I created iron pyrite nanocluster in material studio 7.0 and exported it as .pdb file.
I downloaded martinize.py to convert this nanocluster to coarse grain and create simultaneously cg.gro and topology file in GROMACS 4.6.5.
But, the topology file and cg.gro file does not have any coordinates.
Can anyone help me out how to use martinize.py to generate coarse grain structure of iron pyrite nanocluster?
The martinize.py script is for proteins, DNA, and a limited number of lipids. It won't produce an FeS2 topology. I would also be very suspicious of any CG treatment of such a species.
To my knowledge, they are no parameters for iron pyrite nanocluster on Martini. Why not parameterizing them yourself?
http://md.chem.rug.nl/cgmartini/index.php/parametrzining-new-molecule
Parametrizing something like this with a CG force field may not even be possible. Even atomistic FF fail to describe transition metals adequately. There are significant quantum effects whenever a transition metal is involved. A cluster of uncharged CG beads seems likely an inadequate description, in my opinion. CG representations are fine for mesoscopic phenomena, but in cases like this, I think CG is far less valuable.
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