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ccsb-scripps / AutoDock-GPU

AutoDock for GPUs and other accelerators
https://ccsb.scripps.edu/autodock
GNU General Public License v2.0
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energy decomposition of individual terms #155

Open amir-tagh opened 3 years ago

amir-tagh commented 3 years ago

Hello,

I am using Autodock GPU to study RNA-ligand interactions and I was wondering if there is anyway to get the individual contribution of energy terms in the output file. Currently dlg output provides the cumulative energy terms (vdW + Hbond + desolv Energy) for each docked state, but how can I get the value of each individual term (for example desolv)?

Thanks in forward. Best, Amir

UR-Free commented 2 years ago

I have the same question now

diogomart commented 2 years ago

It's possible, but complicated, because the maps for each of the atom types have contributions from vdw, hbond, and desolv terms.

  1. create four versions of the parameter file, which is called "AD4.1_bound.dat" in MGLTools, in which only one term keeps their original weight, while the others have their weight set to zero. Weights are controlled by the "FE_coeff" keywords. Do this for vdw, elec, hbond, and desolv.
  2. Add each of the parameter files to the autogrid configuration file (.gpf) and run autogrid four times, to generate grid maps for each of the terms: vdw, elec, hbond, and desolv.
  3. Evaluate the pose with autodock-vina using the --maps keyword to load the maps, as well as --scoring ad4 and --score_only. Also set the weights of each term to zero according to which map is being used (e.g. --weight_ad4_vdw 0).

The energies printed in each of the four calculations are associated with of the terms.