On 3/27/17 8:42 AM, Juan José Galano Frutos wrote:
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?
You need distance as well as orientational restraints. This is done with [intermolecular_interactions], which was a new feature in 5.1. For theory, see dx.doi.org/10.1021/ci300505n
-Justin
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)
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