You can reparameterize the current types with the --custom_atoms flag (vinardo scoring has different parameters). See the output of --print_atom_types for the format.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello, could you please give more details about using --custom_atoms ? I'm trying to add boron atom, so I created file named 'boron' with 1 line: "B ...." with all ten numeric parameters with spaces as delimiters. However, when I try to use it I receive an error: Line 1: omitting atom type name B. I also tried to write parameters in file atom_constants.h, but the output of --print_atom_types showed no changes.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Thank you for your answer!
Can you explain, how to add them in source code, or where I can read about it?
I know about gnina, I extracted parameters from it. However, I use smina running on the server without root access to install and use gnina. So if it possible, I'd like to solve this issue with smina.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Take the Boron related changes in atom_constants.h from gnina and put them in smina.
If you can't install custom software, you aren't going to be use the version of smina you want to make, although I don't see why you wouldn't be able to use an executable.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Thank you! I managed to use the gnina binaries. I suppose, it's the best solution. I'm not so familiar with *nix systems, so when I changed atom_constants.h, I didn't recompile smina.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello, is it possible to include new atom types or any way to customize the existing ones with different parameters? Thank you so much!
You can reparameterize the current types with the --custom_atoms flag (vinardo scoring has different parameters). See the output of --print_atom_types for the format.
Hello, could you please give more details about using --custom_atoms ? I'm trying to add boron atom, so I created file named 'boron' with 1 line: "B ...." with all ten numeric parameters with spaces as delimiters. However, when I try to use it I receive an error: Line 1: omitting atom type name B. I also tried to write parameters in file atom_constants.h, but the output of --print_atom_types showed no changes.
You can't create new atom types with --custom_atoms, you can only redefine the existing ones. To add atom types you need to change the source code.
gnina already has a Boron type, so maybe use that?
Thank you for your answer!
Can you explain, how to add them in source code, or where I can read about it?
I know about gnina, I extracted parameters from it. However, I use smina running on the server without root access to install and use gnina. So if it possible, I'd like to solve this issue with smina.
Take the Boron related changes in atom_constants.h from gnina and put them in smina.
If you can't install custom software, you aren't going to be use the version of smina you want to make, although I don't see why you wouldn't be able to use an executable.
Thank you! I managed to use the gnina binaries. I suppose, it's the best solution. I'm not so familiar with *nix systems, so when I changed atom_constants.h, I didn't recompile smina.
Hi, how to put Boron related changes in smina when I use Jupyter virtual environment?
You can't. Smina doesn't support Boron as an atom type. gnina does and is a fork of smina though.