Hi,
I have downloaded some molecules from ZINC20 in mol2 format.
I then have used mk_prepare_ligand.py to convert the molecules to the pdbqt format.
For an high percentage of them mk_prepare_ligand.py takes in input a molecule with total charge
of -2 ( I have checked with openbabel GetTotalCharge() ) and return a pdbqt converted ligand with
a TOT CHARGE of +/.-0.00 as reported using the -v option.

Why these different values of total charge of the same molecule with different formats?

This different values of total charge of the ligands can have effects on the docking results?

For example for ZINC000001644610.mol2 openbabel evaluate a total charge equal -2 whereas
mk_prepare_ligand.py returns the following output when the previous molecule is processed:

Processing ./ZINC000001644610.mol2 file
Molecule setup

==============[ ATOMS ]===================================================
idx | coords | charge |ign| atype | connections
-----+----------------------------+--------+---+----------+--------------- . . .
0 | 0.002 -0.004 0.002 | -0.258 | 0 | OA | [1]
1 | -0.014 1.214 0.009 | 0.062 | 0 | N | [0, 2, 3]
2 | 1.032 1.837 0.002 | -0.258 | 0 | OA | [1]
3 | -1.306 1.936 0.019 | 0.271 | 0 | A | [1, 29, 4]
4 | -1.322 3.320 0.021 | 0.020 | 0 | A | [3, 5, 30]
5 | -2.522 4.006 0.030 | -0.006 | 0 | A | [4, 6, 31]
6 | -3.719 3.311 0.038 | 0.204 | 0 | A | [5, 7, 8]
7 | -4.899 3.984 0.048 | -0.288 | 0 | OA | [6]
8 | -3.709 1.909 0.036 | 0.117 | 0 | A | [6, 9, 29]
9 | -4.885 1.212 0.043 | -0.252 | 0 | NA | [8, 10]
10 | -5.000 0.135 0.768 | 0.035 | 0 | C | [9, 11, 32]
11 | -6.266 -0.614 0.776 | -0.007 | 0 | A | [10, 28, 12]
12 | -7.345 -0.173 0.001 | -0.053 | 0 | A | [11, 13, 33]
13 | -8.520 -0.869 0.008 | -0.053 | 0 | A | [12, 14, 34]
14 | -8.645 -2.023 0.791 | -0.007 | 0 | A | [13, 15, 27]
15 | -9.911 -2.772 0.799 | 0.035 | 0 | C | [14, 16, 35]
16 | -10.028 -3.847 1.527 | -0.252 | 0 | NA | [15, 17]
17 | -11.204 -4.543 1.535 | 0.117 | 0 | A | [16, 25, 18]
18 | -11.919 -4.727 0.349 | 0.046 | 0 | A | [17, 19, 36]
19 | -13.105 -5.431 0.364 | 0.271 | 0 | A | [18, 20, 23]
20 | -13.862 -5.626 -0.893 | 0.062 | 0 | N | [19, 21, 22]
21 | -13.436 -5.167 -1.938 | -0.258 | 0 | OA | [20]
22 | -14.910 -6.247 -0.883 | -0.258 | 0 | OA | [20]
23 | -13.591 -5.955 1.550 | 0.020 | 0 | A | [19, 24, 37]
24 | -12.893 -5.778 2.730 | -0.006 | 0 | A | [23, 25, 38]
25 | -11.698 -5.080 2.732 | 0.204 | 0 | A | [17, 24, 26]
26 | -11.011 -4.907 3.892 | -0.288 | 0 | OA | [25]
27 | -7.566 -2.465 1.565 | -0.053 | 0 | A | [14, 28, 39]
28 | -6.389 -1.771 1.554 | -0.053 | 0 | A | [11, 27, 40]
29 | -2.490 1.228 0.021 | 0.046 | 0 | A | [3, 8, 41]
30 | -0.391 3.868 0.015 | 0.070 | 0 | H | [4]
31 | -2.526 5.086 0.032 | 0.067 | 0 | H | [5]
32 | -4.166 -0.207 1.363 | 0.085 | 0 | H | [10]
33 | -7.248 0.717 -0.603 | 0.063 | 0 | H | [12]
34 | -9.353 -0.529 -0.589 | 0.063 | 0 | H | [13]
35 | -10.744 -2.432 0.201 | 0.085 | 0 | H | [15]
36 | -11.543 -4.320 -0.577 | 0.072 | 0 | H | [18]
37 | -14.521 -6.504 1.552 | 0.070 | 0 | H | [23]
38 | -13.279 -6.190 3.651 | 0.067 | 0 | H | [24]
39 | -7.662 -3.355 2.168 | 0.063 | 0 | H | [27]
40 | -5.557 -2.112 2.152 | 0.063 | 0 | H | [28]
41 | -2.474 0.148 0.018 | 0.072 | 0 | H | [29]
-----+----------------------------+--------+---+----------+--------------- . . .
TOT CHARGE: 0.000

Thanks.

Saverio

PS: I have posted this problem on [email protected] but I guess that this place is more appropriated an the question
is made more clear.
Sorry if this way is an error.

ZINC000001644610.pdbqt.txt
ZINC000001644610.mol2.txt