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

[Justin Lemkul]

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
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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