication for each of the '''force field''' is also listed.

To learn further, learner is referred to the publication listed.

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|| Type '''4''' as seen here and press the '''Enter''' key.
|| Learner must know their system to select the desired force field.

'''Lysozyme''', is a protein without unnatural modifications. 

I want to select '''AMBER99'''. 

To select '''AMBER''', type '''4''' and press the '''Enter''' key.

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|| Cursor and highlight the response on the '''terminal'''.
|| '''Gromacs''' returns the '''force field''' as '''amber99.ff''' that will be used . 

By convention, '''.ff''' extension denotes '''force field '''files.

The path of the file is also seen.

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|| Highlight solvent environment options.

Type '''2''' and press '''Enter'''.
|| Next, the user is prompted to add a water model to the system.

Notice that only an aqueous environment is present in the list.

Type '''2''' for '''tip4p''' and press the '''Enter''' key.

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|| Show output and total charge of the system.
|| In the output notice the total charge on the system listed.
Learner is encouraged to pause the video and explore the solvent addition.
 
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|| Show file manager with the newly created files.
|| Open the file manager and notice the newly created files.

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|| Cursor on the file manager showing the newly generated files.
|| Three files, with '''.gro,''' '''.top''' and '''.itp '''extension are created with this command.

'''top''' is the '''topology''' file and '''.itp''' is '''include topology''' file.

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|| Open '''first.gro''' in text editor.
|| Let’s open the generated '''first.gro''' file in a text editor.

Notice that, this command has also added hydrogens.

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|| Cursor on 4-6 columns.
|| The 4th, 5<sup>th</sup> and 6<sup>th</sup> columns are the atomic coordinate positions of the atom.

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|| Close the '''firstmd.gro''' file.

Press '''Ctrl+L'''.
|| Let’s close the file.

I will clear the '''terminal''' for clarity in the video.

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|| Type '''gmx editconf -f first.gro -o box-added.gro -c -d 1 -bt cubic'''.
|| Next, enter the '''editconf''' command, which adds a solvent box to the system.

This is to define the volume where the simulation will be performed.

'''Editconf''' does not create a new conformational state for the protein.

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|| Cursor on '''-f''' and '''-o''' flag.
|| This command also generates '''.gro''' file like before '''pdb2gmx''' command.

Again '''-f''' denotes input file and '''-o''' denotes output file.

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|| Type''' -c '''.
|| The '''hyphen c''' flag places the center of the molecule in the center box.

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|| Type''' -d 1 '''.
|| The''' -d''' flag denotes distance from the center of the box to the boundary.

Here 1 denotes 1 nm, which is half of the length of the box.

Increasing the box size will considerably lengthen the '''MD''' run time.

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|| 
|| So the box length is a little bigger than the molecule under study.

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|| Type''' -bt cubic '''.
|| Next, enter the shape of the box, which is cubic.

If another shape is desired, use the '''bt''' flag with the shape name.

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|| Press '''Enter''' to run the command.
|| Let’s run the command.

Cubic and hexagonal shapes are popularly used for the bounding box.

This generates another input '''gro''' file, with box size and file name.

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|| Cursor on the details.
|| The box volume that is created is displayed in cubic nanometers.

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|| 
|| The extent of shift of the coordinates is also mentioned.

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|| Show screenshot of''' box-added.gro'''.
||
Notice that, the coordinates have shifted to accommodate aligning with the box.

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|| Close the text editor.
|| Learner may pause the video, and explore the options further.

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|| Show '''Gromacs''' manual website on '''getting started'''.

[https://manual.gromacs.org/archive/5.0.4/online/getting_started.html#setup https://manual.gromacs.org/archive/5.0.4/online/getting_started.html#setup] 
|| Learner may go through the '''Gromacs''' website on '''getting started'''.

The link is shown here.

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|| '''Slide Number'''

'''Summary 8'''
|| Now let’s summarize. In this tutorial, we learned about,
* Steps in a '''MD''' run for a protein in a solvent box
* The '''pdb2gmx''' command and syntax
* About adding a '''force field'''
* Generated .'''gro''' and '''.top '''files
* About '''editconf''' command

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|| '''Slide Number'''

'''Summary 9'''
|| 
* Define the size of a bounding box 
* Set the position of the molecule in the box

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|| '''Slide Number'''

'''Assignment 10'''
|| For assignment activity, please do the following. 
* Use a '''PDB''' ID of another protein of your choice.
* Practice the commands learnt in this tutorial.
* Read publications of your choice which use '''Gromacs'''.

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|| '''Slide Number'''

'''Assignment 11'''

'''http://www.mdtutorials.com/gmx/'''
||
* Go to the website seen below.
* Choose a tutorial of your choice and read it.

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|| '''Slide Number 12'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 13'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates. 

Please write to us.

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|| '''Slide Number 14'''

'''Forum for questions'''
|| Post your timed queries in this forum.

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|| '''Slide Number 15'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

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|| 
|| This is Rani from IIT, Bombay. Thank you for joining.

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