I would like to know if there is any software that can be used to generate molecular surfaces functionalized/decorated with other molecular groups. For example, I want to start with a given XYZ/MOL2 file for a pristine structure (i.e. a carbon nanotube) and them, generate several other structures with other fragment (i.e. organic group -OH) attached randomly to its surface.
What do you mean "software to produce"? If you want to model their structure, you could perform semiempiric QC or DFT calculations, but please specifiy what you actually want so someone can give a more meaningful answer.
OK, so you just want s drawing with maybe a simple optimization? You can use most structure editors like Avogadro, Molden or others to draw and perform a simple force field optimization:
https://en.wikipedia.org/wiki/Comparison_of_force-field_implementations
Jürgen Weippert I need to select the representative structure for functionalizing a given percent of the surface. As the coating process is random, I need to generate thousands of structures, then calculate the entropy of all of them, I finally chose the representative as the one with higher entropy.
I can not do that manually, drawing each structure.
The method that I will use to study those structures will depend on the size of them (moving between DFT, semi-empirical and Molecular Mechanics).
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