The .gro coordinates of the ligand do not match with pdb coordinates after pdb2gmx

User discussions
1

GROMACS version: 5.1.4
GROMACS modification: No
I am working on a protein-ligand simulation. My ligand happens to be a cholesterol molecule. I am using the Charmm36-jul2021.ff which already contains the parameters of cholesterol as (CHL1). To begin with, I separated the docked cholesterol from the protein by using pymol and saved the coordinates of cholesterol in a new pdb file. I manually changed the name of cholesterol and the atom numbers etc according to the structure and specifications mentioned in the top_all36_cgenff.rtf file in top_all36_cgenff.rtf folder. Then I gave this “modified” cholesterol.pdb file to the pdb2gmx and selected CHARMM36 all-atom force field and TIP3P_CHARMM CHARMM-modified TIP3P water model so as to generate the topology and coordinate (.gro) file of cholesterol. This process was successful; however, the location of the H atom of the OH in cholesterol is changed in the gro file generated by pdb2gmx. Manual inspection of the cholesterol.gro file generated after pdb2gmx and the initial cholesterol.pdb file clearly indicates that the coordinates of H3’ atom have changed in the cholesterol.gro file.

PDB File of Cholesterol:

ATOM 1 C1 CHL1 1 39.319 45.363 28.473 0.00 0.00 C

ATOM 2 C2 CHL1 1 40.064 46.074 27.345 0.00 0.00 C

ATOM 3 C3 CHL1 1 39.151 46.304 26.142 0.00 0.00 C

ATOM 4 C4 CHL1 1 38.863 44.962 25.452 0.00 0.00 C

ATOM 5 C5 CHL1 1 38.782 43.911 26.547 0.00 0.00 C

ATOM 6 C10 CHL1 1 38.301 44.384 27.892 0.00 0.00 C

ATOM 7 C6 CHL1 1 39.131 42.691 26.292 0.00 0.00 C

ATOM 8 C7 CHL1 1 39.116 41.594 27.315 0.00 0.00 C

ATOM 9 C8 CHL1 1 39.182 42.200 28.723 0.00 0.00 C

ATOM 10 C9 CHL1 1 38.044 43.227 28.848 0.00 0.00 C

ATOM 11 C14 CHL1 1 38.932 41.107 29.747 0.00 0.00 C

ATOM 12 C13 CHL1 1 39.023 41.759 31.153 0.00 0.00 C

ATOM 13 C12 CHL1 1 37.797 42.642 31.307 0.00 0.00 C

ATOM 14 C11 CHL1 1 37.922 43.769 30.270 0.00 0.00 C

ATOM 15 C15 CHL1 1 40.011 40.023 29.838 0.00 0.00 C

ATOM 16 C16 CHL1 1 39.806 39.446 31.265 0.00 0.00 C

ATOM 17 C17 CHL1 1 39.114 40.559 32.091 0.00 0.00 C

ATOM 18 C19 CHL1 1 36.980 45.130 27.694 0.00 0.00 C

ATOM 19 C18 CHL1 1 40.292 42.608 31.254 0.00 0.00 C

ATOM 20 C20 CHL1 1 39.957 40.911 33.319 0.00 0.00 C

ATOM 21 C21 CHL1 1 39.038 41.150 34.518 0.00 0.00 C

ATOM 22 C22 CHL1 1 40.911 39.755 33.629 0.00 0.00 C

ATOM 23 C23 CHL1 1 40.597 39.194 35.018 0.00 0.00 C

ATOM 24 C24 CHL1 1 41.263 37.827 35.179 0.00 0.00 C

ATOM 25 C25 CHL1 1 41.249 37.422 36.655 0.00 0.00 C

ATOM 26 C26 CHL1 1 42.683 37.208 37.139 0.00 0.00 C

ATOM 27 C27 CHL1 1 40.592 38.531 37.481 0.00 0.00 C

ATOM 28 O3 CHL1 1 37.922 46.886 26.582 0.00 0.00 O

ATOM 29 H3’ CHL1 1 37.688 47.566 25.934 0.00 0.00 H

END

Gro file after PDB2GMX

74

1CHL1 C3 1 3.915 4.630 2.614

1CHL1 H3 2 3.955 4.696 2.551

1CHL1 O3 3 3.792 4.689 2.658

1CHL1 H3’ 4 3.811 4.776 2.703

1CHL1 C4 5 3.886 4.496 2.545

1CHL1 H4A 6 3.960 4.473 2.481

1CHL1 H4B 7 3.800 4.501 2.496

1CHL1 C5 8 3.878 4.391 2.655

1CHL1 C6 9 3.913 4.269 2.629

1CHL1 H6 10 3.943 4.247 2.536

1CHL1 C7 11 3.912 4.159 2.731

1CHL1 H7A 12 3.990 4.100 2.716

1CHL1 H7B 13 3.827 4.106 2.721

1CHL1 C8 14 3.918 4.220 2.872

1CHL1 H8 15 4.008 4.261 2.888

1CHL1 C14 16 3.893 4.111 2.975

1CHL1 H14 17 3.806 4.070 2.946

1CHL1 C15 18 4.001 4.002 2.984

1CHL1 H15A 19 4.092 4.042 2.973

1CHL1 H15B 20 3.987 3.932 2.914

1CHL1 C16 21 3.981 3.945 3.126

1CHL1 H16A 22 3.923 3.863 3.123

1CHL1 H16B 23 4.069 3.921 3.167

1CHL1 C17 24 3.911 4.056 3.209

1CHL1 H17 25 3.821 4.028 3.243

1CHL1 C13 26 3.902 4.176 3.115

1CHL1 C18 27 4.029 4.261 3.125

1CHL1 H18A 28 4.034 4.302 3.216

1CHL1 H18B 29 4.109 4.202 3.115

1CHL1 H18C 30 4.022 4.339 3.064

1CHL1 C12 31 3.780 4.264 3.131

1CHL1 H12A 32 3.777 4.302 3.223

1CHL1 H12B 33 3.697 4.211 3.114

1CHL1 C11 34 3.792 4.377 3.027

1CHL1 H11A 35 3.874 4.431 3.048

1CHL1 H11B 36 3.711 4.435 3.032

1CHL1 C9 37 3.804 4.323 2.885

1CHL1 H9 38 3.718 4.277 2.862

1CHL1 C10 39 3.830 4.438 2.789

1CHL1 C19 40 3.698 4.513 2.769

1CHL1 H19A 41 3.630 4.451 2.731

1CHL1 H19B 42 3.664 4.545 2.858

1CHL1 H19C 43 3.712 4.590 2.707

1CHL1 C1 44 3.932 4.536 2.847

1CHL1 H1A 45 3.997 4.486 2.904

1CHL1 H1B 46 3.884 4.604 2.903

1CHL1 C2 47 4.006 4.607 2.734

1CHL1 H2A 48 4.039 4.696 2.768

1CHL1 H2B 49 4.084 4.551 2.706

1CHL1 C20 50 3.996 4.091 3.332

1CHL1 H20 51 4.048 4.174 3.314

1CHL1 C21 52 3.904 4.115 3.452

1CHL1 H21A 53 3.851 4.032 3.470

1CHL1 H21B 54 3.841 4.191 3.432

1CHL1 H21C 55 3.959 4.138 3.532

1CHL1 C22 56 4.091 3.976 3.363

1CHL1 H22A 57 4.185 4.009 3.361

1CHL1 H22B 58 4.080 3.903 3.294

1CHL1 C23 59 4.060 3.919 3.502

1CHL1 H23A 60 3.961 3.910 3.512

1CHL1 H23B 61 4.095 3.982 3.572

1CHL1 C24 62 4.126 3.783 3.518

1CHL1 H24A 63 4.076 3.715 3.464

1CHL1 H24B 64 4.221 3.788 3.486

1CHL1 C25 65 4.125 3.742 3.665

1CHL1 H25 66 4.073 3.657 3.676

1CHL1 C26 67 4.268 3.721 3.714

1CHL1 H26A 68 4.311 3.648 3.660

1CHL1 H26B 69 4.267 3.694 3.810

1CHL1 H26C 70 4.320 3.806 3.703

1CHL1 C27 71 4.059 3.853 3.748

1CHL1 H27A 72 3.965 3.867 3.716

1CHL1 H27B 73 4.058 3.827 3.845

1CHL1 H27C 74 4.111 3.938 3.737

0.69031 1.12760 1.36305

I have highlighted the problematic Hydrogen atom with bold font in both the files. What can be the reason for this discrepancy? Am I doing something wrong? How can this be rectified? Thanks in advance.

2

You didn’t provide you pdb2gmx command, but I’m guessing you used -ignh and the H atoms that were present in the input file got rebuilt.

3

Thank you Dr. Lemkul for your valuable suggestion. Indeed the culprit was -ignh flag that i had used with the pdb2gmx command. Now after removing -ignh flag the coordinates in the .gro file are exactly matching with the coordinates in the initial pdb file used as an input. Once again thanks for helping me out.