Hi,
we are using Open Babel 2.4.1 and we have found a very strange
behaviour when converting pdbqt format; for instance:
a) babel 3CQA.pdbqt 3CQA_2.pdbqt
(file is pasted below)
it makes unnecessary modifications to several parts of the file
or
b) babel *.pdbqt -opdbqt test_join.pdbqt
in our case this could be
babel 3CQA.pdbqt 3CQA.pdbqt -opdbqt test_join.pdbqt
when we want to join all pdbqt files into a single one, it distorts
some of the pdbqt files
What can be the reason?
Thanks
=============== 3CQA.pdbqt =====
REMARK 12 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: C1_1 and C16_40
REMARK 2 A between atoms: C1_1 and O7_41
REMARK 3 A between atoms: C3_5 and O6_38
REMARK 4 A between atoms: C4_7 and O5_36
REMARK 5 A between atoms: C5_9 and O1_14
REMARK 6 A between atoms: O1_14 and C7_15
REMARK 7 A between atoms: C7_15 and C8_17
REMARK 8 A between atoms: C7_15 and O2_19
REMARK 9 A between atoms: C9_21 and C10_23
REMARK 10 A between atoms: C13_28 and O3_32
REMARK 11 A between atoms: C14_29 and O4_34
REMARK 12 A between atoms: C16_40 and O9_44
ROOT
ATOM 1 C1 <1> d 1 -5.339 2.673 -0.768 0.00 0.00
0.141 C
ATOM 2 C2 <1> d 1 -5.512 3.793 -1.794 0.00 0.00
-0.096 C
ATOM 3 H21 <1> d 1 -6.503 4.255 -1.674 0.00 0.00
0.079 H
ATOM 4 H22 <1> d 1 -5.532 3.384 -2.813 0.00 0.00
0.079 H
ATOM 5 C3 <1> d 1 -4.427 4.866 -1.699 0.00 0.00
0.153 C
ATOM 6 H3 <1> d 1 -3.474 4.479 -2.074 0.00 0.00
0.104 H
ATOM 7 C4 <1> d 1 -4.255 5.402 -0.271 0.00 0.00
0.075 C
ATOM 8 H4 <1> d 1 -3.426 6.119 -0.264 0.00 0.00
0.052 H
ATOM 9 C5 <1> d 1 -4.032 4.272 0.749 0.00 0.00
0.127 C
ATOM 10 H5 <1> d 1 -4.049 4.682 1.767 0.00 0.00
0.054 H
ATOM 11 C6 <1> d 1 -5.144 3.220 0.654 0.00 0.00
-0.102 C
ATOM 12 H61 <1> d 1 -4.922 2.389 1.336 0.00 0.00
0.076 H
ATOM 13 H62 <1> d 1 -6.089 3.654 1.007 0.00 0.00
0.076 H
ENDROOT
BRANCH 9 14
ATOM 14 O1 <1> d 1 -2.801 3.581 0.554 0.00 0.00
-0.449 OA
BRANCH 14 15
ATOM 15 C7 <1> d 1 -1.660 4.418 0.690 0.00 0.00
0.364 C
ATOM 16 H7 <1> d 1 -1.848 5.393 0.240 0.00 0.00
-0.371 H
BRANCH 15 17
ATOM 17 C8 <1> d 1 -0.527 3.740 -0.014 0.00 0.00
0.121 C
ATOM 18 H8 <1> d 1 -0.754 3.451 -1.040 0.00 0.00
-0.190 H
ATOM 19 C9 <1> d 1 0.682 3.466 0.497 0.00 0.00
-0.337 C
ATOM 20 H9 <1> d 1 0.943 3.761 1.510 0.00 0.00
0.216 H
BRANCH 19 21
ATOM 21 C10 <1> d 1 1.728 2.772 -0.260 0.00 0.00
-0.114 A
ATOM 22 C11 <1> d 1 3.040 3.277 -0.228 0.00 0.00
0.135 A
ATOM 23 H11 <1> d 1 3.261 4.187 0.327 0.00 0.00
-0.050 H
ATOM 24 C15 <1> d 1 4.075 2.632 -0.914 0.00 0.00
0.065 A
ATOM 25 C14 <1> d 1 3.792 1.470 -1.619 0.00 0.00
0.206 A
ATOM 26 H15 <1> d 1 5.078 3.047 -0.880 0.00 0.00
-0.001 H
ATOM 27 C13 <1> d 1 2.500 0.954 -1.640 0.00 0.00
-0.073 A
ATOM 28 C12 <1> d 1 1.465 1.592 -0.970 0.00 0.00
-0.117 A
ATOM 29 H12 <1> d 1 0.468 1.161 -0.995 0.00 0.00
0.138 H
BRANCH 25 30
ATOM 30 O4 <1> d 1 4.749 0.781 -2.312 0.00 0.00
-0.493 OA
ATOM 31 H4 <1> d 1 5.586 1.270 -2.230 0.00 0.00
0.437 HD
ENDBRANCH 25 30
BRANCH 27 32
ATOM 32 O3 <1> d 1 2.256 -0.203 -2.325 0.00 0.00
-0.417 OA
ATOM 33 H3 <1> d 1 3.131 -0.454 -2.689 0.00 0.00
0.337 HD
ENDBRANCH 27 32
ENDBRANCH 19 21
ENDBRANCH 15 17
BRANCH 15 34
ATOM 34 O2 <1> d 1 -1.363 4.691 2.048 0.00 0.00
-0.108 OA
ATOM 35 H2 <1> d 1 -1.190 3.852 2.482 0.00 0.00
0.450 HD
ENDBRANCH 15 34
ENDBRANCH 14 15
ENDBRANCH 9 14
BRANCH 7 36
ATOM 36 O5 <1> d 1 -5.439 6.147 0.051 0.00 0.00
-0.542 OA
ATOM 37 H5 <1> d 1 -5.301 6.565 0.921 0.00 0.00
0.430 HD
ENDBRANCH 7 36
BRANCH 5 38
ATOM 38 O6 <1> d 1 -4.805 5.961 -2.541 0.00 0.00
-0.599 OA
ATOM 39 H6 <1> d 1 -5.461 6.464 -2.013 0.00 0.00
0.409 HD
ENDBRANCH 5 38
BRANCH 1 40
ATOM 40 C16 <1> d 1 -4.215 1.701 -1.170 0.00 0.00
0.013 C
ATOM 41 O8 <1> d 1 -3.226 1.928 -1.845 0.00 0.00
-0.500 OA
BRANCH 40 42
ATOM 42 O9 <1> d 1 -4.457 0.459 -0.673 0.00 0.00
-0.070 OA
ATOM 43 H9 <1> d 1 -3.689 -0.077 -0.972 0.00 0.00
-0.142 HD
ENDBRANCH 40 42
ENDBRANCH 1 40
BRANCH 1 44
ATOM 44 O7 <1> d 1 -6.557 1.903 -0.767 0.00 0.00
-0.060 OA
ATOM 45 H7 <1> d 1 -6.306 1.026 -0.407 0.00 0.00
0.494 HD
ENDBRANCH 1 44
TORSDOF 12
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