Hello Folks,
I want to dock nano-particle like Fe2O3 in protein. I need to optimize the geometry of such nano-particle structure. Is there any online approach to assign partial charge and optimize geometry of nano-particle (single) or unit cell?
Thanks in advance!
~Amir
Well the most common geometry that is natural are sphere and hexagon !!!
May be you have to look at chirality of molecular structures compatible to biological systems , I do not know much of chemistry !!!
Thanks Aparna,
Well, I want to optimize the geometry of a single molecule, because we don't know the number of molecules in a single clump. I would like to dock that optimized structure, so I need to assign the partial charges to all the atoms. My question to you people, is there any online server or package like to optimize the geometry in terms of partial charges?
Thanks!
Oh !!!! nano software you say ...
Did you check in here :https://nanohub.org/resources/downloads
This paper says GA : http://www.mdpi.com/1999-4893/2/1/410 (old paper)
Check this , they say editor : https://dasher.wustl.edu/chem430/software/learning-avogadro.pdf
May be you have buy it !! They say based on primitive cell structure , single clump - how do you define this (just asking) . Check for chirality and its association with geometry (face , etc etc) .I seem to have forgotten ...
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