the calculation of transitions between ligands with different total charges about pmx HOT 2 OPEN

Hi.

One can use the double-system/single-box method, where you have two copies of the hybrid ligand in the simulation box but at opposite states. Eg. first one in the binding pocket and transitioning from A to B state and the second one in the solvent simultaneously transitioning from B to A. The solvent copy should be kept far away from the protein to avoid interactions between them, eg. by using a restraint between the two and a fairly large simulation box size to also prevent interactions across the periodic boundary. See Figure 3 in doi:10.1007/978-1-4939-1465-4_9.

Cheers,
Yuriy.

from pmx.

Hello,

Thank you for your prompt response.

If I understand correctly, with the pmx command, I should employ "pmx double box" to create a pdb file for the complex of StateA and the ligand of StateB (the complex of StateB and the ligand of StateA). From there, I can generate a topology file.

Additionally, when applying restraints, should I use NPT run with restraints based on parameters such as the distance between ligand centers of mass?

I appreciate your further guidance on this matter.

from pmx.