From: Sruthi Sudhakar <sruthisudhakarraji.gmail.com>
Date: Mon, 10 Feb 2020 16:26:43 +0530

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
AMBER mailing list
Received on Mon Feb 10 2020 - 02:30:02 PST
Custom Search