Dear Gromacs users I was wondering if there exists any technique that sets distance restraint between specified ligand (atoms) and the protein(atoms) in Gromacs. I am simulating a system which contains metal ions coordinated to the Ligand. I looked in to the mailing list and Gromacs manual and figured out that *genrster* can be employed, to set distance, position and dihedral restraints. Unfortunately i also stumbled on the fact that restraints between systems is not possible.
Since force fields are not good at handling chelation between metal atoms, i find that the metals drifting away from the coordinated ligand atoms during the course of simulation, hence i introduced position constraints for the metal and ended up realizing that the coordination distance between the ligand and the metal exceeds the permissible range and the angles between the chelating atoms gets distorted and some coordinating residues like Histidine and Aspartic acid also moves away from the metal. Hence, i was wondering if l anyone knows of any method (apart from QM/MM) that can help to set distance restraints between the protein (metal ion ) and the ligand, also any suggestion that could help in handling ligand metal chelation is welcomed. Thanking in advance Regards Vijayan.R
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