ADL: Alternative to MGLTools prepare_ligand4.py

Price, Gareth Gareth.Price at warwick.ac.uk
Tue Jul 23 16:32:31 PDT 2013


Dear Steffen and Ruth

Thank you very much for your swift responses!

Steffen,  I will definitely look into attending that - it seems like it would be very useful with respect to what I am trying to achieve!

Ruth, thank you for alerting me to obabel/babel's ability to do this. I already use obabel, and somehow I managed to miss this feature! I would be interested to see if obabel consistently produces the same atom typing as the prepare_ligand4.py script. Preliminary tests seem to indicate that it does, which is great news!

Thank you for your help :)

Gareth

On 23 Jul 2013, at 23:19, Ruth Huey <rhuey at scripps.edu>
 wrote:

> Hi,
> You could use Open Babel 2.3.2 for this:
>   babel -ipdb ind.pdb -opdbqt ind.pdbqt -p 7.0
> Here's the resulting file, ind.pdbqt... poorly formatted by my mail tool (MS Office Outlook):
> ============================================================
> 
> REMARK  Name = ind.pdb
> REMARK                            x       y       z     vdW  Elec       q    Type
> REMARK                         _______ _______ _______ _____ _____    ______ ____
> ROOT
> ATOM      1  C   LIG    1        0.179  -0.499  -6.803  0.00  0.00    +0.160 C 
> ENDROOT
> BRANCH   1   2
> ATOM      2  O   LIG    1        0.484  -0.830  -8.124  0.00  0.00    -0.387 OA
> ATOM      3  H   LIG    1       -0.010  -0.251  -8.725  0.00  0.00    +0.210 HD
> ENDBRANCH   1   2
> BRANCH   1   4
> ATOM      4  C   LIG    1       -1.311  -0.822  -6.920  0.00  0.00    +0.164 C 
> BRANCH   4   9
> ATOM      5  N   LIG    1       -3.884  -2.421  -3.900  0.00  0.00    +0.247 N 
> ATOM      6  H   LIG    1       -4.598  -2.680  -4.581  0.00  0.00    +0.204 HD
> ATOM      7  C   LIG    1       -3.646  -0.958  -4.031  0.00  0.00    +0.197 C 
> ATOM      8  C   LIG    1       -3.232  -0.342  -5.352  0.00  0.00    +0.198 C 
> ATOM      9  N   LIG    1       -1.962  -1.090  -5.654  0.00  0.00    +0.253 N 
> ATOM     10  H   LIG    1       -1.423  -0.636  -4.917  0.00  0.00    +0.205 HD
> ATOM     11  C   LIG    1       -1.905  -2.547  -5.378  0.00  0.00    +0.184 C 
> ATOM     12  C   LIG    1       -2.680  -3.065  -4.184  0.00  0.00    +0.183 C 
> BRANCH   8  13
> ATOM     13  C   LIG    1       -3.013   1.132  -5.140  0.00  0.00    +0.267 C 
> ATOM     14  O   LIG    1       -2.070   1.525  -4.464  0.00  0.00    -0.269 OA
> ATOM     15  N   LIG    1       -3.881   1.953  -5.698  0.00  0.00    -0.306 N 
> ATOM     16  H   LIG    1       -4.630   1.512  -6.160  0.00  0.00    +0.149 HD
> BRANCH  15  17
> ATOM     17  C   LIG    1       -3.908   3.380  -5.739  0.00  0.00    +0.026 C 
> ATOM     18  C   LIG    1       -3.878   4.005  -4.413  0.00  0.00    +0.031 C 
> ATOM     19  C   LIG    1       -5.273   3.785  -6.326  0.00  0.00    +0.031 C 
> ATOM     20  C   LIG    1       -2.879   3.927  -6.487  0.00  0.00    +0.031 C 
> ENDBRANCH  15  17
> ENDBRANCH   8  13
> BRANCH   5  21
> ATOM     21  C   LIG    1       -4.558  -2.886  -2.682  0.00  0.00    +0.169 C 
> BRANCH  21  22
> ATOM     22  C   LIG    1       -5.993  -2.460  -2.351  0.00  0.00    +0.015 A 
> ATOM     23  C   LIG    1       -6.168  -1.520  -1.359  0.00  0.00    +0.012 A 
> ATOM     24  C   LIG    1       -7.470  -1.143  -1.039  0.00  0.00    +0.020 A 
> ATOM     25  C   LIG    1       -8.548  -1.719  -1.719  0.00  0.00    +0.111 A 
> ATOM     26  N   LIG    1       -8.459  -2.673  -2.731  0.00  0.00    -0.263 NA
> ATOM     27  C   LIG    1       -7.118  -2.997  -2.993  0.00  0.00    +0.119 A 
> ENDBRANCH  21  22
> ENDBRANCH   5  21
> ENDBRANCH   4   9
> ENDBRANCH   1   4
> BRANCH   1  28
> ATOM     28  C   LIG    1        0.740   0.907  -6.523  0.00  0.00    +0.049 C 
> BRANCH  28  29
> ATOM     29  C   LIG    1        2.252   1.135  -6.391  0.00  0.00    +0.082 C 
> BRANCH  29  30
> ATOM     30  C   LIG    1        2.866   0.277  -5.291  0.00  0.00    +0.217 C 
> ATOM     31  O   LIG    1        2.350   0.233  -4.164  0.00  0.00    -0.275 OA
> ATOM     32  N   LIG    1        4.027  -0.296  -5.596  0.00  0.00    -0.306 N 
> ATOM     33  H   LIG    1        4.309  -0.339  -6.538  0.00  0.00    +0.149 HD
> BRANCH  32  34
> ATOM     34  C   LIG    1        4.890  -0.860  -4.571  0.00  0.00    +0.132 C 
> ATOM     35  C   LIG    1        4.800  -2.382  -4.287  0.00  0.00    -0.022 A 
> ATOM     36  C   LIG    1        6.203  -2.978  -3.983  0.00  0.00    -0.040 A 
> ATOM     37  C   LIG    1        6.370  -4.317  -3.716  0.00  0.00    +0.004 A 
> ATOM     38  C   LIG    1        5.237  -5.138  -3.712  0.00  0.00    +0.000 A 
> ATOM     39  C   LIG    1        3.963  -4.609  -3.972  0.00  0.00    +0.000 A 
> ATOM     40  C   LIG    1        7.079  -1.760  -4.129  0.00  0.00    +0.069 C 
> ATOM     41  C   LIG    1        3.766  -3.264  -4.254  0.00  0.00    +0.006 A 
> ATOM     42  C   LIG    1        6.361  -0.677  -4.902  0.00  0.00    +0.143 C 
> BRANCH  42  43
> ATOM     43  O   LIG    1        6.561  -0.743  -6.306  0.00  0.00    -0.389 OA
> ATOM     44  H   LIG    1        6.235  -1.594  -6.639  0.00  0.00    +0.210 HD
> ENDBRANCH  42  43
> ENDBRANCH  32  34
> ENDBRANCH  29  30
> BRANCH  29  45
> ATOM     45  C   LIG    1        2.599   2.609  -6.125  0.00  0.00    +0.048 C 
> BRANCH  45  46
> ATOM     46  C   LIG    1        4.061   2.833  -5.989  0.00  0.00    -0.047 A 
> ATOM     47  C   LIG    1        4.490   3.460  -4.832  0.00  0.00    +0.003 A 
> ATOM     48  C   LIG    1        5.856   3.665  -4.630  0.00  0.00    +0.000 A 
> ATOM     49  C   LIG    1        6.774   3.236  -5.596  0.00  0.00    +0.000 A 
> ATOM     50  C   LIG    1        6.339   2.611  -6.767  0.00  0.00    +0.000 A 
> ATOM     51  C   LIG    1        4.978   2.414  -6.953  0.00  0.00    +0.003 A 
> ENDBRANCH  45  46
> ENDBRANCH  29  45
> ENDBRANCH  28  29
> ENDBRANCH   1  28
> TORSDOF 14
> 
> =====================================================================
> To see more information use:
>  babel -H
> 
>   Best wishes,
>       Ruth
> 
> ________________________________________
> From: autodock-bounces at scripps.edu [autodock-bounces at scripps.edu] On Behalf Of Price, Gareth [Gareth.Price at warwick.ac.uk]
> Sent: Tuesday, July 23, 2013 2:46 PM
> To: autodock at scripps.edu
> Subject: ADL: Alternative to MGLTools prepare_ligand4.py
> 
> Dear all,
> 
> I am developing a small suite of python applications, one of which uses AutoDock Vina.
> 
> Currently, to prepare the PDBQT for screening, I am using  prepare_ligand4.py, which uses the pythonsh binary, both provided by the MGLTools package.
> 
> I am wanting to move the application to a cluster where it may not be possible to either a) access/run the pythonsh binary or b) run the prepare_ligand4.py program in an environment which means that it will work properly.
> 
> Thus, is there an alternative to prepare_ligand4.py? I am aware that it is assigning partial charges and atom types - is there a way to do this without the MGLTools dependency?
> 
> Many thanks,
> Gareth Price
> University of Warwick, UK.
> 
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