[gmx-users] Restraining Protein-ligand distance

[Juan José Galano Frutos]

Hi there,

I am trying AFEC simulations in complex (ligand-protein), but sometimes I
get the ligands out the binding site, but I dont want that scenary. I was
thinking the situation of applying distance retraints between a ligand and
a protein was already solved in GROMACS version later 5.0... without any
necessity of making a hybrid system. But, I'm using version 5.1, and it
seems that's not possible doing so, because I'm obtaining errors.
Is there currently any happy solution to restraint ligand-protein distance?
or Has one to still go through the unbrella pulling option to do that?

In the case I need to do a hybrid system what would be a good procedure?

Thank you very much.


Juan José Galano Frutos

Department of Biochemistry and
Molecular and Cellular Biology,
Faculty of Sciences,
University of Zaragoza
Pedro Cerbuna # 12, 50009
Zaragoza (Spain)
+34 976 76 28 06

Institute for Biocomputation and
Physics of Complex Systems (BIFI)
Mariano Esquillor, Edificio I + D - 50018
Zaragoza (Spain)