ADL: vina virtual
horse16031603 at yahoo.co.jp
horse16031603 at yahoo.co.jp
Sat Nov 21 23:19:48 PST 2020
Dear honorable Autodock users:I try to virtual screening by Vina and ZINC ligands (9872 molecules, file 1).But error shows up (file 2).
Bash file (file 3) is the one I used for my publication (attached file: vsdk.pdf )which worlked well.
I appreciate your advice to solve this error.
All the best.
Eiichi
*** file 1***REMARK 2
REMARK Name = ZINC000000517234
REMARK 4 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: C2_2 and C4_4
REMARK 2 A between atoms: C4_4 and C5_5
REMARK 3 A between atoms: C5_5 and C6_6
REMARK 4 A between atoms: N8_8 and C9_9
REMARK x y z vdW Elec q Type
REMARK _______ ______________ _____ _____ ______ ____
REMARK
ATOM 9 C9 <0> d -6.176 1.669 0.147 0.00 0.00 -0.010 C
ATOM 10 C10 <0> d -7.186 1.421 -0.721 0.00 0.00 +0.320 C
ATOM 11 N11 <0> d -8.373 2.097 -0.591 0.00 0.00 -0.630 N
ATOM 12 C12 <0> d -8.542 3.002 0.389 0.00 0.00 +0.700 C
ATOM 13 O13 <0> d -9.602 3.590 0.484 0.00 0.00 -0.550 OA
ATOM 14 N14 <0> d -7.556 3.269 1.265 0.00 0.00 -0.650 N
ATOM 15 C15 <0> d -6.375 2.624 1.179 0.00 0.00 +0.550 C
ATOM 16 O16 <0> d -5.484 2.865 1.973 0.00 0.00 -0.480 OA
ATOM 18 H23 <0> d -9.096 1.920 -1.212 0.00 0.00 +0.440 HD
ATOM 19 H24 <0> d -7.697 3.925 1.965 0.00 0.00 +0.430 HD
ENDREMARK
BRANCH 9 8
ATOM 6 C6 <0> d -3.809 1.679 -0.140 0.00 0.00 +0.520 C
ATOM 7 O7 <0> d -3.845 2.883 -0.285 0.00 0.00 -0.520 OA
ATOM 8 N8 <0> d -4.952 0.987 0.031 0.00 0.00 -0.670 N
ATOM 17 H21 <0> d -4.931 0.018 0.074 0.00 0.00 +0.410 HD
BRANCH 6 5
ATOM 5 C5 <0> d -2.485 0.958 -0.151 0.00 0.00 +0.080 C
BRANCH 5 4
ATOM 4 C4 <0> d -1.356 1.968 -0.361 0.00 0.00 -0.050 C
BRANCH 4 2
ATOM 1 O1 <0> d 0.004 0.037 -0.226 0.00 0.00 -0.700 OA
ATOM 2 C2 <0> d -0.033 1.247 -0.372 0.00 0.00 +0.490 C
ATOM 3 O3 <0> d 1.002 1.873 -0.532 0.00 0.00 -0.700 OA
ENDBRANCH 4 2
ENDBRANCH 5 4
ENDBRANCH 6 5
ENDBRANCH 9 8
TORSDOF 4
REMARK
REMARK 3
REMARK Name = ZINC000000517234
REMARK 4 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: C2_2 and C4_4
REMARK 2 A between atoms: C4_4 and C5_5
REMARK 3 A between atoms: C5_5 and C6_6
REMARK 4 A between atoms: N8_8 and C9_9
REMARK x y z vdW Elec q Type
REMARK _______ ______________ _____ _____ ______ ____
REMARK
ATOM 6 C6 <0> d -3.809 1.679 -0.140 0.00 0.00 +0.510 C
ATOM 7 O7 <0> d -3.845 2.883 -0.285 0.00 0.00 -0.520 OA
ATOM 8 N8 <0> d -4.952 0.987 0.031 0.00 0.00 -0.670 N
ATOM 17 H21 <0> d -4.931 0.018 0.074 0.00 0.00 +0.390 HD
ENDREMARK
BRANCH 8 9
ATOM 9 C9 <0> d -6.176 1.669 0.147 0.00 0.00 -0.040 C
ATOM 10 C10 <0> d -7.186 1.421 -0.721 0.00 0.00 +0.240 C
ATOM 11 N11 <0> d -8.373 2.097 -0.591 0.00 0.00 -0.670 N
ATOM 12 C12 <0> d -8.542 3.002 0.389 0.00 0.00 +0.640 C
ATOM 13 O13 <0> d -9.602 3.590 0.484 0.00 0.00 -0.630 OA
ATOM 14 N14 <0> d -7.556 3.269 1.265 0.00 0.00 -0.700 NA
ATOM 15 C15 <0> d -6.375 2.624 1.179 0.00 0.00 +0.520 C
ATOM 16 O16 <0> d -5.484 2.865 1.973 0.00 0.00 -0.570 OA
ATOM 18 H23 <0> d -9.096 1.920 -1.212 0.00 0.00 +0.390 HD
ENDBRANCH 8 9
BRANCH 6 5
ATOM 5 C5 <0> d -2.485 0.958 -0.151 0.00 0.00 +0.060 C
BRANCH 5 4
ATOM 4 C4 <0> d -1.356 1.968 -0.361 0.00 0.00 -0.040 C
BRANCH 4 2
ATOM 1 O1 <0> d 0.004 0.037 -0.226 0.00 0.00 -0.710 OA
ATOM 2 C2 <0> d -0.033 1.247 -0.372 0.00 0.00 +0.490 C
ATOM 3 O3 <0> d 1.002 1.873 -0.532 0.00 0.00 -0.710 OA
ENDBRANCH 4 2
ENDBRANCH 5 4
ENDBRANCH 6 5
TORSDOF 4
Partially omitted
REMARK
REMARK 9781
REMARK Name = ZINC000739742645
REMARK 9 active 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 C7_7
REMARK 4 A between atoms: C5_5 and N8_8
REMARK 5 A between atoms: C9_9 and C11_11
REMARK 6 A between atoms: C11_11 and O12_12
REMARK 7 A between atoms: O12_12 and C13_13
REMARK 8 A between atoms: C13_13 and C14_14
REMARK 9 A between atoms: C14_14 and N15_15
REMARK x y z vdW Elec q Type
REMARK _______ ______________ _____ _____ ______ ____
REMARK
ATOM 7 N8 <0> d -2.510 -2.708 0.011 0.00 0.00 -0.720 N
ATOM 8 C9 <0> d -2.771 -3.936 0.501 0.00 0.00 +0.520 C
ATOM 9 O10 <0> d -1.869 -4.622 0.932 0.00 0.00 -0.510 OA
ATOM 19 H26 <0> d -3.232 -2.159 -0.334 0.00 0.00 +0.410 HD
ENDREMARK
BRANCH 7 5
ATOM 5 C5 <0> d -1.135 -2.201 0.001 0.00 0.00 +0.250 C
ATOM 6 C7 <0> d -0.419 -2.694 -1.258 0.00 0.00 +0.050 C
BRANCH 5 3
ATOM 1 C1 <0> d -0.018 1.461 0.010 0.00 0.00 +0.290 C
ATOM 2 N2 <0> d 0.002 -0.004 0.002 0.00 0.00 -0.730 N
ATOM 3 C3 <0> d -1.156 -0.694 0.009 0.00 0.00 +0.510 C
ATOM 4 O4 <0> d -2.214 -0.102 0.023 0.00 0.00 -0.530 OA
ATOM 18 H22 <0> d 0.849 -0.478 -0.009 0.00 0.00 +0.410 HD
ENDBRANCH 5 3
ENDBRANCH 7 5
BRANCH 8 10
ATOM 10 C11 <0> d -4.185 -4.458 0.511 0.00 0.00 +0.200 C
BRANCH 10 11
ATOM 11 O12 <0> d -4.204 -5.771 1.074 0.00 0.00 -0.350 OA
BRANCH 11 12
ATOM 12 C13 <0> d -5.505 -6.360 1.131 0.00 0.00 +0.160 C
BRANCH 12 13
ATOM 13 C14 <0> d -5.405 -7.757 1.747 0.00 0.00 +0.260 C
BRANCH 13 14
ATOM 14 N15 <0> d -4.968 -7.646 3.141 0.00 0.00 -0.780 N
ATOM 15 C16 <0> d -4.810 -8.756 3.889 0.00 0.00 +0.660 C
ATOM 16 O17 <0> d -5.031 -9.857 3.403 0.00 0.00 -0.730 OA
ATOM 17 O18 <0> d -4.446 -8.663 5.052 0.00 0.00 -0.730 OA
ATOM 20 H33 <0> d -4.793 -6.773 3.526 0.00 0.00 +0.370 HD
ENDBRANCH 13 14
ENDBRANCH 12 13
ENDBRANCH 11 12
ENDBRANCH 10 11
ENDBRANCH 8 10
TORSDOF 7
***file 2***attached file:pri_scr_line12.png***
***file 3***1 #!/bin/bash
2 for f inZINC*.pdbqt; do b=`basename $f .pdbqt`;echo Processing ligand $b; mkdir -p data01; ./Vina/vina --config conf.txt--ligand $f --out data01/$f.pdbqt --log data01/$f.txt; done
3 #result analysis
4 cd data01
5 grep " 1 " *.txt | cut -c1-12,35-42>>result
6 cat result
********************
-------------- next part --------------
A non-text attachment was scrubbed...
Name: vsdk.pdf
Type: application/pdf
Size: 122895 bytes
Desc: not available
URL: <http://mgldev.scripps.edu/pipermail/autodock/attachments/20201122/7534824a/attachment-0001.pdf>
More information about the autodock
mailing list