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I am trying to convert a MOL2 file (includes partial charges and hydrogen atoms) into a PDBQT file for re-scoring in AutoDock Vina. However, both approaches that I tried don't keep the hydrogen atoms from the MOL2 file (the PDBQT file doesn't contain hydrogen atoms).

The command I used for OpenBabel is

babel -i mol2 my.mol2 -o my.pdbqt

When I look at the documentation, they babel has a dedicated "-d" flag for removing hydrogens. So I assume that this shouldn't happen by default?

The same thing happens if I use MGLTools

prepare_ligand4.py -l  my.mol2 

Any ideas of what might be going on here?

Thanks for your help!

will append the MOL2 file if someone wants to try it:

@<TRIPOS>MOLECULE
mymol2
   25    25     0     0     0
SMALL
USER_CHARGES
@<TRIPOS>ATOM
      1 C1         -1.0341   29.2934  -14.5590 C.ar      1 <0>       -0.1745 
      2 C2         -0.1917   29.9513  -13.6630 C.ar      1 <0>       -0.1483 
      3 C3         -2.3919   29.1585  -14.2689 C.ar      1 <0>       -0.1608 
      4 C4         -0.7068   30.4744  -12.4770 C.ar      1 <0>       -0.0956 
      5 C5         -2.9070   29.6816  -13.0828 C.ar      1 <0>       -0.1543 
      6 C6         -2.0573   30.3323  -12.2033 C.ar      1 <0>       -0.0209 
      7 C7         -5.0136   30.3602   -8.9792 C.2       1 <0>        0.9092 
      8 C8         -1.1556   29.8264   -9.1470 C.2       1 <0>        0.9071 
      9 C9         -2.6151   30.8987  -10.9189 C.3       1 <0>       -0.0262 
     10 C10        -3.5221   30.2951   -8.6255 C.3       1 <0>       -0.1568 
     11 C11        -2.5717   29.8912   -9.7583 C.3       1 <0>       -0.1554 
     12 O1         -5.7013   31.2223   -8.3667 O.co2     1 <0>       -0.8817 
     13 O2         -0.7003   30.9084   -8.6799 O.co2     1 <0>       -0.8929 
     14 O3         -5.3714   29.5329   -9.8669 O.co2     1 <0>       -0.8807 
     15 O4         -0.6188   28.6818   -9.1887 O.co2     1 <0>       -0.8571 
     16 H1         -0.6331   28.8861  -15.4824 H         1 <0>        0.0899 
     17 H2          0.8655   30.0564  -13.8891 H         1 <0>        0.1079 
     18 H3         -3.0478   28.6460  -14.9665 H         1 <0>        0.0917 
     19 H4         -0.0427   30.9855  -11.7849 H         1 <0>        0.2049 
     20 H5         -3.9661   29.5717  -12.8653 H         1 <0>        0.1145 
     21 H6         -2.0757   31.8190  -10.6595 H         1 <0>        0.0142 
     22 H7         -3.6485   31.2140  -11.1119 H         1 <0>        0.0547 
     23 H8         -3.4370   29.5769   -7.7988 H         1 <0>       -0.0109 
     24 H9         -3.2268   31.2722   -8.2199 H         1 <0>        0.0482 
     25 H10        -2.8394   28.8903  -10.1212 H         1 <0>        0.0739 
@<TRIPOS>BOND
    1     1     2 ar
    2     1     3 ar
    3     2     4 ar
    4     3     5 ar
    5     4     6 ar
    6     5     6 ar
    7     6     9 1
    8     7    10 1
    9     7    12 1
   10     7    14 2
   11     8    11 1
   12     8    13 1
   13     8    15 2
   14     9    11 1
   15    10    11 1
   16     1    16 1
   17     2    17 1
   18     3    18 1
   19     4    19 1
   20     5    20 1
   21     9    21 1
   22     9    22 1
   23    10    23 1
   24    10    24 1
   25    11    25 1
@<TRIPOS>SUBSTRUCTURE

EDIT:

The solution to the problem with prepare_ligand4.py would be

prepare_ligand4.py -l  my.mol2  -U \""" -C

to keep the partial charges and hydrogen atoms (oddly, -U "" didn't work for me: prepare_ligand4.py: option -U requires argument)

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You saw my last answer of your question? you can do that easily, just use

prepare_ligand4.py -l  my.mol2 -A "hydrogens"
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  • $\begingroup$ Thanks, I didn't see that you updated it. But one important question: in the help menu it says "-A type(s) of repairs to make:" does it add hydrogens or does it preserve the original ones? $\endgroup$ – user6881 Jul 21 '14 at 16:31
  • $\begingroup$ It will add all hydrogens. The algorithm is like that. You can always manually edit the hydrogen in a pdbqt file. $\endgroup$ – Devashish Das Jul 21 '14 at 16:32
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    $\begingroup$ -U "" alone might stop merging of hydrogen to the nearest carbon. $\endgroup$ – Devashish Das Jul 21 '14 at 16:49
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    $\begingroup$ Same problem with and without the -C, somehow it is not accepting the empty string for the -U parameter. Thanks for all your help btw, I really appreciate it! $\endgroup$ – user6881 Jul 21 '14 at 18:11
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    $\begingroup$ Thanks a lot, just got it to work if I use -U \""" Thanks for all your help, problem solved :) $\endgroup$ – user6881 Jul 21 '14 at 18:20
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In babel:

babel my.mol2 my.pdbqt -xh

-x states options for writing .pdbqt files -h says keep hydrogens

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