Minimization problem

[Manuel Llanos]

Hi !
I have a problem regarding the minimization. When I use this option, the ligands are not translated into the active site, instead they are minimized in other coordinates and of course the simulation occurs in seconds. If I don't use this option instead, the program works fine for docking the ligands or re-scoring a particular pose. I've tried both, rigid and flexible sidechains, with the same results.
I'm using Smina Apr 2 2016, downloaded as binaries from here.
Finally, I would like to ask you for some options of the program which I don't really understand what they mean:
--local_only
--factor (suggested values)
--force_cap (suggested values)

Thanks in advance!

Manu

[David Koes]

Minimization will find the local optimum from the current position. I'm not sure what you mean by "they are minimized in other coordinates", but I suspect it is doing exactly what it is suppose to. If the ligand isn't already positioned in the active site, you should use docking.

localy_only provides backwards compatibility with the AutoDock Vina option with the same name, It is very unlikely you want to use it.

--factor arg approximation factor: higher results in a
finer-grained approximation
--force_cap arg max allowed force; lower values more gently
minimize clashing structures

These are already set to reasonable defaults. factor should probably be a hidden argument; I'm not going to bother to explain it more than it already is.

force_cap places a cap on forces. If you are starting with a severely clashing ligand, it will have a very large force on it that will fling it out of the binding site. Lower the cap results in smaller forces and less dramatic movement. It generally only have a meaningful impact if you start with significant clashes.