Dear open babel community
I used MOPAC to minimize the ligand and obtain the output in PDB format with
atomic charges. When I converted the PDB file to mol2 using babel the atomic
charges were found to be modified. Can anyone help me to preserve the
charges during conversion or any other mode of way to obtain the ligand
output with atomic charges preserved? Below am pasting the PDB file and mol2
file for reference.
The PDB file
ATOM 1 O LIG A 1 -2.264 -1.020 0.122 1.00 -0.39
PROT O
ATOM 2 O LIG A 1 2.796 0.538 -0.113 1.00 -0.39 PROT
O
ATOM 3 C LIG A 1 -1.114 -0.659 0.066 1.00 0.41
PROT C
ATOM 4 C LIG A 1 -0.751 0.792 -0.005 1.00 0.00
PROT C
ATOM 5 C LIG A 1 0.001 -1.641 0.066 1.00 -0.22
PROT C
ATOM 6 C LIG A 1 0.532 1.171 -0.065 1.00 -0.28
PROT C
ATOM 7 C LIG A 1 1.275 -1.250 0.008 1.00 -0.20
PROT C
ATOM 8 C LIG A 1 1.640 0.192 -0.062 1.00 0.43
PROT C
ATOM 9 C LIG A 1 -1.893 1.734 -0.003 1.00 -0.45
PROT C
ATOM 10 H LIG A 1 -0.305 -2.687 0.117 1.00 0.18
PROT H
ATOM 11 H LIG A 1 0.839 2.216 -0.119 1.00 0.19
PROT H
ATOM 12 H LIG A 1 2.118 -1.944 0.006 1.00 0.18
PROT H
ATOM 13 H LIG A 1 -2.493 1.632 0.919 1.00 0.18
PROT H
ATOM 14 H LIG A 1 -1.591 2.787 -0.085 1.00 0.16
PROT H
ATOM 15 H LIG A 1 -2.589 1.523 -0.834 1.00 0.18
PROT H
END
Converted mol2 file using babel
@<TRIPOS>MOLECULE
A_lig1.pdb
15 15 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 O -2.2640 -1.0200 0.1220 O.2 1 LIG1 -0.2876
2 O 2.7960 0.5380 -0.1130 O.2 1 LIG1 -0.2879
3 C -1.1140 -0.6590 0.0660 C.2 1 LIG1 0.1821
4 C -0.7510 0.7920 -0.0050 C.2 1 LIG1 -0.0002
5 C 0.0010 -1.6410 0.0660 C.2 1 LIG1 -0.0111
6 C 0.5320 1.1710 -0.0650 C.2 1 LIG1 -0.0084
7 C 1.2750 -1.2500 0.0080 C.2 1 LIG1 -0.0113
8 C 1.6400 0.1920 -0.0620 C.2 1 LIG1 0.1795
9 C -1.8930 1.7340 -0.0030 C.3 1 LIG1 -0.0360
10 H -0.3050 -2.6870 0.1170 H 1 LIG1 0.0657
11 H 0.8390 2.2160 -0.1190 H 1 LIG1 0.0659
12 H 2.1180 -1.9440 0.0060 H 1 LIG1 0.0657
13 H -2.4930 1.6320 0.9190 H 1 LIG1 0.0279
14 H -1.5910 2.7870 -0.0850 H 1 LIG1 0.0279
15 H -2.5890 1.5230 -0.8340 H 1 LIG1 0.0279
@<TRIPOS>BOND
1 15 9 1
2 11 6 1
3 2 8 2
4 14 9 1
5 6 8 1
6 6 4 2
7 8 7 1
8 4 9 1
9 4 3 1
10 9 13 1
11 12 7 1
12 7 5 2
13 3 5 1
14 3 1 2
15 5 10 1
--
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