ADL: Alternative to MGLTools prepare_ligand4.py

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ADL: Alternative to MGLTools prepare_ligand4.py

Price, Gareth
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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Re: ADL: Alternative to MGLTools prepare_ligand4.py

Ruth Huey
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: [hidden email] [[hidden email]] On Behalf Of Price, Gareth [[hidden email]]
Sent: Tuesday, July 23, 2013 2:46 PM
To: [hidden email]
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.

________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
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Re: ADL: Alternative to MGLTools prepare_ligand4.py

Price, Gareth
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 <[hidden email]>
 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: [hidden email] [[hidden email]] On Behalf Of Price, Gareth [[hidden email]]
> Sent: Tuesday, July 23, 2013 2:46 PM
> To: [hidden email]
> 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.
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>



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Re: ADL: Alternative to MGLTools prepare_ligand4.py

HOUSTON Douglas
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/


Quoting "Price, Gareth" <[hidden email]> 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 <[hidden email]>
>  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: [hidden email] [[hidden email]]  
>> On Behalf Of Price, Gareth [[hidden email]]
>> Sent: Tuesday, July 23, 2013 2:46 PM
>> To: [hidden email]
>> 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.
>>
>> ________________________________________________
>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>>
>> ________________________________________________
>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>>
>
>
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
>




_____________________________________________________
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

--
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Scotland, with registration number SC005336.


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Re: ADL: Alternative to MGLTools prepare_ligand4.py

Brian Moldover
In reply to this post by Price, Gareth
Hi Gareth,

I am also interested in your apps, especially as you move it to a cluster.
Thanks!

Brian

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On
Behalf Of Price, Gareth
Sent: Tuesday, July 23, 2013 7:33 PM
To: <[hidden email]>
Subject: Re: ADL: Alternative to MGLTools prepare_ligand4.py

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 <[hidden email]>
 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: [hidden email] [[hidden email]] On
> Behalf Of Price, Gareth [[hidden email]]
> Sent: Tuesday, July 23, 2013 2:46 PM
> To: [hidden email]
> 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.
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list 
> ---
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list 
> ---
>



________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

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Re: ADL: Alternative to MGLTools prepare_ligand4.py

HOUSTON Douglas
In reply to this post by Price, Gareth
[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" <[hidden email]> 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 <[hidden email]>
> 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: [hidden email] [[hidden email]]  
>> On Behalf Of Price, Gareth [[hidden email]]
>> Sent: Tuesday, July 23, 2013 2:46 PM
>> To: [hidden email]
>> 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.
>>
>> ________________________________________________
>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>>
>> ________________________________________________
>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>>
>
>
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
>




_____________________________________________________
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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Re: ADL: Alternative to MGLTools prepare_ligand4.py

Ruth Huey
>From the 710 bug report, it appears that using -h instead is ok .

babel -isdf molecule.sdf -omol2 molecule_H.mol2 -h

      Ruth

________________________________________
From: [hidden email] [[hidden email]] On Behalf Of Douglas Houston [[hidden email]]
Sent: Wednesday, July 24, 2013 5:59 AM
To: [hidden email]
Subject: Re: Alternative to MGLTools prepare_ligand4.py

[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" <[hidden email]> 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 <[hidden email]>
> 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: [hidden email] [[hidden email]]
>> On Behalf Of Price, Gareth [[hidden email]]
>> Sent: Tuesday, July 23, 2013 2:46 PM
>> To: [hidden email]
>> 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.
>>
>> ________________________________________________
>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>>
>> ________________________________________________
>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>>
>
>
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
>




_____________________________________________________
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.


________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---