Answers.Body: <p>Docking is a computational calculation in the field of <strong>molecular mechanisms</strong>.
  It can be argued that whereas it is true one can 'wing it' without knowing the basics, it is best to know them —akin to the fact that it is possible to drive a car fine without knowing the road code or how a car works: many do for sure but it is not a good idea as something will go wrong.</p>
  <p>So I would suggest having a gander at the very least at:</p>
  <ul>
  <li><a href="https://en.wikipedia.org/wiki/Molecular_modelling" rel="nofollow noreferrer">https://en.wikipedia.org/wiki/Molecular_mechanics</a></li>
  <li><a href="https://en.wikipedia.org/wiki/Force_field_(chemistry)" rel="nofollow noreferrer">https://en.wikipedia.org/wiki/Force_field_(chemistry)</a></li>
  <li><a href="https://en.wikipedia.org/wiki/Lennard-Jones_potential" rel="nofollow noreferrer">https://en.wikipedia.org/wiki/Lennard-Jones_potential</a></li>
  <li><a href="https://en.wikipedia.org/wiki/Solvent_model" rel="nofollow noreferrer">https://en.wikipedia.org/wiki/Solvent_model</a></li>
  <li><a href="https://manual.gromacs.org/documentation/current/reference-manual/topologies/particle-type.html" rel="nofollow noreferrer">https://manual.gromacs.org/documentation/current/reference-manual/topologies/particle-type.html#atom-types</a></li>
  </ul>
  <p>So a forcefield is a sum of different terms that mathematically describes the forces acting between atoms. A thing to note is that these terms may be have some basis in chemistry or some may be just fudge factors to make the data fit.</p>
  <p>Regarding the atom types, in a full atom model, each atom is represented as a particle (or node in graph theory speak) and the bonds are fixed (edges).
  An element behaves different depending on its hybridisation and charge etc. Therefore, each atom is classified not as an element, but as an atom type. Say, nitrogen in a ring and amine are generally different atom types. With parameterising a small molecule an atomtype may not be a perfect fit.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-02-15T15:25:42.200Z
Answers.LastActivityDate: 2022-02-15T15:25:42.200Z
Answers.UserDisplayName: Matteo Ferla
Body: <p>I know that before performing docking with <a href="https://autodock-vina.readthedocs.io/en/latest/docking_python.html" rel="nofollow noreferrer">AutoDock Vina</a>, we have to compute &quot;vina maps&quot; like below</p>
  <pre><code>v.set_ligand_from_file('1iep_ligand.pdbqt')
  v.compute_vina_maps(center=[15.190, 53.903, 16.917], box_size=[20, 20, 20])
  </code></pre>
  <p>but I do not quite understand what those maps exactly are.
  I found from the manual that</p>
  <blockquote>
  <p>...and then compute the affinity maps for each ligand atom types accroding to the Vina forcefield.</p>
  </blockquote>
  <p>but again, what are affinity maps and Vina forcefield. I checked the <a href="https://github.com/ccsb-scripps/AutoDock-Vina/blob/ea68a7abd8d90d2f8ab296521c0d07ee828f9d46/src/lib/vina.cpp#:%7E:text=Vina%3A%3Acompute_vina_maps" rel="nofollow noreferrer">source code</a> to see that it creates some kind of a grid which will be then used for scoring. What kind of information does this grid data type contains? I would greatly appreciate any help.</p>
  
Tags: <docking>
Title: Affinity maps and forcefields
ThreadText: # Affinity maps and forcefields
  
  (Asked by: username_0 on 2022-02-15)
  
  I know that before performing docking with [AutoDock Vina](https://autodock-vina.readthedocs.io/en/latest/docking_python.html), we have to compute "vina maps" like below
  
  ```
  v.set_ligand_from_file('1iep_ligand.pdbqt')
  v.compute_vina_maps(center=[15.190, 53.903, 16.917], box_size=[20, 20, 20])
  
  ```
  
  but I do not quite understand what those maps exactly are.
  I found from the manual that
  
  > ...and then compute the affinity maps for each ligand atom types accroding to the Vina forcefield.
  
  but again, what are affinity maps and Vina forcefield. I checked the [source code](https://github.com/ccsb-scripps/AutoDock-Vina/blob/ea68a7abd8d90d2f8ab296521c0d07ee828f9d46/src/lib/vina.cpp#:%7E:text=Vina%3A%3Acompute_vina_maps) to see that it creates some kind of a grid which will be then used for scoring. What kind of information does this grid data type contains? I would greatly appreciate any help.
  
  **Tags:** docking
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2022-02-15. Score: 1
  
  Docking is a computational calculation in the field of **molecular mechanisms**.
  It can be argued that whereas it is true one can 'wing it' without knowing the basics, it is best to know them —akin to the fact that it is possible to drive a car fine without knowing the road code or how a car works: many do for sure but it is not a good idea as something will go wrong.
  
  So I would suggest having a gander at the very least at:
  
  * [https://en.wikipedia.org/wiki/Molecular\_mechanics](https://en.wikipedia.org/wiki/Molecular_modelling)
  * <https://en.wikipedia.org/wiki/Force_field_(chemistry)>
  * <https://en.wikipedia.org/wiki/Lennard-Jones_potential>
  * <https://en.wikipedia.org/wiki/Solvent_model>
  * [https://manual.gromacs.org/documentation/current/reference-manual/topologies/particle-type.html#atom-types](https://manual.gromacs.org/documentation/current/reference-manual/topologies/particle-type.html)
  
  So a forcefield is a sum of different terms that mathematically describes the forces acting between atoms. A thing to note is that these terms may be have some basis in chemistry or some may be just fudge factors to make the data fit.
  
  Regarding the atom types, in a full atom model, each atom is represented as a particle (or node in graph theory speak) and the bonds are fixed (edges).
  An element behaves different depending on its hybridisation and charge etc. Therefore, each atom is classified not as an element, but as an atom type. Say, nitrogen in a ring and amine are generally different atom types. With parameterising a small molecule an atomtype may not be a perfect fit.
  
  
  ---
  
  