Gromacs/C2/Creating-Input-Files/English
{border=1 || 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,
- 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
|- || Slide Number 3
Learning Objectives || * About selecting a force field
- Specifiy the size and shape of bounding box for MD
- editconf command
|- || Slide Number 4
System and Software Requirement || To record this tutorial, I am using
- Ubuntu Linux v20.04 OS
- Firefox web browser v92
- gedit 3.36
- Gromacs v2021.2
|- || Slide Number 5
Pre-requisites
https://spoken-tutorial.org || To follow this tutorial,
- Learner must be familiar with basic computer skills.
- For pre-requisite tutorials, please visit this site.
|- || 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.
|- || 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 Documents before changing path with cd command.
|- || Type mkdir firstmd and press Enter. || I will create a new directory and name it firstmd.
|- || Type cd firstmd and press Enter. || Change path to the newly created firstmd directory.
|- || 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.
|- || Open the File Manager. || Open the File Manager.
|- || Copy 1AKI.pdb to the firstmd directory. || Copy the 1AKI.pdb file input file to this directory.
For Windows users this path is likely to be in C drive.
|- || 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 well studied, stable and 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 the user later on.
|- || || 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 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 forcefieds are listed, for the user to pick from.
|- || Cursor on the details page. || The details off 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.
Hence I want to select AMBER99.
To select AMBER, type 4 as seen here and press the Enter key.
|- || Cursor and highlight the response on the terminal. || Gromacs returns the force field that will be used as amber99.ff.
By convention, .ff 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 more on 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 screen 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 pdb2gmx command.
Again -f denotes input file and -o denotes output file.
|- || Type -c . || Cubic and hexagonal shapes are popularly used for the bounding box.
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 1nm, 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 in nanometer.
|- || Show screenshot of box-added.gro. || Let’s open the box-added.gro in a text editor.
Notice that, the coordinates have shifted to accommodate aligning in 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,
- 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
|- || Slide Number
Summary 9 ||
- Define the size of a bounding box
- Set the position of the molecule in the box
|- || 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.
|- || Slide Number
Assignment 11
http://www.mdtutorials.com/gmx/ || * Go to the website seen below.
- Choose a tutorial of your choice and read it.
|- || 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.
|- |}
