Re: [AMBER] DNA-ligand system

From: David A Case <>
Date: Mon, 21 Jan 2019 08:52:36 -0500

On Mon, Jan 21, 2019, maya nair wrote:
>Can anyone help with me for doing a MD simulation of a docked structure of
>DNA-ligand system.
>When I am trying to do this so many errors are coming. I am attaching the
>screenshots and the files herewith.

Just to add to what Bill said: your DNA has really unusual hydrogen
positions. As just one example, nucleotide DA 5 in the "C" complex has
protons on both the N3 and N7 positions(!). These don't match the
standard tautomer for DA, and are quite unreasonable chemically.

You should look at how you created the PDB files you are using. The
residue and atom names in the PDB file must match exactly the residue
and atom names in the Amber library, or in any ligand libraries you
load. Once you get used to reading them, the error messages from tleap
are pretty clear in pointing you directly to places where this
one-to-one comparison breaks down. As a start, just remove all
hydrogens from the DNA, and let tleap build them back in. You can then
examine the structure to see if there are any tautomers that are not the
ones you want.

...good luck....dac

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Received on Mon Jan 21 2019 - 06:00:06 PST
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