ligand_docking: ligand preparation

This topic has 0 replies, 1 voice, and was last updated 4 years, 6 months ago by Anonymous.

Viewing 0 reply threads

Author

Posts
- July 2, 2020 at 2:05 pm #3490
  Anonymous
  Hi, I am using mol-to-param script to generate param files of my conformer. the sdf file looks normal before generation. But the PDB looks weird with some bonds connected to each other when I visualize it in pymol software however it looks totally fine in chemdoodle3D. Anyone has any clue about this?
  
  The PDB with weird structure looks like this:
  
  HETATM 1 P1 FMN X 1 9.575 -36.329 -12.137 1.00 20.00 P
  
  HETATM 2 C1 FMN X 1 8.227 -34.156 -12.834 1.00 20.00 C
  
  HETATM 3 N1 FMN X 1 3.372 -35.765 -10.079 1.00 20.00 N
  
  HETATM 4 O1 FMN X 1 10.967 -36.829 -12.467 1.00 20.00 O
  
  HETATM 5 C2 FMN X 1 6.902 -34.774 -12.377 1.00 20.00 C
  
  HETATM 6 N2 FMN X 1 1.340 -35.396 -8.874 1.00 20.00 N
  
  HETATM 7 O2 FMN X 1 8.606 -37.496 -12.186 1.00 20.00 O
  
  HETATM 8 C3 FMN X 1 6.268 -35.660 -13.449 1.00 20.00 C
  
  HETATM 9 N3 FMN X 1 1.081 -38.492 -10.841 1.00 20.00 N
  
  HETATM 10 O3 FMN X 1 9.547 -35.681 -10.765 1.00 20.00 O
  
  HETATM 11 C4 FMN X 1 4.937 -36.263 -13.003 1.00 20.00 C
  
  HETATM 12 N4 FMN X 1 3.628 -37.651 -11.468 1.00 20.00 N
  
  HETATM 13 O4 FMN X 1 9.108 -35.193 -13.184 1.00 20.00 O
  
  HETATM 14 C5 FMN X 1 5.031 -37.159 -11.740 1.00 20.00 C
  
  HETATM 15 O5 FMN X 1 6.032 -33.717 -12.030 1.00 20.00 O
  
  HETATM 16 C6 FMN X 1 2.622 -35.008 -9.213 1.00 20.00 C
  
  HETATM 17 O6 FMN X 1 7.160 -36.716 -13.767 1.00 20.00 O
  
  HETATM 18 C7 FMN X 1 0.818 -36.561 -9.401 1.00 20.00 C
  
  HETATM 19 O7 FMN X 1 4.395 -36.962 -14.125 1.00 20.00 O
  
  HETATM 20 C8 FMN X 1 1.577 -37.328 -10.281 1.00 20.00 C
  
  HETATM 21 O8 FMN X 1 3.109 -33.982 -8.748 1.00 20.00 O
  
  HETATM 22 C9 FMN X 1 1.853 -39.255 -11.702 1.00 20.00 C
  
  HETATM 23 O9 FMN X 1 -0.323 -36.912 -9.083 1.00 20.00 O
  
  HETATM 24 C10 FMN X 1 1.348 -40.432 -12.255 1.00 20.00 C
  
  HETATM 25 C11 FMN X 1 2.124 -41.196 -13.132 1.00 20.00 C
  
  HETATM 26 C12 FMN X 1 1.591 -42.470 -13.730 1.00 20.00 C
  
  HETATM 27 C13 FMN X 1 3.408 -40.769 -13.450 1.00 20.00 C
  
  HETATM 28 C14 FMN X 1 4.261 -41.580 -14.383 1.00 20.00 C
  
  HETATM 29 C15 FMN X 1 3.908 -39.592 -12.898 1.00 20.00 C
  
  HETATM 30 C16 FMN X 1 3.140 -38.834 -12.018 1.00 20.00 C
  
  HETATM 31 C17 FMN X 1 2.852 -36.916 -10.613 1.00 20.00 C
  
  HETATM 32 H1 FMN X 1 11.217 -37.525 -11.840 1.00 20.00 H
  
  HETATM 33 H2 FMN X 1 8.059 -33.526 -13.682 1.00 20.00 H
  
  HETATM 34 H3 FMN X 1 8.649 -33.569 -12.046 1.00 20.00 H
  
  HETATM 35 H4 FMN X 1 7.085 -35.412 -11.537 1.00 20.00 H
  
  HETATM 36 H5 FMN X 1 5.309 -34.058 -11.480 1.00 20.00 H
  
  HETATM 37 H6 FMN X 1 6.078 -35.041 -14.301 1.00 20.00 H
  
  HETATM 38 H7 FMN X 1 7.531 -37.084 -12.949 1.00 20.00 H
  
  HETATM 39 H8 FMN X 1 4.287 -35.472 -12.694 1.00 20.00 H
  
  HETATM 40 H9 FMN X 1 3.443 -37.096 -13.993 1.00 20.00 H
  
  HETATM 41 H10 FMN X 1 5.393 -36.592 -10.909 1.00 20.00 H
  
  HETATM 42 H11 FMN X 1 5.708 -37.975 -11.890 1.00 20.00 H
  
  HETATM 43 H12 FMN X 1 0.802 -34.846 -8.260 1.00 20.00 H
  
  HETATM 44 H13 FMN X 1 0.393 -40.742 -12.015 1.00 20.00 H
  
  HETATM 45 H14 FMN X 1 0.595 -42.641 -13.377 1.00 20.00 H
  
  HETATM 46 H15 FMN X 1 2.217 -43.289 -13.441 1.00 20.00 H
  
  HETATM 47 H16 FMN X 1 1.581 -42.387 -14.796 1.00 20.00 H
  
  HETATM 48 H17 FMN X 1 3.716 -42.443 -14.705 1.00 20.00 H
  
  HETATM 49 H18 FMN X 1 5.150 -41.890 -13.875 1.00 20.00 H
  
  HETATM 50 H19 FMN X 1 4.524 -40.987 -15.233 1.00 20.00 H
  
  HETATM 51 H20 FMN X 1 4.859 -39.279 -13.144 1.00 20.00 H
  
  TER
Author

Posts

Viewing 0 reply threads

You must be logged in to reply to this topic.