Respected researchers:
I have just done md simulation through gromacs, also total binding energy calculation of protein ligand complex through g-mmpbsa tool. Now i want to analyze hydogen bonding and other interaction between protein and ligand complex. What should i do?
i am waiting for your extreme answer.
Thanks a lot
GROMACS has a built-in program specifically for analyzing hydrogen bonding, called gmx hbond. I suggest you investigate the manual for the other analysis tools that are built into GROMACS, as there are many.
Beyond that, issues of protein-ligand interactions are discussed in one of my tutorials (http://www.mdtutorials.com/gmx/complex/index.html)
Article From Proteins to Perturbed Hamiltonians: A Suite of Tutorial...
GROMACS has a built-in program specifically for analyzing hydrogen bonding, called gmx hbond. I suggest you investigate the manual for the other analysis tools that are built into GROMACS, as there are many.
Beyond that, issues of protein-ligand interactions are discussed in one of my tutorials (http://www.mdtutorials.com/gmx/complex/index.html)
Article From Proteins to Perturbed Hamiltonians: A Suite of Tutorial...
VMD also has a built-in analysis for hydrogen bonding and salt bridges. It is extremely easy to use directly in the GUI. Just load your coordinates and trajectory, the extensions tab of the main window, analysis submenu, and select either hydrogen bonds or salt bridges. You can customize your cutoff distance and angle (e.g. to look at only strong hydrogen bonds), select only specific residues, or a neat trick for example is to select 1 as chain A (enzyme) and select 2 as chain B (ligand) to get only the hydrogen bonds that occur at the interface. This outputs the %occupancy of the hydrogen bond, i.e. what % of the simulation the donor-acceptor pair are within the specified distance/angle of each other. I'd play with a few MD data analysis programs to figure out which you like better for your typical analysis workup.
Justin Lemkul respected sir, i am doing md simulation on gromacs and i have to perform 50 ns simulation so what kind of changes i have to perform in my .mdp file.
kindly find the attachment of .mdp file and after changes then send back it to me.
I shall be very thankful to you.
Said, simply change the nsteps to 25000000 inorder to give a 50 ns mdrun.
thanks for the reply
respected sir, i changed it but it didn't work.
could you perform that changes in .mdp and sent it to me?
- Badges
- Science topic