# Procedure to validate glide docking without a reference ligand on Autodock vina

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.

• 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 – lewiso1 Apr 22 at 4:37

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