[gmx-users] constraints between protein ligand - metal chelation
biovijayan at gmail.com
Sun May 20 03:42:25 CEST 2012
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
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