ADL: virtual screening

horse16031603 at yahoo.co.jp horse16031603 at yahoo.co.jp
Fri Aug 28 22:40:02 PDT 2020


Dear Diogo and all:Thank you for your response for my virtual screening problem.Answering your request the following is my pdbqt file downloaded from ZINC15 (Note1) and the Cygwin files and run result indicating the error (Note2).I appreciate your help from the bottom of my heart.Eiichi
◎(Note1)     File 9783 ligand 3D pdbqt  molecules downloaded from ZINC15 (it shows thefirst one and the last one)


 

 
MODEL       1

REMARK  Name= ZINC000000011175

REMARK  5active torsions:

REMARK status: ('A' for Active; 'I' for Inactive)

REMARK   1  A    between atoms: C1_1  and C2_2

REMARK   2  A    between atoms: N4_4  and C5_5

REMARK   3  A    between atoms: C8_8  and C10_10

REMARK   4  A    between atoms: C10_10  and O11_11

REMARK   5  A    between atoms: C13_13  and O15_15

REMARK                            x       y      z     vdW  Elec      q    Type

REMARK                         _______ ______________ _____ _____    ______ ____

ROOT

ATOM     1  C1  <0> A  1      -0.018   1.503  0.010  0.00  0.00   +0.140 C 

ATOM      2 C2  <0> A   1      0.002  -0.004   0.002 0.00  0.00    -0.270 C 

ATOM     3  C3  <0> A  1      -1.153  -0.704  0.004  0.00  0.00   +0.370 C 

ATOM     4  N4  <0> A  1      -1.116  -2.072 -0.004  0.00  0.00   -0.520 N 

ATOM    13  C16 <0> A   1      0.060  -2.726  -0.013 0.00  0.00    +0.710 C 

ATOM    14  O17 <0> A   1      0.069  -3.942  -0.020 0.00  0.00    -0.540 OA

ATOM    15  N18 <0> A   1      1.226  -2.053  -0.016 0.00  0.00    -0.660 N 

ATOM    16  C19 <0> A   1      1.232  -0.705  -0.013 0.00  0.00    +0.550 C 

ATOM    17  O20 <0> A   1      2.287  -0.095  -0.016 0.00  0.00    -0.510 OA

ATOM    20  H31 <0> A   1      2.064  -2.540  -0.023 0.00  0.00    +0.430 HD

ENDROOT

BRANCH  4   5

ATOM     5  C5  <0> A  1      -2.369  -2.831 -0.002  0.00  0.00   +0.440 C 

ATOM     6  O7  <0> A  1      -3.500  -1.935 -0.062  0.00  0.00   -0.360 OA

ATOM     7  C8  <0> A  1      -4.597  -2.740 -0.547  0.00  0.00   +0.170 C 

ATOM    10  C12 <0> A   1     -3.978  -3.629  -1.647 0.00  0.00    +0.010 C 

ATOM    11  C13 <0> A   1     -2.477  -3.693  -1.280 0.00  0.00    +0.160 C 

BRANCH 11  12

ATOM    12  O15 <0> A   1     -1.680  -3.138  -2.328 0.00  0.00    -0.550 OA

ATOM    19  H30 <0> A   1     -1.759  -3.605  -3.171 0.00  0.00    +0.390 HD

ENDBRANCH 11  12

BRANCH  7   8

ATOM     8  C10 <0> A   1     -5.693  -1.847  -1.133 0.00  0.00    +0.210 C 

BRANCH  8   9

ATOM     9  O11 <0> A   1     -6.280  -1.066  -0.090 0.00  0.00    -0.570 OA

ATOM    18  H27 <0> A   1     -6.985  -0.476  -0.391 0.00  0.00    +0.390 HD

ENDBRANCH  8   9

ENDBRANCH  7   8

ENDBRANCH  4   5

TORSDOF 4

ENDMDL

|

|

|

MODEL    9783

REMARK  Name= ZINC000739744108

REMARK  6active torsions:

REMARK status: ('A' for Active; 'I' for Inactive)

REMARK   1  A    between atoms: C1_1  and N2_2

REMARK   2  A    between atoms: C3_3  and C5_5

REMARK   3  A    between atoms: C5_5  and C6_6

REMARK    4 A    between atoms: N8_8  and C9_9

REMARK   5  A    between atoms: C9_9  and C10_10

REMARK   6  A    between atoms: C10_10  and N11_11

REMARK                            x       y      z     vdW  Elec      q    Type

REMARK                         _______ _______ _______ _____ _____    ______ ____

ROOT

ATOM     6  C6  ZIN A  1       0.667  -2.924  0.161  0.00  0.00   +0.560 C 

ATOM     7  O7  ZIN A  1       1.353  -3.920  0.250  0.00  0.00   -0.530 OA

ATOM     8  N8  ZIN A  1      -0.037  -2.493  1.227  0.00  0.00   -0.710 N 

ATOM    18  H21 ZIN A   1     -0.527  -1.658   1.179 0.00  0.00    +0.410 HD

ENDROOT

BRANCH  6   5

ATOM     5  C5  ZIN A  1       0.601  -2.167 -1.140  0.00  0.00   -0.200 C 

ATOM    15  C15 ZIN A   1     -0.616  -2.405  -2.036 0.00  0.00    +0.090 C 

ATOM    16  C16 ZIN A   1      0.749  -2.971  -2.433 0.00  0.00    +0.100 C 

BRANCH  5   3

ATOM     1  C1  ZIN A  1       3.029   0.770 -1.492  0.00  0.00   +0.290 C 

ATOM     2  N2  ZIN A  1       2.486  -0.588 -1.409  0.00  0.00   -0.730 N 

ATOM     3  C3  ZIN A  1       1.185  -0.778 -1.115  0.00  0.00   +0.560 C 

ATOM     4  O4  ZIN A  1       0.484   0.170 -0.829  0.00  0.00   -0.520 OA

ATOM    17  H20 ZIN A   1      3.064  -1.351  -1.567 0.00  0.00    +0.410 HD

ENDBRANCH  5   3

ENDBRANCH  6   5

BRANCH  8   9

ATOM     9  C9  ZIN A  1      -0.062  -3.288  2.458  0.00  0.00   +0.250 C 

BRANCH  9  10

ATOM    10  C10 ZIN A   1     -0.926  -2.581   3.504 0.00  0.00    +0.230 C 

BRANCH 10  11

ATOM    11  N11 ZIN A   1     -0.951  -3.375   4.735 0.00  0.00    -0.780 N 

ATOM    12  C12 ZIN A   1     -1.655  -2.945   5.800 0.00  0.00    +0.660 C 

ATOM    13  O13 ZIN A   1     -2.273  -1.891   5.740 0.00  0.00    -0.720 OA

ATOM    14  O14 ZIN A   1     -1.675  -3.608   6.828 0.00  0.00    -0.720 OA

ATOM    19  H26 ZIN A   1     -0.460  -4.211   4.782 0.00  0.00    +0.370 HD

ENDBRANCH 10  11

ENDBRANCH  9  10

ENDBRANCH  8   9

TORSDOF 5

ENDMDL


 

 
◎ (Note2)    Virtual screening run by CYGDRIVE whichshows error message.


 

 

 
Eiichi Akaho at DESKTOP-EF6R6S2 /cygdrive/c/my_document/zinc9783

$ ls

19aug.pdbqt    1t64.pdb          1t64_lg_lock.pdbqt  AutoDockTools VS01.bash  cAutoDock  data01

19aug2020.mol2 1t64_lg_lock.pdb  AutoDockFR          PyAutoDock     Vina      conf.txt   out3.bash


 
Eiichi Akaho at DESKTOP-EF6R6S2 /cygdrive/c/my_document/zinc9783

$ ./VS01.bash

Processing ligand ZINC*

Command line parse error: too many positionaloptions


 
Correct usage:


 
Input:

  --receptorarg        rigid part of the receptor(PDBQT)

  --flexarg            flexible side chains, ifany (PDBQT)

  --ligandarg          ligand (PDBQT)


 
Search space (required):

  --center_xarg        X coordinate of the center

  --center_yarg        Y coordinate of the center

  --center_zarg        Z coordinate of the center

  --size_xarg          size in the X dimension(Angstroms)

  --size_y arg          size in the Y dimension (Angstroms)

  --size_zarg          size in the Z dimension(Angstroms)


 
Output (optional):

  --outarg             output models (PDBQT),the default is chosen based on

                        the ligand file name

  --logarg             optionally, write logfile


 
Misc (optional):

  --cpuarg                 the number of CPUs touse (the default is to try to

                            detect the numberof CPUs or, failing that, use 1)

  --seedarg                explicit random seed

 --exhaustiveness arg (=8) exhaustiveness of the global search (roughly

                            proportional totime): 1+

  --num_modesarg (=9)      maximum number of bindingmodes to generate

 --energy_range arg (=3)   maximumenergy difference between the best binding

                            mode and the worstone displayed (kcal/mol)


 
Configuration file (optional):

  --config arg          the above options can be put here


 
Information (optional):

  --help                print this message

 --version             printprogram version


 
ZINC02584527 -3.9

ZINC02584532 -4.1

ZINC02584527 -3.7

ZINC02584532 -4.1

ZINC02584527 -4.1

ZINC02584532 -4.1

ZINC02584527 -3.8

ZINC02584532 -4.1

ZINC02584527 -4.5

ZINC02584532 -4.1

ZINC02584527 -4.1

ZINC02584532 -4.1

ZINC02584527 -3.8

ZINC02584532 -4.9

ZINC02584527 -3.8

ZINC02584532 -4.9

ZINC02584527 -4.1

ZINC02584532 -4.1

ZINC02584532 -4.2

ZINC02584532 -4.1

ZINC02584532 -4.0

ZINC02584532 -4.1

ZINC02584532 -4.1

ZINC02584532 -4.9

ZINC02584532 -4.1

ZINC02584532 -4.1

ZINC19aug_1t   -5.1

ZINC02584532 -4.0

ZINC19aug_1t   -5.1

ZINC02584532 -4.9

ZINC19aug_1t   -5.4

ZINC02584532 -3.8

ZINC19aug_1t   -5.3

ZINC02584532 -4.1

ZINC19aug_1t   -5.3

ZINC02584532 -4.0

ZINC19aug_1t   -5.2

ZINC02584532 -4.1

ZINC19aug_1t   -5.1

ZINC02584532 -4.1

ZINC19aug_1t   -5.2

ZINC02584532 -4.1

ZINC19aug_1t   -5.3

ZINC02584532 -4.1

ZINC19aug_1t   -5.3

ZINC02584532 -4.1

ZINC19aug_1t   -5.3


 
Eiichi Akaho at DESKTOP-EF6R6S2 /cygdrive/c/my_document/zinc9783

$



     ----- Original Message -----
 From: Diogo Martins <diogo.stmart at gmail.com>
 To: autodock at scripps.edu; horse16031603 at yahoo.co.jp 
 Date: 2020/8/29, Sat 01:56
 Subject: Re: ADL: virtual screening
   
Dear Eiichi,
It could be, for example, a ROOT or BRANCH keyword in the receptor .pdbqt. Can you post the exact error message?
Best regards,
On Fri, 28 Aug 2020 at 00:10, <horse16031603 at yahoo.co.jp> wrote:


Dear honorable AutoDock users:I have downloaded over 500 pdbqt 3D molecules from ZINC15, and tried to perform virtual screening by using AutoDock Vina. But I get error massages saying "in line  and such line, there is unknown or inappropriate tag". Is there any way to download the file avoiding these error massage. Or is there any way to do the virtual screeningavoiding the error.Your help is greatly appreciated.Eiichi
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