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

Jennifer Williams Jennifer.Williams at ed.ac.uk
Fri Oct 22 13:03:24 CEST 2010


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  

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       
HETATM    2  ONO NOO     1       0.000   0.000   0.000  1.00 0.00       
CONECT    1    2

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.

I am using gromacs 4.0.7



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