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

[Quin K]

Hi
Thank you!!!

Let's say during restraining of ligand, if I increased  the -fc value to
10000 (i had 1000) or higher and equilibrated it for longer time like 1 or
2 ns (I had 100ps), would it help?
Also would  restraining the protein and ligand independently help?
Or is generating a better ligand topology the only way to solve this issue?

Thanks in advance.
Regards

On Sun, Dec 15, 2019 at 11:07 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/15/19 11:47 AM, Quin K wrote:
> > Hi All,
> >
> > Further to following email, i just noted that the ligand has detached
> from
> > binding site.
> > Is there a way to prevent this from happening?
> > It happened to me once before with the same complex.
>
> If the ligand is dissociating on a time scale that it shouldn't (e.g.
> you expect it should stay bound), that suggests the ligand topology is
> insufficiently accurate, arising from interactions with the protein that
> are too weak and/or interactions with water that are too strong.
>
> > Doesn't boundary conditions prevent ligand from detaching from binding
> site
> > in protein during MD simulation?
>
> No, PBC does not do this. A periodic system contains copies of whatever
> is happening in the central image.
>
> -Justin
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
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