Respected group members,
I have been trying to run a md simulation using the best docked structure
of my ligand with nucleic acids. I obtained the docked structure from the
dlg file in pdb format. But I cannot add the missing hydrogens or generate
the parameter files for the same.
I used the gaussian ESP charge calculated ligand conformation for docking
and when I used the same for running MD, using "combine" command in tleap,
my MD runs fine and I could generate all the parameters. But the same
cannot be done for the docked ligand conformation. So should I continue
with the charge fitted initial conformation of the ligand. If not please
suggest a way to use the docked ligand conformation for running MD
simulation(including the addition of hydrogen).
Thanking you in advance.
Sruthi Sudhakar
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Received on Mon Feb 10 2020 - 02:30:02 PST
