Dear researcher,
I did a protein ligand Molecular Dynamic simulation and protein MDS for 50 ns both. In the Protein simulation, the RMSD is stable till 50ns. But when i add the ligand and simulate same protein was stable till 15ns and after that it shows abrupt pattern of RMSD (Fig attached). After 15 ns the ligand is detached from protein(Figure attached). it is the problem with the MDS parameters? I did the simulation using GROMACS 4.5.6.
Please provide the probable reason for this kind of results.
Thanks in advance.
This looks simply like an issue of the ligand jumping across periodic boundaries. Correct for PBC effects and run the analysis again. It should also be obvious from visualization if the complex reaches a boundary at the instant the RMSD spikes.
This looks simply like an issue of the ligand jumping across periodic boundaries. Correct for PBC effects and run the analysis again. It should also be obvious from visualization if the complex reaches a boundary at the instant the RMSD spikes.
There may be a problem associated with simulation parameters. I suggest you to simulate using desmond which generates protein-ligand contact for entire simulation time.
Thanks justin sir and Dev sir
Dear Justin sir,
I used this command for correct the PBC
trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact
After that i visualize result in to VMD and i also created a movie. Which i attached with this mail. In this movie ligand is detached from protein. For that reason RMSD look like this type.
Please suggest me sir, I am a learner of GROMACS.
The ligand does not seem to be very much "in" in the beginning of the simulation. Is there a deep pocket on the protein surface to which the ligand was docked?
The "dissociation" is still extremely sudden and seems artificial to me. Without showing the box (and therefore the position of the protein relative to the periodic boundaries) it is still impossible to say. Note that a single pass through trjconv is often insufficient for post-processing complex systems. Please follow: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
It is also possible that your ligand topology is simply of inadequate quality and thus the dissociation is real (in the context of the simulation) but ultimately artificial (with respect to reality). What force field are you using? How did you parametrize the ligand? Is the affinity of the ligand for this site known? If it is a weak-binding ligand, maybe this isn't unrealistic.
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