Extension of Numbers of Conformations and Configurations

[Akira Suma]

I would like to ask you concerning how to extend the space
to be explored by smina; i.e., I want to increase the numbers
of conformations and configurations of the ligands, that
are taken as the candidates (of the structures) by the
algorithms.

(e.g. I want to increase the number of the positions and
orientations of the ligands that are arranged in the binding
pockets of the receptors)

However, I cannot find the parameters that determine the
size of the conformational and configurational spaces to be
explored, in the source code of smina.

If you would let me know the above-mentioned parameters
relevant to the size of the space to be explored, and the module
files where the parameter values are included, I could much
appreciate it.

Thank you in advance.

[David Koes]

--num_modes sets the number of ligand poses to output (default is 9).

[Akira Suma]

Hi, David,

OK. Thank you. But my issue is as follows.

The structures that I obtained employing smina were not enough
in terms of the accuracy when I compared them with the experimental
structures.

I believe that this problem is derived from the restricted numbers
of trial structures (i.e., conformations and configurations of ligand
generated by the default setting of sumina).

So, I want to perform much more extended conformational and
configurational searches, by increasing the number of
generated structures in smina. Which parameters should I modify ?

Thank you in advance.

[David Koes]

You can try increasing the exhaustiveness.

[André Filipe Pereira]

Hi David,
Congratulations, great software.
Apart from decreasing the exhaustiveness, is there any way to speed up smina?
Thank you in advance.

[David Koes]

Not really. You can be faster by sampling less which is what exhaustiveness controls. Make sure your --cpu option matches your cores but isn't larger than your exhaustiveness. If you have free cores, run multiple smina jobs.

[André Filipe Pereira]

Is it possible to take advantage of hardware accelerators like GPUs and TPUs offered by Google Colab?

[David Koes]

Not with smina. gnina has GPU acceleration but it isn't actually faster.