Difference between revisions of "Gromacs/C2/Creating-Input-Files/English"
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|| Let’s select all the lines starting with '''HOH''' molecules and delete them. | || Let’s select all the lines starting with '''HOH''' molecules and delete them. | ||
− | Lysozyme is a well studied | + | Lysozyme is a stable, well studied model protein. |
Hence we will also use it for learning the steps of protein '''MD''' for beginners. | Hence we will also use it for learning the steps of protein '''MD''' for beginners. | ||
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We will not add them. | We will not add them. | ||
− | The '''Gromacs''' commands will add the hydrogens for | + | The '''Gromacs''' commands will add the hydrogens for us. |
|- | |- | ||
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|- | |- | ||
|| Annotation: '''Windows''' users use appropriate path in your system. | || Annotation: '''Windows''' users use appropriate path in your system. | ||
− | || Let’s learn a few '''terminal''' commands to generate input files for '''MD'''. | + | || Let’s learn a few '''terminal''' commands to generate the input files for '''MD'''. |
|- | |- | ||
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|| Selection of '''force field''' and '''solvent''' addition is interactive in this command. | || Selection of '''force field''' and '''solvent''' addition is interactive in this command. | ||
− | First, several force | + | First, several force fields are listed, for the user to pick from. |
|- | |- | ||
|| Cursor on the details page. | || Cursor on the details page. | ||
− | || The details | + | || The details of publication for each of the '''force field''' is also listed. |
To learn further, learner is referred to the publication listed. | To learn further, learner is referred to the publication listed. | ||
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'''Lysozyme''', is a protein without unnatural modifications. | '''Lysozyme''', is a protein without unnatural modifications. | ||
− | + | I want to select '''AMBER99'''. | |
− | To select '''AMBER''', type '''4''' | + | To select '''AMBER''', type '''4''' and press the '''Enter''' key. |
|- | |- | ||
|| Cursor and highlight the response on the '''terminal'''. | || Cursor and highlight the response on the '''terminal'''. | ||
− | || Gromacs returns the force field | + | || '''Gromacs''' returns the '''force field''' as '''amber99.ff''' that will be used . |
− | By convention, '''.ff''' denotes '''force field '''files. | + | By convention, '''.ff''' extension denotes '''force field '''files. |
The path of the file is also seen. | The path of the file is also seen. | ||
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|| Show output and total charge of the system. | || Show output and total charge of the system. | ||
|| In the output notice the total charge on the system listed. | || In the output notice the total charge on the system listed. | ||
− | Learner is encouraged to pause the video and explore | + | Learner is encouraged to pause the video and explore the solvent addition. |
|- | |- | ||
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|| Three files, with '''.gro,''' '''.top''' and '''.itp '''extension are created with this command. | || 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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|| Let’s close the file. | || Let’s close the file. | ||
− | I will clear the '''terminal''' | + | I will clear the '''terminal''' for clarity in the video. |
|- | |- | ||
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|- | |- | ||
|| Cursor on '''-f''' and '''-o''' flag. | || Cursor on '''-f''' and '''-o''' flag. | ||
− | || This command also generates '''.gro''' file like '''pdb2gmx''' command. | + | || This command also generates '''.gro''' file like before '''pdb2gmx''' command. |
Again '''-f''' denotes input file and '''-o''' denotes output file. | Again '''-f''' denotes input file and '''-o''' denotes output file. | ||
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|- | |- | ||
|| Type''' -c '''. | || Type''' -c '''. | ||
− | || | + | || The '''hyphen c''' flag places the center of the molecule in the center box. |
− | + | ||
− | The '''hyphen c''' flag places the center of the molecule in the center box. | + | |
|- | |- | ||
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|| The''' -d''' flag denotes distance from the center of the box to the boundary. | || The''' -d''' flag denotes distance from the center of the box to the boundary. | ||
− | Here 1 denotes | + | 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. | Increasing the box size will considerably lengthen the '''MD''' run time. | ||
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|| Next, enter the shape of the box, which is cubic. | || Next, enter the shape of the box, which is cubic. | ||
− | If another shape is desired, use the ''' | + | If another shape is desired, use the '''bt''' flag with the shape name. |
|- | |- | ||
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Cubic and hexagonal shapes are popularly used for the bounding box. | Cubic and hexagonal shapes are popularly used for the bounding box. | ||
− | This generates another input ''' | + | This generates another input '''gro''' file, with box size and file name. |
|- | |- | ||
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|- | |- | ||
|| | || | ||
− | || The extent of shift of the coordinates is also mentioned | + | || The extent of shift of the coordinates is also mentioned. |
|- | |- | ||
|| Show screenshot of''' box-added.gro'''. | || Show screenshot of''' box-added.gro'''. | ||
− | || | + | || |
− | + | Notice that, the coordinates have shifted to accommodate aligning with the box. | |
− | Notice that, the coordinates have shifted to accommodate aligning | + | |
|- | |- | ||
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* Steps in a '''MD''' run for a protein in a solvent box | * Steps in a '''MD''' run for a protein in a solvent box | ||
* The '''pdb2gmx''' command and syntax | * The '''pdb2gmx''' command and syntax | ||
− | * About adding a force field | + | * About adding a '''force field''' |
* Generated .'''gro''' and '''.top '''files | * Generated .'''gro''' and '''.top '''files | ||
* About '''editconf''' command | * About '''editconf''' command |
Latest revision as of 11:14, 27 October 2021
Visual Cue | Narration |
Slide Number 1
Title Slide |
Welcome to the spoken tutorial on Creating Input Files. |
Slide Number 2
Learning Objectives |
In this tutorial, we will learn about,
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Slide Number 3
Learning Objectives |
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Slide Number 4
System and Software Requirement |
To record this tutorial, I am using
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Slide Number 5
Pre-requisites |
To follow this tutorial,
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Slide Number 6
Code Files |
* Files used in this tutorial are provided in the Code files link.
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Open a web browser and go to 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. |
Cursor on the flow chart. | I will demonstrate parts of this procedure till the addition of a bounding box. |
Let’s consolidate all our input files into one folder.
From now on, I will not mention this separately. | |
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. |
Type cd Documents and press Enter. | Linux users can change directory to Documents using the cd command as seen. |
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. |
Type mkdir firstmd and press Enter. | I will create a new directory and name it firstmd. |
Type cd firstmd and press Enter. | Change directory to the newly created firstmd directory. |
Slide Number 7
File path for Windows Users |
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Open the File Manager. | Open the File Manager. |
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. |
Open the 1AKI.pdb file in a text editor. | Then, open the pdb file in a text editor. |
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. |
Show water molecules HOH from 1AKI.pdb file. | They are denoted as HOH and present at the end, before the model ends. |
Highlight the HOH from 1AKI.pdb. | If so, be sure to delete them and save the file, before proceeding further. |
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. |
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. |
Structures determined by NMR methods may not contain the water molecules. | |
Save the file and quit the text editor. | Now, save the file and quit the text editor. |
Annotation: Windows users use appropriate path in your system. | Let’s learn a few terminal commands to generate the input files for MD. |
Go to the terminal. | GO back to the terminal. |
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. |
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. |
Highlight -f 1AKI.pdb . | The hyphen f flag denotes the input file and it is 1AKI.pdb. |
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. |
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. |
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. |
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. |
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. |
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. |
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. |
Show file manager with the newly created files. | Open the file manager and notice the newly created files. |
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. |
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. |
Cursor on 4-6 columns. | The 4th, 5th and 6th columns are the atomic coordinate positions of the atom. |
Close the firstmd.gro file.
Press Ctrl+L. |
Let’s close the file.
I will clear the terminal for clarity in the video. |
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. |
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. |
Type -c . | The hyphen c flag places the center of the molecule in the center box. |
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. |
So the box length is a little bigger than the molecule under study. | |
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. |
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. |
Cursor on the details. | The box volume that is created is displayed in cubic nanometers. |
The extent of shift of the coordinates is also mentioned. | |
Show screenshot of box-added.gro. |
Notice that, the coordinates have shifted to accommodate aligning with the box. |
Close the text editor. | Learner may pause the video, and explore the options further. |
Show Gromacs manual website on getting started.
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. |
Slide Number
Summary 8 |
Now let’s summarize. In this tutorial, we learned about,
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Slide Number
Summary 9 |
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Slide Number
Assignment 10 |
For assignment activity, please do the following.
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Slide Number
Assignment 11 |
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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. |
Slide Number 14
Forum for questions |
Post your timed queries in this forum. |
Slide Number 15
Acknowledgment |
Spoken Tutorial Project is funded by MoE, Government of India. |
This is Rani from IIT, Bombay. Thank you for joining. |