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

[Jennifer Williams]

Hi Justin,

The .pdb I sent with my last e-mail was a result of trying to add 500  
molecules. The max of 168 were added and then genconf couldn't add  
anymore despite the large vacant space. Trying to add more molecules  
to this .pdb won't work. This is what makes me think the space was  
somehow inaccessible.

If I carry out an mdrun on this structure, the NO molecules distribute  
themselves into this empty space. If I take the structure file  
following MD I can add an extra 24 molecules with genbox.

The worry is not for these small NO molecules where I can use MD to  
create more space. I am also trying to insert larger organic molecules  
and if parts of the unit cell are seen as inaccessible I won't be able  
to get the molecules in there in the first place.


Jenny




Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

>
>
> 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
>
> ========================================
> -- 
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Dr. Jennifer Williams
Institute for Materials and Processes
School of Engineering
University of Edinburgh
Sanderson Building
The King's Buildings
Mayfield Road
Edinburgh, EH9 3JL, United Kingdom
Phone: ++44 (0)131 650 4 861


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