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PostPosted: Fri Aug 23, 2013 7:12 pm 
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Hello,

I would like to calculate the binding energy of a ligand to a receptor protein and compare this to binding energies to mutant versions of the same protein. I will be generating or modifying Autodock Vina calculated poses of the ligand to the protein, but I am mainly interested in calculating the binding energy directly. That is, I do not want to go through the docking if I don't need to.

I realize this may not be the intended purpose of Autodock Vina, but I wanted to ask, can this software perform this?

Thanks very much in advance.


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PostPosted: Fri Aug 23, 2013 10:15 pm 
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This can be done using the advanced option 'score_only'

To see all the vina options type:

vina --help_advanced

Input:
--receptor arg rigid part of the receptor (PDBQT)
--flex arg flexible side chains, if any (PDBQT)
--ligand arg ligand (PDBQT)

Search space (required):
--center_x arg X coordinate of the center
--center_y arg Y coordinate of the center
--center_z arg Z coordinate of the center
--size_x arg size in the X dimension (Angstroms)
--size_y arg size in the Y dimension (Angstroms)
--size_z arg size in the Z dimension (Angstroms)

Output (optional):
--out arg output models (PDBQT), the default is chosen based on
the ligand file name
--log arg optionally, write log file

Advanced options (see the manual):
--score_only score only - search space can be omitted
--local_only do local search only
--randomize_only randomize input, attempting to avoid clashes
--weight_gauss1 arg (=-0.035579) gauss_1 weight
--weight_gauss2 arg (=-0.005156) gauss_2 weight
--weight_repulsion arg (=0.84024500000000002) repulsion weight
--weight_hydrophobic arg (=-0.035069000000000003) hydrophobic weight
--weight_hydrogen arg (=-0.58743900000000004) Hydrogen bond weight
--weight_rot arg (=0.058459999999999998) N_rot weight

Misc (optional):
--cpu arg the number of CPUs to use (the default is to try to
detect the number of CPUs or, failing that, use 1)
--seed arg explicit random seed
--exhaustiveness arg (=8) exhaustiveness of the global search (roughly
proportional to time): 1+
--num_modes arg (=9) maximum number of binding modes to generate
--energy_range arg (=3) maximum energy difference between the best binding
mode and the worst one displayed (kcal/mol)

Configuration file (optional):
--config arg the above options can be put here

Information (optional):
--help display usage summary
--help_advanced display usage summary with advanced options
--version display program version


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PostPosted: Sat Aug 24, 2013 2:26 am 
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I will try this. Thank you so much.


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