the atom order in ligand shows mismatch and thus i cannot proceed to next step
Prefer taking the best docked posed complex and then proceed towards MD.
Anwesh Pandey i could not proceed to MD. running charmm shows ligand mismatch between old and new ligand. further gauss view of docked compound shows the bond of macrocycle broken at nitrogen atom
Anwesh Pandey i docked the ligand and protein using PyRX. then i generated a single pdb file for docked ligand-protein complex using edu-PyMol. then when i load my pdb file in CHARMM, it shows ligand mismatch.
Hi Siddartha Gautam,
May be it is a problem with parametrization of the ligand?
which software are you using for MD? I would suggest you to consider AMBER forcefields. If you are using GROMACS, parametrization of the ligand could be achieved using a semi QM/MM procedure using ACPYPE. You will have to install AMBERTOOLS (available free of cost).
All the best.
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