Aw: Re: [gmx-users] Umbrella Sampling

[lloyd riggs]

I did this with a small molecule and the ions were in the solvent, but associated with the ligand, and conversly if the site has a Mg or something etc...it wouldn't be restrained in the normal posres.itp unless you made one for them.  It is in the end a matter of view, but I am assuming the change in the binding sites energy would reflect also the ions or the ions being attached to the ligand would not represent a completly solvated ligand (ie energy missing).  The positional restraint I stated meant you can just make a two ion -posres_ion and include it in an .mdp however it might screw your system up if your protein is not positionally restrained, or calphas etc...thus I dont know based on your experiment.  If the ions move into solution it probably doesnt matter (a quick visual of the simulation).  But somone else might have better ideas to help out.

 

Stephan

 

Gesendet: Mittwoch, 31. Juli 2013 um 12:46 Uhr
Von: "Steven Neumann" <s.neuman...@gmail.com>
An: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Betreff: Re: [gmx-users] Umbrella Sampling

They do not dissociate...Are you sure? My mdp specifies only ligand as a
pull_group1. I think it would change having ions in this group included.


On Wed, Jul 31, 2013 at 11:01 AM, lloyd riggs <lloyd.ri...@gmx.ch> wrote:

>
> >will get the PMF profile for my
> >ligand binding or ligand and two ions binding?
>
> It would be the ligand and two ions unless the ions also at some point
> discossiate from the ligand once in solvent. Could add positional restraint
> for them, but dont know how that effects the calculation?
> *Gesendet:* Mittwoch, 31. Juli 2013 um 09:29 Uhr
> *Von:* "Steven Neumann" <s.neuman...@gmail.com>
> *An:* "Discussion list for GROMACS users" <gmx-users@gromacs.org>
> *Betreff:* [gmx-users] Umbrella Sampling
> Dear Gmx Users,
>
> I run SMD to extract the windows for US calculations. The system involves
> negatively charged ligand and protein. I generated the protein-ligand
> complex within self assembly MD simulations.
>
> I pulled my molecule away and two ions were also detached from the protein
> surface being attached to my ligand.
>
> My question: if I run my US caluclation and combine windows by WHAM (I
> specified in my umbrella.mdp my ligand as a pull_group1 and same protein
> residues I pulled it from as pull_group0) will get the PMF profile for my
> ligand binding or ligand and two ions binding?
>
> Steven
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