I have done 10 ns complex simulation for Protein-ligand complex using Gromacs 5.0. the ligand moved out of pocket after 6 ns. Now i want to choose best stable conformation. How can i find the lowest energy conformation from my trajectory?
@Mehul: "Average structure" is not the lowest energy conformer. Consider a torsion angle with two minima; the average structure of the two minima can very well be a maximum.
Cluster the snapshots and energy-minimize the representative structures.
---
But why do you need "the lowest [potential] energy conformation of [the] protein-ligand complex" in the first place?
Hi sana saeed , you do 10ns MD of your complex protein and you get stable on 6 ns . you find a average md trajectory file in folder . It's consider as a lowest energy confermer ...
@Mehul: "Average structure" is not the lowest energy conformer. Consider a torsion angle with two minima; the average structure of the two minima can very well be a maximum.
Hi Sana Saeed, you may want to try the subroutines g_enemat or g_energy to calculate an approximation of the free energy of different groups in your system or the different types of energy involved as a function of time. However, if the ligand spontaneously moved out of its pocket after 6 ns, it seems to me that this complex is not stable at all. If it is a biologically natural complex, than there must be something wrong with your simulation or starting conformation.
thank you all. i did it already. actually i wanted to select minimum energy conformer from trajectory for further simulation as an initial structure. it was just to test if the result can be improved (binding free energy). but it didnt improve.
i did it through clustering.
It may be best to take the minimum energy between the ligand-protein residues (non-bonding) instead of the total energy minimum.
@Sana Saeed, How did you choose the structure with lowest energy after using the clustering command?
Thanks for your help in advance,
Manasa
- Badges
- Science topic