In our latest experiments, we did a molecular docking simulation by using "CHARMm" forcefield and it went well. However when we were doing molecular dynamics simulation by using an exact same forcefield, the ligand-protein complex seems to have an issue (the ligand 'fly' away from the protein when the production stage begin'. So we try again by using "GROMOS" forcefield and surprisingly the issue seems to be gone. But was that acceptable ? Thanks.
note: we're using MOE software for docking, and GROMACS for MD simulation
Molecular dynamics (MD) trajectories (of protein-ligand complexes) will differ if there are differences in the initial atomic coordinates, velocities, simulation protocol/method, and/or force field.
Artificial dissociation of a ligand likely indicates a poor-quality ligand topology. What "worked" for an in vacuo docking may not be suitable for MD in solution. The fact that a different force field "works" likely indicates a better-quality ligand topology. How did you generate each?
The theoretical analysis of biomolecules permits the study of relationship between structure, function and dynamics at atomic and sub atomic level. it is not yet feasible to treat these systems using quantum mechanics. many force field predicted tools based on potential energy functions like AMBER, CHARMM. It does not analyze the 3D structure of biomolecules which are drastically modified. as possible to keep the structure of protein (receptor) in original state and try again molecular dynamic simulation using CHARMM, U get the similar result obtained by GROMOCS.
Concentrate on to check the accuracy of protein structure. number of softwares have an ability to correct the error prone structure of protein automatically.
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