[gmx-users] RMSD analysis of protein-ligand complex

[Quin K]

Thank you
Your advice is very helpful
I will try to reparametrize the molecule, which I think is a better
strategy.

On Sun, Oct 6, 2019 at 6:38 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/5/19 1:58 PM, Quin K wrote:
> > Thank you.
> >
> > I examined the trajectory using VMD and noted that ligand had come out of
> > the binding site and is running around.
> > How is this possible? I have used the guidelines in mdtutorials.com to
> set
> > up the system.
> > However it's worth noting that there was a power failure around the same
> > time (23ns) and I had to restart MD with append command.
> > Could this have had an affect on MD? Do I have to recreate trajectory
> file
> > after restarting MD, instead of using the default trajectory?
>
> I imagine it's possible that the power failure caused a corruption in
> some file, and it's too much of a coincidence that just when the power
> failed, your simulation changed radically. I would re-run it.
>
> Also note that a ligand can dissociate from the binding site if the
> topology is not well parametrized, leading to insufficiently strong
> interactions. You shouldn't likely encounter such a problem if you get a
> reasonable CGenFF topology, but it's worth noting as a general problem
> with any ligand parametrization.
>
> -Justin
>
> > Regards
> >
> > On Sat, Oct 5, 2019 at 9:53 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >> On 10/5/19 11:59 AM, Quin K wrote:
> >>> Thank you.
> >>>
> >>> I got following when I analysed Ligand RMSD protein backbone as east
> >> square
> >>> fit.
> >>> Graph <https://photos.app.goo.gl/JZJaLt1BxJi1qgwV7>
> >>> Can you please comment why there's high fluctuation after like 23 ns?
> >>> What could this mean?
> >> Watch the trajectory and see what is going on. Make sure you've properly
> >> re-imaged to account for PBC effects.
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
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> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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