[gmx-users] genconf to insert small molecules triclinic unit cell

[Justin A. Lemkul]

Jennifer Williams wrote:
> 
> Hi Justin,
> 
> Thanks for the response (again!).
> 
> I would be happy if genbox inserted molecules randomly (within the box 
> defined by my .pdf file) but the output doesn't look random but subject 
> to some strange (symmetry?)constraints which don't allow random 
> insertions into some areas of my unit cell.
> 
> The molecules will crowd into one space leaving another portion of the 
> cell completely empty. The inserted molecules assume the shape of a box 
> whilst the rest of my structure is a triclinic cell.
> 
> One pic is probably worth a thousand words. I've attached a .pdb of the 
> final structure. I'd appreciate if you could tell me if this is normal 
> output for genbox,
> 

I see nothing wrong with it.  Looks like genbox started adding molecules on one 
"side" of your box, and continued adding until it reached 100, then stopped. 
Looks like you simply have more than enough space to add more of your NO 
molecules, that's all.  The molecules are all within the unit cell, so I see no 
issue.

If you want a more homogeneous distribution of NO, you may have to come up with 
a different method.

-Justin

> Thanks very much
> 
> Jenny
> 
> 
> 
> 
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
> 
>>
>>
>> Jennifer Williams wrote:
>>> Hi,
>>>
>>> I have a strange problem when I try to insert small molecules into  
>>> my cell using genconf. Here the cell is a crystalline metal-organic 
>>>  framework with lots of space for the molecules inside. The edges of  
>>> the metal organic framework defined the pbcs.
>>>
>>> When I view the final structure, the inserted molecules appear to  
>>> have a different symmetry to that of the MOF/cell. They notieably  
>>> avoid some empty regions inside the box and are inserted outside  
>>> regions of my triclinic cell. The inserted molecules don?t occupy a 
>>>  triclinic shape at all.
>>>
>>> I have used this feature before on a similar triclinic cell and it  
>>> worked perfectly. I can?t tell what I am doing wrong this time.
>>>
>>> I outline the steps I take below.
>>>
>>> 1. I am trying to insert a number of molecules of NO into a  
>>> triclinic crystal cell. The pdb file of the crystal cell has the  
>>> following cell parameters.
>>>
>>> CRYST1   25.885   25.885    6.806  90.00  90.00 120.00 P 1           1
>>>
>>> This is the pdb file of the small molecule I am trying to insert:
>>>
>>> CRYST1   25.885   25.885   27.2232  90.00  90.00 120.00 P 1           1
>>> HETATM    1  NNO NOO     1       1.150   0.000   0.000  1.00 0.00   
>>>           N
>>> HETATM    2  ONO NOO     1       0.000   0.000   0.000  1.00 0.00   
>>>           O
>>> CONECT    1    2
>>> END
>>>
>>> I use the following commands:
>>>
>>>  To centre the cell:
>>> editconf -c -f  MOF.pdb -o MOF_centered.pdb
>>>
>>> To make a 1x1x4 box ( I need to increase the length in z) so that I 
>>>  can use sensible cut-offs later on
>>>
>>> genconf -nbox 1 1 4 -f MOF_centered.pdb -o MOF_4c.pdb
>>>
>>>
>>> To add the NO molecules:
>>>
>>> genbox ?cp MOF_4c.pdb -ci NOO.pdb -nmol 100 -o inserted_NO.pdb
>>>
>>> Any ideas appreciated as I have been going around in circles.
>>>
>>>
>>
>> When using genbox -ci, there is no guarantee of any type of symmetry.
>> It inserts molecules randomly, wherever it finds space.  I don't think
>> you're doing anything wrong, I think you're just encountering a
>> limitation of genbox.
>>
>> -Justin
>>
>>> I am using gromacs 4.0.7
>>>
>>> Thanks
>>>
>>> Jenny
>>>
>>>
>>
>> -- 
>> ========================================
>>
>> 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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> 
> 
> 
> 
> 

-- 
========================================

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

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