[gmx-users] sphere around a protein

[Justin A. Lemkul]

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

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