ADL: Q: Vina virtual screening with 9873 molecules downloaded from ZINC15

horse16031603 at yahoo.co.jp horse16031603 at yahoo.co.jp
Mon Sep 21 22:40:59 PDT 2020


Dearhonorable AutoDock users:


 
I downloaded 9873 small moleculesfrom ZINC, and I did my AutoDock Vina with failure. The following is therelated files and troubles.


 
◎    (Note1)  File 9783 ligand 3D pdbqt  molecules downloaded from ZINC15 (it shows thefirst molecule 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 CYGDRIVEwhich shows error message.


 

 
Eiichi Akaho at DESKTOP-EF6R6S2 /cygdrive/c/my_document/vd_1t64_zinc100

$./VS01.bash

Processingligand ZINC19aug

##############################################################

#If you used AutoDock Vina in your work, please cite:       #

#                                                           #

#O. Trott, A. J. Olson,                                     #

#AutoDock Vina: improving the speed and accuracy of docking #

#with a new scoring function, efficient optimization and    #

#multithreading, Journal of Computational Chemistry (2009)  #

#                                                            #

#DOI 10.1002/jcc.21334                                      #

#                                                           #

#Please see http://vina.scripps.edu for more information.   #

##############################################################


 
Detected2 CPUs

Readinginput ...


 
Parse error on line 1 in file"ZINC19aug.pdbqt": Unknown or inappropriate tag


 

 
***What Idid as a tentative trial solution (not a completesolution) is as follows ****


 
I thought that since the line 1 is “MODEL   1”, Putting REMARK in front might work. It worked, but another error,”Parse error on line 43 infile "ZINC19aug.pdbqt": Unknown or inappropriate tag” appeared.

Then  again sinceline 43 is “ENDMOL”, Putting REMARK in frontof “ENDMOL” I thought it might work. It worked,  but another error,”Parse error on line 44 infile "ZINC19aug.pdbqt": Unknown or inappropriate tag” appeared.Unfortunately line 44 is “MODEL 2”. Therefore, this is just a tentative trialsolution (not a complete solution). Since I have 9873 ZINC pdbqt molecules, youknow that my trial solution is not a perfect solution. Please advise me how tosolve this problem satisfactorily.


 

 

 
◎    (Note 3)VS01.bash file


 

 
1. for f in ZINC*.pdbqt; do  b=`basename $f .pdbqt`; echo Processingligand $b; mkdir -p data01; ./Vina/vina --config conf.txt --ligand $f --outdata01/$f.pdbqt --log data01/$f.txt; done

2. #result analysis

3. cd data01

4. grep "   1 " *.txt | cut -c1-12,35-42>>result

5. cat result


 
◎    (Note 4) Conf.txt file


 
receptor = 1t64_lg_lock.pdbqt


 
center_x = 65.825 

center_y = 77.714

center_z = 0.682


 
size_x = 60

size_y = 60

size_z = 60


 
num_modes = 10


 

 

 
Thank you very much for your help in advance.


 
Sincerely yours,


 
Eiichi



More information about the autodock mailing list