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.

  • 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 $\endgroup$
    – 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:

  --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
  --local_only                          do local search only
  --randomize_only                      randomize input, attempting to avoid
  --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
  --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
  --version                             display program version
  • $\begingroup$ Thank you so much. $\endgroup$
    – Giu
    Apr 28 at 11:31

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.