Hi all,
I have used UCSF Chimera for several years and find that Chimera has a perfect behavior in adding hydrogen atoms for small molecules. It is easier to add wrong hydrogen atoms onto nitrogen heterocycles
groups with other software, including openbabel, MGLTools, PyMol, etc. Now I want to add hydrogen atoms for a dataset, which contains more than 10 thousands ligands for virtual screening. And a great number of compounds in this dataset have nitrogen heterocycle
groups.
So I want to add hydrogen atoms for all these compounds by Chimera.
When I try to run a script in Favorites > Command line by read a MOL, addh and delete the MOL in cycle. I found that the memory usage of Chimera keep growing although I have delete the previous MOLs.
My question is:
How can I avoid this problem while I want to handle numerous molecules with Chimera?
If there is a way to run Chimera in a real terminal without run Chimera in graphic interface? Or
Which bin file in Chimera_HOME can add hydrogen atoms for a molecule?
Sincerely look forward to your reply.
Thanks
Best
Shengfu Zhou
2019.11.19