[gmx-users] sphere around a protein

[shivangi nangia]

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.


------------------------------------------------------

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> 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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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