How can I perform a score-in-place procedure with autodock to validate ma glide docking? It is a new software for me and I don't Know how to use it and how to proceed. Thanks in advance for help.
$\begingroup$
$\endgroup$
1
-
1$\begingroup$ there are several tutorials ideal for this situation at autodock.scripps.edu/faqs-help/tutorial - if you find something in particular you are stuck with, maybe update the question to ask about it $\endgroup$– lewiso1Commented Apr 22, 2021 at 4:37
Add a comment
|
1 Answer
$\begingroup$
$\endgroup$
1
You need to use the advanced option --score_only which means:
score only - search space can be omitted
To get info about advanced options you run vina --help_advanced that will return:
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
