search

forlilab / Meeko

Interfacing RDKit and AutoDock
GNU Lesser General Public License v2.1
182 stars 43 forks source link

ATOM 'G' created by mk_prepare_ligand. #10

Closed luwei0917 closed 2 years ago

luwei0917 commented 2 years ago

Hello, I'm trying to convert SDF file into pdbqt format using following command:

mk_prepare_ligand.py -I a.sdf -o a.pdbqt --pH 7.4

But my a.pdbqt file contains sometime I don't understand:

ATOM 27 G UNL 1 -0.000 -4.585 0.000 1.00 0.00 0.000 G0

what is this atom G? will this affect further docking?

a.sdf is copied below.


     RDKit          2D

 25 28  0  0  0  0  0  0  0  0999 V2000
   -5.1962  -13.5850    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -3.8971  -12.8350    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5981  -13.5850    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2990  -12.8350    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2990  -11.3350    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5981  -10.5850    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8971  -11.3350    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5981   -9.0850    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2990   -8.3350    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -9.0850    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000  -10.5850    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2990   -6.8350    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -6.0850    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -4.5850    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3515   -3.9342    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6852   -2.4718    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7500   -1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7500   -1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6852   -2.4718    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3515   -3.9342    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5242   -4.8694    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7500    1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7500    1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
  9 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  1  0
 20 21  2  0
 18 22  1  0
 22 23  2  0
 23 24  1  0
 24 25  2  0
  7  2  1  0
 20 14  1  0
 11  5  1  0
 25 17  1  0
M  END

Thanks!

diogomart commented 2 years ago

Hello,

G atoms are for macrocycles. See: https://autodock-vina.readthedocs.io/en/latest/docking_macrocycle.html

luwei0917 commented 2 years ago

thanks a lot!