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

[Justin A. Lemkul]

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
> 
> 

-- 
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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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