[gmx-users] sphere around a protein

[shivangi nangia]

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?

Thanks,
SN





On Wed, May 25, 2011 at 3:43 PM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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