From: Elvis Martis <>
Date: Mon, 10 Feb 2020 17:43:14 +0530

The dlg format is not the correct one for adding hydrogens.
I would recommend converting the best conformation from the dlg file to pdb
or mol2 and define bond orders correctly.
Then use this pdb/mol2 in Gaussian.
Best Regards

On Mon, 10 Feb 2020 at 15:54, Sruthi Sudhakar <>

> 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 - 04:30:02 PST
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