[Chimera-users] Question

Damjanovic Marko damjanovic at uni-heidelberg.de
Thu Jul 2 00:05:24 PDT 2015


To whom it may concern,

I am trying to solve a problem that is more of mathematical nature, and 
I would be very grateful if I could get any advice or pointers on how it 
may be possible to do this (in Chimera or some other program I am not 
aware of).

I have a molecule that is more or less of cylindrical shape (quite 
simple shape). I would need a way to surround this molecule with a 
certain number of layers of solvent molecules that fit around the 
surface of a cylinder (preferably 1 layer and then going up gradually). 
The solvent molecules should be packed around the central molecule 
efficiently (closest packing). An alternative way to approach this would 
be to take a sphere made out of solvent molecules, put in the centre of 
the sphere the one cylindrical molecule what is of interest, and let the 
big sphere accommodate the new molecule. Also, for the sake of 
simplicity, the solvent molecules can be approximated as small spheres 
as well (their exact shape is not that relevant).

When this is done, all I would need is to get this file in a format like 
cif, mol or gjf. I underline here that I am looking for a relatively 
crude model.

Could anyone please advise me on how to do something like this?

Thanks in advance and best wishes,
Damjanovic Marko


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