Pdb file for the lowest energy conformation of protein

User discussions
1

GROMACS version:2020
I have done 100 ns simulation for my Protein using Gromacs 2020… Now i want to choose best stable conformation . How can i find the lowest energy conformation from my trajectory?
actually i need a pdb file of lowest energy conformation for computing cavities, tunnels,…in MOL2 package.

…

2

Hi,

To extrand a pdb file from a xtc file you can use gmx trjconv, select a time (-dump) and then ask to save as pdb -o name.pdb

Concerning the conformation selection, if you are interest at the lowest free energy conformation (then you have to look at the most populated conformation), assuming that your simulation is converged. Or?

Kind regards
Alessandra

3

Hi dear alevilla,
I am a new user and dont know how can i find the lowest energy conformation from my trajectory…
lf you have the command lines, can you send me them?

Best regards
Azam

4

Hi Azam,
Before production run in Gromacs, we do energy minimization and NVT and NPT equilibration. So we already have a nice conformation to start. In your production run, you can check if RMSD and energy is changing with time. If not, then it is already in equilibrium conformation and you can do analysis using this structure. After sufficient run, MD simulation gives the most stable conformation. I have attached two researchgate links, which may be helpful.
https://www.researchgate.net/post/How_can_I_find_the_lowest_energy_conformation_of_Protein-ligand_complex_after_10_ns_simulation
https://www.researchgate.net/post/molecular_dynamics_and_conformation_analysis
Thank you, hope this will help :)
Anirban

5

There is no guarantee of this, and MD simulations are not driven by free energy, which is what is truly necessary to say one has the most “stable” conformation. The total potential energy in the MD simulation is not something that force fields are generally parametrized to ascribe any meaningful value, so there is no way to know if you are in a global energy minimum at any point during the trajectory.

6

Thank you Justin for the correction and valuable comments :)