Take the 2-minute tour ×
Biology Stack Exchange is a question and answer site for biology researchers, academics, and students. It's 100% free, no registration required.

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)

share|improve this question

1 Answer 1

up vote 4 down vote accepted

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

prepare_ligand4.py -l  my.mol2 -A "hydrogens"
share|improve this answer
    
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? –  Sebastian Raschka Jul 21 at 16:31
    
It will add all hydrogens. The algorithm is like that. You can always manually edit the hydrogen in a pdbqt file. –  Devashish Das Jul 21 at 16:32
1  
-U "" alone might stop merging of hydrogen to the nearest carbon. –  Devashish Das Jul 21 at 16:49
1  
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! –  Sebastian Raschka Jul 21 at 18:11
1  
Thanks a lot, just got it to work if I use -U \""" Thanks for all your help, problem solved :) –  Sebastian Raschka Jul 21 at 18:20

Your Answer

 
discard

By posting your answer, you agree to the privacy policy and terms of service.

Not the answer you're looking for? Browse other questions tagged or ask your own question.