Re: [AMBER] Simulation of 10 ns DNA - ligand intercalation

From: David A Case <>
Date: Mon, 7 Sep 2020 08:37:07 -0400

On Mon, Sep 07, 2020, Erdem Yeler wrote:
> I docked my boron containing a ligand (with boron's force field) with DNA.
> After 10 ns it seems ligand is intercalating DNA. Potential energy diagram
> seems OK it is very stable. But RMSD increases up to 9A and it¬ is still
> increasing (after 10 ns). is it normal or should it be lower? if it should
> be lower how can I fix this?¬ I attached first and the last frame of
> simulation. if amber members checked and shared their valuable comments I
> would be very happy.¬
> here is first and the last frame of simulation:

You "after" structure looks pretty bad. If the starting structure comes from
something experimental (e.g. and Xray structure), I'd say that something has
gone wrong. Make sure that a WC helix of DNA alone (in your hands) stays
stable. You might also look for any bad contacts in your starting structure.

Also, check whether the structural distortion occurs early or late in the
simulation. And make sure that you have run a long-ish equilibration with
restraints on the starting structure, so the the water and ions are
well-equilibrated, before allowing the DNA-ligand complex to move very much.


AMBER mailing list
Received on Mon Sep 07 2020 - 06:00:05 PDT
Custom Search