[gmx-users] sphere around a protein

[shivangi nangia]

Dear Justin,

No.

I am still preparing the system. I want the protein in the solvent sphere.



On Sun, May 8, 2011 at 9:29 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> shivangi nangia wrote:
>
>> 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.
>>
>>
> I presume this is from mdrun?  Your system is collapsing.  Without an .mdp
> file, it is not possible to diagnose anything.
>
> -Justin
>
>  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<mailto:
>> 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 <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
>
> ========================================
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