[gmx-users] sphere around a protein

[Justin A. Lemkul]

shivangi nangia wrote:
> Dear Justin,
> 
> No.
> 
> I am still preparing the system. I want the protein in the solvent sphere.
> 
> 

I see now.  You're setting a 12-nm cubic box, but then using a shell of 6 nm, 
which causes neighbor searching to occur throughout the entire box.  The maximum 
value of -shell must be less than 1/2 the shortest box vector, so either set up 
a larger box, or a smaller value of -shell.

-Justin

> 
> On Sun, May 8, 2011 at 9:29 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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>
>         <mailto: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> <http://vt.edu> | (540)
>         231-9080 <tel:%28540%29%20231-9080>
>            <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 <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

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