Dear Dr. Case,
thanks for your valuable suggestions. I will apply your suggestions and
repeat the simulation.
Thank you again,
Erdem
David A Case <david.case.rutgers.edu>, 7 Eyl 2020 Pzt, 15:37 tarihinde şunu
yazdı:
> 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.Â
> > 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.
>
> ....regards....dac
>
>
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Received on Mon Sep 07 2020 - 06:30:03 PDT
