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

[Quin K]

I generated ligand topology using parachem website, I didn't do any
adjustments after, just used it as it is.

On Tue, 17 Dec 2019, 1:11 pm Justin Lemkul, <jalemkul at vt.edu> wrote:

>
>
> On 12/15/19 1:18 PM, Quin K wrote:
> > 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?
>
> Possibly.
>
> > Also would  restraining the protein and ligand independently help?
> > Or is generating a better ligand topology the only way to solve this
> issue?
>
> It depends on how you validated the ligand topology. Do you have
> evidence that it is of sufficiently high quality?
>
> -Justin
>
> > 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
> >>
> >> --
> >> ==================================================
> >>
> >> 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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> >>
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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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