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akiyamalab / restretto

REstretto (REuse of sub-STRuctures as an Effective Technique for protein-ligand docking TOol): An virtual screening-oriented protein-ligand docking tool with reuse of fragments
MIT License
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Minimum RMSD does not work #19

Closed keisuke-yanagisawa closed 9 months ago

keisuke-yanagisawa commented 9 months ago

I found an wrong behavior about the RMSD argument.

Here is my test sample, fragment.sdf, fragment_docking.in. Other data is the same as in testdata directory. Though I set POSE_RMSD=10 but the RMSD of outputs seems much lower than the threshold. Could you check the bug?

fragment_docking.in

INNERBOX 10, 10, 10
OUTERBOX 20, 20, 20
BOX_CENTER 0.3826, 81.705, 109.195
SEARCH_PITCH 1, 1, 1
SCORING_PITCH 0.25, 0.25, 0.25
MEMORY_SIZE 8000
RECEPTOR testdata/2HU4_A_r.pdbqt
LIGAND testdata/fragment.sdf
OUTPUT testdata/fragment_docked.sdf
GRID_FOLDER testdata/grid
NO_LOCAL_OPT false
POSE_RMSD 10
POSES_PER_LIG 10

fragment.sdf

ligprep_1.smi:1
  -OEChem-10092314143D

 20 21  0     1  0  0  0  0  0999 V2000
    1.9431   -0.9280   -0.0056 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0078    0.0264   -0.4042 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2402   -0.8999   -0.5217 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3651    1.0144   -1.3210 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5995    0.0893   -1.4406 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6642    1.0414   -1.8369 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9496    0.1853   -2.0314 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0654    2.0739   -2.8058 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0000   -0.8247   -1.6340 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2908    1.0994   -2.8850 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3666    2.0151   -3.2564 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2639    2.9276   -3.1737 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6614   -1.6963    0.7089 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0001    0.0002 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9437   -1.6575   -0.1909 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6226    1.7493   -1.6191 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9511   -1.6694   -2.3119 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8091   -1.1511   -0.6175 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9771   -0.3578   -1.6898 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6571    2.7208   -3.9258 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  2  0  0  0  0
  4  6  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  8  1  0  0  0  0
  7  9  1  0  0  0  0
  7 10  2  0  0  0  0
  8 11  1  0  0  0  0
  8 12  2  0  0  0  0
 10 11  1  0  0  0  0
  1 13  1  0  0  0  0
  2 14  1  0  0  0  0
  3 15  1  0  0  0  0
  4 16  1  0  0  0  0
  9 17  1  0  0  0  0
  9 18  1  0  0  0  0
  9 19  1  0  0  0  0
 11 20  1  0  0  0  0
M  END
$$$$
keisuke-yanagisawa commented 9 months ago

The result says min_rmsd = inf image