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#541 Results of obminimize/obenergy differ for MOL/SD files

2.2.x
open
nobody
Command-line Tools (114)
5
2015-01-12
2009-08-07
reiss
No

Given 2 MOL files (0.mol and 1.mol) and an SD file containing these MOL files in the order 0/1 (01.sdf) I do get different results for the second compound in the SD file (actually, for any compound other than the first, if this example is extended to more compounds). The results in detail are:

  1. Feeding MOL files 0.mol and 1.mol:

0.mol:
E N E R G Y

 TOTAL BOND STRETCHING ENERGY =  885.142 kJ/mol
 TOTAL ANGLE BENDING ENERGY =    0.000 kJ/mol
 TOTAL TORSIONAL ENERGY =    0.000 kJ/mol
 TOTAL VAN DER WAALS ENERGY =   28.637 kJ/mol

TOTAL ENERGY = 913.77844 kJ/mol

1.mol:
E N E R G Y

 TOTAL BOND STRETCHING ENERGY =  885.082 kJ/mol
 TOTAL ANGLE BENDING ENERGY =    0.000 kJ/mol
 TOTAL TORSIONAL ENERGY =    0.000 kJ/mol
 TOTAL VAN DER WAALS ENERGY =   40.619 kJ/mol

TOTAL ENERGY = 925.70114 kJ/mol

  1. Feeding SD file 01.sdf:
    E N E R G Y

    TOTAL BOND STRETCHING ENERGY = 885.142 kJ/mol
    TOTAL ANGLE BENDING ENERGY = 0.000 kJ/mol
    TOTAL TORSIONAL ENERGY = 0.000 kJ/mol
    TOTAL VAN DER WAALS ENERGY = 28.637 kJ/mol

TOTAL ENERGY = 913.77844 kJ/mol

E N E R G Y

 TOTAL BOND STRETCHING ENERGY = 25051.011 kJ/mol
 TOTAL ANGLE BENDING ENERGY = 4739.340 kJ/mol
 TOTAL TORSIONAL ENERGY =    0.000 kJ/mol
 TOTAL VAN DER WAALS ENERGY = 30521.391 kJ/mol

TOTAL ENERGY = 60311.74191 kJ/mol

One cleary sees that the result for compound 1 from the SD file is not even close to the one which processing the MOL file of the compound gives (e.g. total energy 925.70114 kJ/mol (MOL) vs. 60311.74191 kJ/mol (SDF).

The behaviour is reproducible on both Windows and Linux (OB 2.2.1 and 2.2.3) .

The same is true for obminimize. If I minimize the above compounds (e.g. obminimize -h -c 1e-4 -o mol 0.mol > 0.min.mol), I do get these results:

0.min.mol:

OpenBabel08070915532D

21 21 0 0 0 0 0 0 0 0999 V2000
-2.4575 5.8304 0.0019 C 0 0 0 0 0
-1.3334 3.7826 0.0003 C 0 0 0 0 0
-0.0840 1.5542 -0.0001 C 0 0 0 0 0
-1.2704 -0.5623 -0.0000 C 0 0 0 0 0
-2.4873 1.5297 -0.0001 C 0 0 0 0 0
-2.4795 0.1324 -0.0000 C 0 0 0 0 0
-1.2974 2.2633 -0.0001 C 0 0 0 0 0
-0.0744 0.1570 -0.0000 C 0 0 0 0 0
-3.7739 6.5786 -0.0053 C 0 0 0 0 0
1.1240 2.2511 -0.0000 O 0 0 0 0 0
-1.4212 6.4741 -0.0002 O 0 0 0 0 0
-0.2658 4.3741 0.0007 O 0 0 0 0 0
-2.4936 4.4784 0.0002 O 0 0 0 0 0
-1.2579 -1.6475 0.0000 H 0 0 0 0 0
-3.4377 2.0474 0.0000 H 0 0 0 0 0
-3.4111 -0.4215 0.0000 H 0 0 0 0 0
0.8601 -0.3966 0.0000 H 0 0 0 0 0
-3.5839 7.6653 0.0048 H 0 0 0 0 0
-4.3770 6.3346 0.8821 H 0 0 0 0 0
-4.3580 6.3482 -0.9090 H 0 0 0 0 0
1.8727 1.6653 0.0000 H 0 0 0 0 0
11 1 2 0 0 0
9 1 1 0 0 0
1 13 1 0 0 0
12 2 2 0 0 0
2 7 1 0 0 0
2 13 1 0 0 0
8 3 2 0 0 0
3 7 1 0 0 0
3 10 1 0 0 0
6 4 2 0 0 0
8 4 1 0 0 0
4 14 1 0 0 0
6 5 1 0 0 0
5 7 2 0 0 0
5 15 1 0 0 0
6 16 1 0 0 0
8 17 1 0 0 0
9 18 1 0 0 0
9 19 1 0 0 0
9 20 1 0 0 0
10 21 1 0 0 0
M END

1.min.mol:

CDK 8/6/09,16:11

13 13 0 0 0 0 0 0 0 0999 V2000
2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2990 3.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2990 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.5981 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2990 2.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.8971 2.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.5981 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.5981 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.2990 2.2500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
12 2 2 0 0 0 0
11 1 2 0 0 0 0
6 4 2 0 0 0 0
6 5 1 0 0 0 0
8 4 1 0 0 0 0
8 3 2 0 0 0 0
5 7 2 0 0 0 0
3 7 1 0 0 0 0
3 13 1 0 0 0 0
2 7 1 0 0 0 0
2 10 1 0 0 0 0
9 1 1 0 0 0 0
1 13 1 0 0 0 0
M END

01.min.sdf:

OpenBabel08070915532D

21 21 0 0 0 0 0 0 0 0999 V2000
-2.4575 5.8304 0.0019 C 0 0 0 0 0
-1.3334 3.7826 0.0003 C 0 0 0 0 0
-0.0840 1.5542 -0.0001 C 0 0 0 0 0
-1.2704 -0.5623 -0.0000 C 0 0 0 0 0
-2.4873 1.5297 -0.0001 C 0 0 0 0 0
-2.4795 0.1324 -0.0000 C 0 0 0 0 0
-1.2974 2.2633 -0.0001 C 0 0 0 0 0
-0.0744 0.1570 -0.0000 C 0 0 0 0 0
-3.7739 6.5786 -0.0053 C 0 0 0 0 0
1.1240 2.2511 -0.0000 O 0 0 0 0 0
-1.4212 6.4741 -0.0002 O 0 0 0 0 0
-0.2658 4.3741 0.0007 O 0 0 0 0 0
-2.4936 4.4784 0.0002 O 0 0 0 0 0
-1.2579 -1.6475 0.0000 H 0 0 0 0 0
-3.4377 2.0474 0.0000 H 0 0 0 0 0
-3.4111 -0.4215 0.0000 H 0 0 0 0 0
0.8601 -0.3966 0.0000 H 0 0 0 0 0
-3.5839 7.6653 0.0048 H 0 0 0 0 0
-4.3770 6.3346 0.8821 H 0 0 0 0 0
-4.3580 6.3482 -0.9090 H 0 0 0 0 0
1.8727 1.6653 0.0000 H 0 0 0 0 0
11 1 2 0 0 0
9 1 1 0 0 0
1 13 1 0 0 0
12 2 2 0 0 0
2 7 1 0 0 0
2 13 1 0 0 0
8 3 2 0 0 0
3 7 1 0 0 0
3 10 1 0 0 0
6 4 2 0 0 0
8 4 1 0 0 0
4 14 1 0 0 0
6 5 1 0 0 0
5 7 2 0 0 0
5 15 1 0 0 0
6 16 1 0 0 0
8 17 1 0 0 0
9 18 1 0 0 0
9 19 1 0 0 0
9 20 1 0 0 0
10 21 1 0 0 0
M END
$$$$

OpenBabel08070915532D

21 21 0 0 0 0 0 0 0 0999 V2000
2.5889 1.4557 0.0001 C 0 0 0 0 0
-0.2646 2.9608 -0.3000 C 0 0 0 0 0
-0.9937 2.1520 -0.3002 C 0 0 0 0 0
-1.2674 -0.7325 -0.0021 C 0 0 0 0 0
-2.5829 1.4912 0.3000 C 0 0 0 0 0
-2.5829 0.0087 0.0369 C 0 0 0 0 0
-1.3235 2.2022 0.3000 C 0 0 0 0 0
-0.6217 0.0084 -0.3001 C 0 0 0 0 0
3.8996 2.2528 -0.0004 C 0 0 0 0 0
-2.6800 3.8801 -0.2449 O 0 0 0 0 0
3.2209 0.0641 -0.3553 O 0 0 0 0 0
-0.6533 4.4795 -0.3000 O 0 0 0 0 0
1.4140 2.4476 0.2457 O 0 0 0 0 0
-1.4931 -1.2499 -0.0139 H 0 0 0 0 0
-2.9507 1.4500 -0.0024 H 0 0 0 0 0
-2.9507 0.0500 -0.0084 H 0 0 0 0 0
0.3301 -0.5576 -0.3001 H 0 0 0 0 0
4.7614 1.5120 0.6001 H 0 0 0 0 0
3.9595 2.9287 0.9095 H 0 0 0 0 0
3.3563 2.8945 -0.9342 H 0 0 0 0 0
-2.5949 4.9500 -0.0222 H 0 0 0 0 0
11 1 2 0 0 0
9 1 1 0 0 0
1 13 1 0 0 0
12 2 2 0 0 0
2 7 1 0 0 0
2 10 1 0 0 0
8 3 2 0 0 0
3 7 1 0 0 0
3 13 1 0 0 0
6 4 2 0 0 0
8 4 1 0 0 0
4 14 1 0 0 0
6 5 1 0 0 0
5 7 2 0 0 0
5 15 1 0 0 0
6 16 1 0 0 0
8 17 1 0 0 0
9 18 1 0 0 0
9 19 1 0 0 0
9 20 1 0 0 0
10 21 1 0 0 0
M END
$$$$

Here, one sees different coordinates for the second compound (which is the same MOL file as 1.mol).

Submitted by: Timo Reiss spaceghost@gmx.li

Discussion

  • reiss

    reiss - 2009-08-07

    Example MOL/SD files

     
    files.zip

  • reiss

    reiss - 2009-08-07

    Dreaded Copy & Paste ... The resulting MOL file of 1.mol is of course not the input but the output: Sorry ... Here is the correct version of 1.min.mol (which still differs from the result of compound 1 from the SD file):

    1.min.mol:

    OpenBabel08070915522D

    21 21 0 0 0 0 0 0 0 0999 V2000
    2.5105 1.4619 0.0030 C 0 0 0 0 0
    -1.2960 3.7419 -0.0000 C 0 0 0 0 0
    -0.0015 1.4855 0.0001 C 0 0 0 0 0
    -1.2936 -0.6432 0.0000 C 0 0 0 0 0
    -2.4365 1.4754 -0.0000 C 0 0 0 0 0
    -2.4850 0.0975 0.0000 C 0 0 0 0 0
    -1.2235 2.2114 -0.0000 C 0 0 0 0 0
    -0.1100 0.0548 0.0000 C 0 0 0 0 0
    3.8173 2.2548 -0.0045 C 0 0 0 0 0
    -2.4895 4.3980 -0.0000 O 0 0 0 0 0
    2.6968 0.2578 -0.0000 O 0 0 0 0 0
    -0.2670 4.3799 0.0000 O 0 0 0 0 0
    1.2859 2.0877 0.0000 O 0 0 0 0 0
    -1.3016 -1.7291 -0.0000 H 0 0 0 0 0
    -3.3772 1.9973 -0.0000 H 0 0 0 0 0
    -3.4290 -0.4497 -0.0000 H 0 0 0 0 0
    0.7677 -0.5599 0.0000 H 0 0 0 0 0
    4.6793 1.5577 0.0039 H 0 0 0 0 0
    3.9209 2.8928 0.8810 H 0 0 0 0 0
    3.9189 2.8675 -0.9078 H 0 0 0 0 0
    -2.4423 5.3543 0.0000 H 0 0 0 0 0
    11 1 2 0 0 0
    9 1 1 0 0 0
    1 13 1 0 0 0
    12 2 2 0 0 0
    2 7 1 0 0 0
    2 10 1 0 0 0
    8 3 2 0 0 0
    3 7 1 0 0 0
    3 13 1 0 0 0
    6 4 2 0 0 0
    8 4 1 0 0 0
    4 14 1 0 0 0
    6 5 1 0 0 0
    5 7 2 0 0 0
    5 15 1 0 0 0
    6 16 1 0 0 0
    8 17 1 0 0 0
    9 18 1 0 0 0
    9 19 1 0 0 0
    9 20 1 0 0 0
    10 21 1 0 0 0
    M END

     

  • reiss

    reiss - 2009-08-07

    I stumbled also over another issue (?) : obenergy uses an empty string as its default force field. The Linux and Windows version seemingly differ in what they return as the default (Windows gets an UFF, wheras Linux gets a Gheminal force field).

     

  • reiss

    reiss - 2009-08-11

    And another issue (maybe) : The results of obminimize and obenergy differ between versions 2.2.1 and 2.2.3. Using the same input files and parameters for both (obminimize -c 1e-4 -ff Ghemical -h resp. obenergy -h -ff UFF).

     

  • reiss

    reiss - 2009-08-11

    Another piece of the puzzle: As zou may already have noticed, the original files I reported the problem for are 'special', i.e. the compounds contained therein are actually different structures for the same sum formula.

    Now, just out of curiosity, I re-ran the test with two completely unrelated compounds (vanilin and morphine). And what can I say? The programs perform as they should, i.e. the results do not differ if the calculations are performed on the individual MOL files or an SD file containing both compounds.

    Maybe this hints you in the correct direction.

     

  • Noel O'Boyle

    Noel O'Boyle - 2009-08-15

    It would be useful if you could file different bug reports for different issues.