How to get Cartesian coordinates for united atoms given the Cartesian coordinates for all atoms?

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Gourav Shrivastav

http://www.ks.uiuc.edu/Research/vmd/plugins/cgtools/

I think you need this as Denis said.

Rino Ragno

Try openbabel, you can transform a given hydrogenated mol to the corresponding containing only polar hydrogens.

You can also use ADT (autodocktools) since autodock used united atoms mols.

Anupam Singh

Hi Prerana,

You can open your PDB in VMD. And try commands mentioned in below link.

https://sites.google.com/site/akohlmey/software/topotools

Cheers!!