[gmx-users] sphere around a protein

[Justin A. Lemkul]

shivangi nangia wrote:
> Hi,
> 
> Please correct me if I am wrong.
> 
> In that case then, I will have polyhisitine in the box size 12 12 12 and 
> then If I add dhb anions and Li cations, they will be placed randomly in 
> the box.
> 
> When I add then the 1 Li cation, water methanol sphere, how is it 
> necessary it will cover/solvate all the ions that I had added in the box?
> Some might still be in open space of the box?
> 

You need to start with whatever molecules you want to solvate in a suitable 
configuration.  Insert them with genbox -ci -nmol and a small box, then solvate 
with the sphere as before.

-Justin

> Thanks,
> SN
> 
> 
> 
> 
> 
> On Wed, May 25, 2011 at 3:43 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Justin A. Lemkul wrote:
> 
> 
> 
>         shivangi nangia wrote:
> 
>             Hi Justin,
> 
>             Thanks a lot!
>             Things worked.
> 
>             Now I, however, have a different problem in extension to
>             what I am doing.
> 
>             I was able to created a sphere of water and methanol around
>             a polypeptide and 1 Li+ ion.
> 
>              editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro
>              genbox -cp onlyli.gro -cs mix.gro -shell 3 -o li_sol.gro
>              genbox -cp li_sol.gro -cs mix.gro -shell 3 -o 6nmshell.gro
>              editconf -f his20.gro -d 0 -o onlyhis.gro
>              editconf -f onlyhis.gro -c -box 12 12 12 -o hisinbox.gro
>              genbox -cp hisinbox.gro -cs 6nmshell.gro -o 6sys.gro
> 
> 
>             Now I need to add few more Li ions and anions in the sphere.
> 
>             I tried doing that,
>             genbox -cp 6sys.gro -ci 1dhb.gro -nmol 20 -o added_dhb.gro
>             -p topol.top
> 
>             (1dhb.gro is 2,5-dihydrobenzoic acid anion)
> 
>             But, since the sphere 6sys.gro is essentially in a box, the
>             dhb anions ...some got randomly placed inside the sphere and
>             some in the open spaces of the box in which 6sys.gro is sitting.
> 
>             How can I place all the anions and then Li+ ions
>             specifically inside the sphere?
> 
> 
>         That's what genion is for.
> 
> 
>     I take that back, genion doesn't work for polyatomic ions.  The
>     better approach is to construct your system with solute, ions (which
>     in this case are just other molecules floating around), etc, before
>     adding the sphere of solvent.
> 
> 
>     -Justin
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================