Difference between revisions of "Gromacs/C2/Creating-Input-Files/English"

Title Slide

Learning Objectives

• 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

Learning Objectives

• Specifiy the size and shape of bounding box for MD
• editconf command

System and Software Requirement

• Ubuntu Linux v20.04 OS
• Firefox web browser v92
• gedit 3.36
• Gromacs v2021.2

Pre-requisites

https://spoken-tutorial.org

• Learner must be familiar with basic computer skills.
• For pre-requisite tutorials, please visit this site.

Code Files

• Please download and extract the files.
• Make a copy and then use them while practising.

Go to the Gromacs manual link as seen here.

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

From now on, I will not mention this separately.

Windows users can open the Ubuntu 20.04 app.

Hence, type mkdir Documents before changing path with cd command.

FIle path for Windows Users

• Detailed instructions are provided with the tutorial.
• Use this path when locating, opening or moving files, which are saved here.

For Windows users this path is likely to be in C drive.

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

Lysozyme is a well studied, stable and model protein.

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

We will not add them.

The Gromacs commands will add the hydrogens for the user later on.

All the commands start with the phrase gmx which calls Gromacs.

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

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

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

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

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.

By convention, .ff denotes force field files.

The path of the file is also seen.

Type 2 and press Enter.

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

Type 2 for tip4p and press the Enter key.

Learner is encouraged to pause the video and explore more on the solvent addition.

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

Notice that, this command has also added hydrogens.

Press Ctrl+L.

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

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

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

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

The hyphen c flag places the center of the molecule in the center box.

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

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

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

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

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

Notice that, the coordinates have shifted to accommodate aligning in the box.

https://manual.gromacs.org/archive/5.0.4/online/getting_started.html#setup

The link is shown here.

Summary 8

• 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

Summary 9

• Define the size of a bounding box
• Set the position of the molecule in the box

Assignment 10

• 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.

Assignment 11

http://www.mdtutorials.com/gmx/

• Choose a tutorial of your choice and read it.

Spoken Tutorial Project

Please download and watch it.

Spoken Tutorial workshops

Please write to us.

Forum for questions

Acknowledgment