Doubt in the understanding of workflow of binding free energy calculations

[Sarthak Trivedi SVNIT]

Dear Sir,

 

I am having a doubt regarding a workflow of binding free energy calculations of MMPBSA. As per my understanding from the workflow image given on website (As I can't attach a file here), the trajectories of complex, receptor, and ligand are analysed and if they are dry then they are going for clean up and if they are not dried then they are sent for the further process. So. what do we mean by dry trajectories? As far as I got it, it means a trajectory without water, right ? if I am wrong them pardon me and please correct my understanding. If I am right, then please comment on the conflict bolded above. 

 

 

 

Thank you in advance.

 

Regards,

Sarthak.

[Mario Sergio Valdes]

Sorry for the confusion. Actually, in this case, it refers to the action, not the state. That is, the question is related to whether it is necessary to generate the dry trajectory, not to whether the trajectory is dry or not. These methods are based on explicit solvent, so all water molecules (in most cases) must be removed. This is done to save time. If the trajectory is passed as such, it is cleaned up, but if the user only passes the complex trajectory (only receptor+ligand, without water, ions, or any other molecules), then this step is omitted (must set solvated_trajectory = 0). We are working on a new version of the documentation that uses configurable diagrams and not images, so we will take this issue into account. Thanks