ADL: Alternative to MGLTools prepare_ligand4.py

Douglas Houston DouglasR.Houston at ed.ac.uk
Wed Jul 24 05:59:18 PDT 2013


[I sent this earlier but my email address has changed so it bounced back]:


I wouldn't use the -p option, there is a serious bug in Open Babel  
which means it currently generates very wrong charges in many cases.

http://sourceforge.net/p/openbabel/bugs/710/

cheers,

Doug



Quoting "Price, Gareth" <Gareth.Price at warwick.ac.uk> on Tue, 23 Jul  
2013 23:32:31 +0000:

> 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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>>
>> ________________________________________________
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>>
>
>
>
> ________________________________________________
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>
>




_____________________________________________________
Dr. Douglas R. Houston
Lecturer
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



----- End forwarded message -----



_____________________________________________________
Dr. Douglas R. Houston
Lecturer
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.




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