[gmx-users] sphere around a protein

Wed May 25 21:39:43 CEST 2011

Hi Justin,

Thanks a lot!
Things worked.

Now I, however, have a different problem in extension to what I am doing.

I was able to created a sphere of water and methanol around a polypeptide
and 1 Li+ ion.

  editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro
  genbox -cp onlyli.gro -cs mix.gro -shell 3 -o li_sol.gro
  genbox -cp li_sol.gro -cs mix.gro -shell 3 -o 6nmshell.gro
  editconf -f his20.gro -d 0 -o onlyhis.gro
  editconf -f onlyhis.gro -c -box 12 12 12 -o hisinbox.gro
  genbox -cp hisinbox.gro -cs 6nmshell.gro -o 6sys.gro

Now I need to add few more Li ions and anions in the sphere.

I tried doing that,
genbox -cp 6sys.gro -ci 1dhb.gro -nmol 20 -o added_dhb.gro -p topol.top

(1dhb.gro is 2,5-dihydrobenzoic acid anion)

But, since the sphere 6sys.gro is essentially in a box, the dhb anions
...some got randomly placed inside the sphere and some in the open spaces of
the box in which 6sys.gro is sitting.

How can I place all the anions and then Li+ ions specifically inside the
sphere?

Thanks a lot,
SN

On Wed, May 25, 2011 at 1:18 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ========================================
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