search

ccsb-scripps / AutoDock-GPU

AutoDock for GPUs and other accelerators
https://ccsb.scripps.edu/autodock
GNU General Public License v2.0
366 stars 101 forks source link

atom types: HS, NS, OS #251

Closed chaninpark0806 closed 2 months ago

chaninpark0806 commented 5 months ago

I don't understand the 3 atom types HS, NS, OS.

Can you tell me what they look like in smilies code?

diogomart commented 5 months ago

We are not using these types, at least not anymore. They were used for non-directional H-bond potentials (the "S" stands for spherical I think). The SMILES would be the same as for the directional counterparts HD, NA, OA. Here are the SMARTS patterns to match these types. Note that the last SMARTS to match, going down the list, takes over preceding matches, which happens often for nitrogen, which is typed as NA first but can loose its H-bonding trait by being typed with N afterwards.