getting the center of mass of each part of a molecule
qasimpars at gmail.com
qasimpars at gmail.com
Sat May 20 12:13:29 EDT 2017
I have more than 100 ligand molecules. The image I showed at the beginning of this discussion was only an example. It had missing atoms.
See it without missing any atom in the pdb format (coordinates in Angstrom unit):
ATOM 1 O1 LIG 1 46.050 50.290 26.860
ATOM 2 O2 LIG 1 46.070 47.530 27.170
ATOM 3 C1 LIG 1 47.630 49.260 23.730
ATOM 4 C2 LIG 1 48.200 49.870 22.500
ATOM 5 C3 LIG 1 47.090 50.070 24.730
ATOM 6 C4 LIG 1 46.570 49.490 25.890
ATOM 7 C5 LIG 1 47.650 47.870 23.890
ATOM 8 C6 LIG 1 46.590 48.100 26.040
ATOM 9 C7 LIG 1 47.120 47.290 25.050
ATOM 10 C8 LIG 1 47.160 50.610 21.680
ATOM 11 C9 LIG 1 46.450 51.660 26.860
ATOM 12 C10 LIG 1 46.910 51.920 21.790
ATOM 13 H1 LIG 1 48.640 49.150 21.820
ATOM 14 H2 LIG 1 48.980 50.600 22.700
ATOM 15 H3 LIG 1 47.080 51.150 24.610
ATOM 16 H4 LIG 1 48.070 47.240 23.110
ATOM 17 H5 LIG 1 47.140 46.210 25.170
ATOM 18 H6 LIG 1 46.580 50.030 20.960
ATOM 19 H7 LIG 1 45.570 52.300 26.810
ATOM 20 H8 LIG 1 47.090 51.850 26.000
ATOM 21 H9 LIG 1 47.000 51.860 27.780
ATOM 22 H10 LIG 1 46.190 48.140 27.920
ATOM 23 H11 LIG 1 46.220 52.400 21.250
ATOM 24 H12 LIG 1 46.750 52.530 22.680
The same ligand coordinate file in gro format (coordinates in nanometer unit) is here as well:
1LIG O1 1 4.605 5.029 2.686
1LIG O2 2 4.607 4.753 2.717
1LIG C1 3 4.763 4.926 2.373
1LIG C2 4 4.820 4.987 2.250
1LIG C3 5 4.709 5.007 2.473
1LIG C4 6 4.657 4.949 2.589
1LIG C5 7 4.765 4.787 2.389
1LIG C6 8 4.659 4.810 2.604
1LIG C7 9 4.712 4.729 2.505
1LIG C8 10 4.716 5.061 2.168
1LIG C9 11 4.645 5.166 2.686
1LIG C10 12 4.691 5.192 2.179
1LIG H1 13 4.864 4.915 2.182
1LIG H2 14 4.898 5.060 2.270
1LIG H3 15 4.708 5.115 2.461
1LIG H4 16 4.807 4.724 2.311
1LIG H5 17 4.714 4.621 2.517
1LIG H6 18 4.658 5.003 2.096
1LIG H7 19 4.557 5.230 2.681
1LIG H8 20 4.709 5.185 2.600
1LIG H9 21 4.700 5.186 2.778
1LIG H10 22 4.619 4.814 2.792
1LIG H11 23 4.622 5.240 2.125
1LIG H12 24 4.675 5.253 2.268
I am doing molecular dynamics simulation of protein-ligand complex. The issue is to keep the ligand in the binding site of the protein during simulation when turned off the interactions (van der waals, coulomb...) between the ligand and protein. In that case, to keep the ligand in the bindind site I need to apply the translational and rotational restraints (distance, angle, dihedral restraints). The more detail is here http://pubs.acs.org/doi/abs/10.1021/jp0217839
My aim is to get the COM of the whole ligand (I already do it) and divide the ligand in two parts and find to the COM of each part. Then I will apply the distance, angle and dihedral restraints on the atoms of the ligand and protein.
-The first distance restraints will be between one of the ligand heavy atom closest to the ligand COM (COM for whole ligand atoms) and one of the protein atoms closest to the ligand COM.
-The second distance restraints will be between one of the ligand heavy atom closest to the COM of the first part of ligand in two parts and one of the protein atoms closest to the COM of the first part of ligand in two parts.
-And the third distance restraints will be between one of the ligand heavy atom closest to the COM of the second part of ligand in two parts and one of the protein atoms closest to the COM of the second part of ligand in two parts.
That is, I will form 3 bonds between ligand and protein. Hope that makes clear what I am trying to do.
Please tell me on the python code what I need to do.
Thanks.
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