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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