[gmx-users] sphere around a protein

[shivangi nangia]

Hello,

Thanks Justin, I am getting somewhere but still running into problems.

     Okay, I have a 6 nm sphere (one Li ion surrounded by 1:1 water-methanol
mixture) in 12 nm box.
      I did the following:
editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro
genbox -cp onlyli.gro -cs mix.gro   -shell 6 -o li_sol.gro


    Then, used genbox -cp protein.gro -cs sphere.gro
with only 1 molecule of histidine I get the same error as with polyhistidine
( 20 )

Fatal error:
One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the cut-off.

How can I resolve this?

help needed.

Thanks,
SN

On Sun, May 8, 2011 at 5:12 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> shivangi nangia wrote:
>
>> Hi Justin and other gmx-users,
>>
>> I want to make a sphere around a protein (5nm).with Li ions and anions.
>>
>> Justin, as you had suggested to use genbox -shell option, I tried using it
>> but i realized that since my protein is a long tube like structure, the
>> shell option generated a cyclinder around the protein.
>>
>> The solvent around the protein is 1:1 water-methanol (pre-prepared mixture
>> n a gro file)
>>
>> If I try to start with a ion and solvate it with my solvent (1:1 water
>> methanol) using -shell option, I do get a sphere but then I am unable to
>> insert the protein in the system.
>>
>>
> And why not?
>
> genbox -cp protein.gro -cs sphere.gro
>
> should do exactly what you want, provided the sphere is large enough for
> the protein.
>
> -Justin
>
>
>  Is there another feasible route to get to my desired configuration of the
>> system ?
>>
>> Thanks in advance
>>
>>
>> Best,
>> SN
>>
>>
>>
>>
> --
> ========================================
>
> 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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