Docking of Ligand in a membrane protein


So I am working on a membrane protein and I want to understand how a particular ligand binds to the binding pocket. So, I want to first do a random search to find the residues which are interacting with the ligand.
In the web-server, for the final refinement step, I would like to use DMSO as the solvent. In that case, what should I keep the value for Eelec?

Also what would be the recommended number of models that I should generate initially?

I would be grateful for the help.

Thank you

Don’t change the dielectric.

And if using the 2.4 server make sure to then to include the solvent for the final refinement.

I would increase the sampling to 10000/400/400 - as explained on our protein-ligand tutorial:

Hi there, I am trying to assess if two proteins interact (docking a ligand on a surface receptor complex), but when I press the submit button, it does not register the job.

Can you please advice on this one?

Thank you


Probably some validation error in your submission that prevents you to submit

At each stage check carefully all messages appearing on top!