[gmx-users] sphere around a protein

[Justin A. Lemkul]

shivangi nangia wrote:
> Hi Justin,
> 
> 
> Revisiting some of the calculations I had tried to do few days back.
> 
> Just as a recap I am trying to build a sphere around the protein.
> 
> As you had suggested in the last messgae of this thread to make a new 
> directory. I did that.
> 
> I used the following commands:
> 
>   editconf -f 1li.gro -c -box 15 15 15 -o onlyli.gro
>   genbox -cp onlyli.gro -cs mix.gro   -shell 6 -o li_sol.gro
>   genbox -cp his1.gro -cs li_sol.gro
> 
> *
> 1li.gro is:*
> 1 Li ion
>   1
>     1LI+     LI    1   1.736   0.839   0.257
>    1.86824   1.86824   1.86824
> 
> *onlyli.gro is:*
> 1 Li ion
>     1
>     1LI+     LI    1   7.500   7.500   7.500
>   15.00000  15.00000  15.00000
> 
> *mix.gro ( pre-made mix of 1:1 :: water: methanol)*
> 
> li_sol.gro des look like a sphere after seeingin vmd.
> 
> his1.gro is:
> UNNAMED
>   14
>     1HISH     N    1   0.000   0.000   0.000
>     1HISH    H1    2  -0.033   0.000  -0.094
>     1HISH    H2    3  -0.033  -0.082   0.047
>     1HISH    CA    4   0.146   0.000   0.000
>     1HISH    CB    5   0.204   0.120  -0.077
>     1HISH    CG    6   0.291   0.076  -0.190
>     1HISH   ND1    7   0.240   0.009  -0.299
>     1HISH   HD1    8   0.145  -0.014  -0.315
>     1HISH   CD2    9   0.425   0.089  -0.215
>     1HISH   CE1   10   0.345  -0.019  -0.382
>     1HISH   NE2   11   0.458   0.027  -0.333
>     1HISH   HE2   12   0.549   0.020  -0.374
>     1HISH     C   13   0.195   0.000   0.146
>     1HISH     O   14   0.118   0.000   0.242
>    2.50220   0.24060   2.47531
> 
> 
> 
> I get the following error yet again:
> 
> 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.
> 
> 

Look at the box vectors of his1.gro - a sphere of solvent with a radius of 6 
cannot fit inside a box that is 2.5 x 0.2 x 2.5 nm^3.

-Justin

> ------------------------------------------------------
> 
> Thanks a lot in advance.
> 
> Sorry about reviving few days old thread.
> 
> 
> Thanks,
> SN
> 
> 
> 
> 
> On Mon, May 9, 2011 at 6:21 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     shivangi nangia wrote:
> 
>         Hi Justin,
> 
>         I used 15 nm cubic box and 6 nm shell.
>         I again tried to insert only 1 histidine molecule in the sphere.
>         I get the same error
> 
>         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.
> 
> 
> 
>     Please provide the exact command that gives the error.  I cannot
>     reproduce this using a shell value less than half a box vector.  You
>     may also want to try starting from a clean directory - get rid of
>     old files and intermediates so you're sure you're using the right files.
> 
>     -Justin
> 
> 
>     -- 
>     ========================================
> 
>     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

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