Subject: problems with MOPAC93 and "real! water molecules

From: [email-masked] (Kay Kreidler)
Date: Thu, 8 Feb 1996 16:49:53 +0000 (WET)

Dear netters!

I have a problem with MOPAC93 (Revision No. 2). I am doing calculations on
organic acids and their corresponding anions in aqueous solution. 
Because of the ability of the molecules to form inter/intramolecular hydrogen 
bonds I would like not to calculate them with a continuum model of solvation.
I added approx. 30 real molecules of water to the system and tried to optimize
it. The calculation started successfully but stopped each time with the 
following error message:

                     CALCULATION ABANDONED AT THIS POINT

           THREE ATOMS BEING USED TO DEFINE THE
           COORDINATES OF A FOURTH ATOM, WHOSE BOND-ANGLE IS
           NOT ZERO OR 180 DEGREEES, ARE IN AN ALMOST STRAIGHT
           LINE.  THERE IS A HIGH PROBABILITY THAT THE
           COORDINATES OF THE ATOM WILL BE INCORRECT.

Is there any chance to avoid this error, which occurs during every calculation
dealing with this scheme of adding the water molecules?

I read the error section of the manual, which didn't sound very hopeful. 
Redefining the starting structure seems not to be the right choice, as the
error occurs after several optimization cycles. 

Using the program "Hyperchem" from Hypercube the calculation is successful, so
it seems, that this kind of calculation is available. 

For better understanding I will add the .out file of the calculation:

 *******************************************************************************
 ** FRANK J. SEILER RES. LAB., U.S. AIR FORCE ACADEMY, COLO. SPGS., CO. 80840 **
 *******************************************************************************

                                 PM3 CALCULATION RESULTS

 *******************************************************************************
 *          MOPAC:  VERSION  6.00               CALC'D.  6- 2 -96               
 *   T=      - A TIME OF100000.0 SECONDS REQUESTED
 *  DUMP=N   - RESTART FILE WRITTEN EVERY  3600.0 SECONDS
 *  EF       - USE EF ROUTINE FOR MINIMUM SEARCH
 *  PM3      - THE PM3 HAMILTONIAN TO BE USED
 *  PRECISE  - CRITERIA TO BE INCREASED BY 100 TIMES
 *  NOINTER  - INTERATOMIC DISTANCES NOT TO BE PRINTED
 ***********************************************************************040BY040
 PRECISE NOINTER PM3 EF
 Name: F:\CHEMIE\MOPAC_GR\BS0_1.DAT
 MOPAC file created on 6/2 0:1:36 1996 by HYPERCHEM

    ATOM   CHEMICAL  BOND LENGTH    BOND ANGLE     TWIST ANGLE
   NUMBER  SYMBOL    (ANGSTROMS)     (DEGREES)      (DEGREES)
    (I)                  NA:I          NB:NA:I      NC:NB:NA:I     NA   NB   NC

      1      C       
      2      C         1.51450  *                                  1
      3      C         1.53560  *     114.62440  *                 2    1
      4      C         1.51390  *     113.47860  *   57.61120  *   3    2    1
      5      O         1.20630  *     126.04380  * -126.02320  *   1    2    3
      6      O         1.33090  *     110.73910  *   55.96760  *   1    2    3
      7      O         1.33150  *     110.96570  *  159.53330  *   4    3    2
      8      O         1.20570  *     126.44750  *  -21.07730  *   4    3    2
      9      H         1.11460  *     108.35960  *   -3.60810  *   2    1    5
     10      H         1.11470  *     107.67780  *  111.93070  *   2    1    5
     11      H         1.11550  *     108.77150  *   56.91870  *   3    2    9
     12      H         1.11490  *     110.00900  *  174.65020  *   3    2    9
     13      H          .97110  *     107.36200  *    1.63810  *   6    1    5
     14      H          .97170  *     107.20710  *   -1.81430  *   7    4    8
     15      O         3.37130  *     118.53960  * -149.11530  *   5    1    6
     16      H          .95710  *      55.16800  *  153.79290  *  15    5    1
     17      H          .95710  *      49.79430  *  -17.35590  *  15    5    1
     18      O         2.77440  *     170.41800  *   27.16110  *  11    3   12
     19      H          .95710  *     157.24840  *  134.67500  *  18   11    3
     20      H          .95710  *      66.92390  * -153.45890  *  18   11    3
     21      O         3.32110  *     110.86470  *  -40.08120  *   9    2   10
     22      H          .95710  *      81.97260  * -161.84020  *  21    9    2
     23      H          .95710  *     116.66430  *   95.89010  *  21    9    2
     24      O         1.94820  *     170.65480  *   26.70960  *  20   18   19
     25      H          .95710  *      90.83970  * -167.69760  *  24   20   18
     26      H          .95710  *     108.20230  *   86.71110  *  24   20   18
     27      O         3.57440  *     109.27570  *  -50.09380  *   8    4    7
     28      H          .95710  *      71.13490  * -163.84750  *  27    8    4
     29      H          .95710  *     157.34040  *  113.66510  *  27    8    4
     30      O         3.62200  *      86.30250  *   86.90500  *   8    4    7
     31      H          .95710  *     149.66550  * -164.72210  *  30    8    4
     32      H          .95710  *      73.25350  *  105.03760  *  30    8    4
     33      O         2.45040  *      79.49190  * -135.76100  *  14    7    4
     34      H          .95710  *      71.68130  * -132.22810  *  33   14    7
     35      H          .95710  *     133.33670  *  134.86490  *  33   14    7
     36      O         2.09870  *     138.61030  *   -6.44240  *  32   30   31
     37      H          .95710  *     143.42860  * -131.76910  *  36   32   30
     38      H          .95710  *     102.97310  *    6.16200  *  36   32   30
     39      O         2.43220  *     115.47740  *   93.83630  *  10    2    9
     40      H          .95710  *      73.03260  *  -66.76660  *  39   10    2
     41      H          .95710  *      32.09440  *  124.75630  *  39   10    2
     42      O         2.46610  *     138.92780  *  124.08390  *   5    1    6
     43      H          .95710  *     125.63330  *  -23.59280  *  42    5    1
     44      H          .95710  *     114.60380  *  108.28320  *  42    5    1
     45      O         3.27860  *      91.79320  * -146.02370  *  13    6    1
     46      H          .95710  *      94.41880  *    9.62620  *  45   13    6
     47      H          .95710  *      84.66390  *  -94.57590  *  45   13    6
     48      O         2.75290  *      90.28310  *  -55.47400  *  27    8    4
     49      H          .95710  *       3.79070  *  -31.97220  *  48   27   28
     50      H          .95710  *     107.52010  *  -69.99370  *  48   27   28
     51      O         3.13600  *     117.35860  *  -25.66320  *  33   14    7
     52      H          .95710  *     118.77810  *  152.23300  *  51   33   35
     53      H          .95710  *      14.45760  *  142.15930  *  51   33   35
     54      O         2.98100  *      80.96320  * -108.93120  *  29   27   28
     55      H          .95710  *      51.61470  *  -16.47660  *  54   29   27
     56      H          .95710  *      67.41590  * -149.00140  *  54   29   27
     57      O         1.85230  *     160.64550  *  -91.24480  *  46   45   47
     58      H          .95710  *     116.63140  *  105.04630  *  57   46   45
     59      H          .95710  *     138.83890  *  -76.29790  *  57   46   45
     60      O         2.80050  *     132.14100  *  119.42860  *   7    4    8
     61      H          .95710  *     102.93820  *   77.53850  *  60    7   14
     62      H          .95710  *     108.84030  * -171.96190  *  60    7   14
     63      O         1.83880  *     172.58340  *  -47.59070  *  19   18   20
     64      H          .95710  *      99.62530  *    9.16330  *  63   19   18
     65      H          .95710  *     118.24220  *  121.48200  *  63   19   18
     66      O         1.89140  *     161.29240  * -118.36700  *  37   36   38
     67      H          .95710  *     102.15610  *  -82.13490  *  66   37   36
     68      H          .95710  *     142.44550  *  143.36200  *  66   37   36
     69      O         2.84310  *     105.90350  *  -63.80740  *  51   33   35
     70      H          .95710  *     105.67290  *  -36.14890  *  69   51   53
     71      H          .95710  *      12.06240  *   50.01470  *  69   51   53
     72      O         2.56480  *     155.31730  * -149.66910  *  23   21   22
     73      H          .95710  *     110.75550  *   74.70700  *  72   23   21
     74      H          .95710  *      85.52560  *  -29.13720  *  72   23   21
     75      O         2.72120  *     126.63700  *   84.12300  *  54   29   27
     76      H          .95710  *       7.01450  *  -56.03410  *  75   54   55
     77      H          .95710  *     111.50650  *  -61.26930  *  75   54   55

          CARTESIAN COORDINATES 

    NO.       ATOM         X         Y         Z

     1         C         .0000     .0000     .0000
     2         C        1.5145     .0000     .0000
     3         C        2.1543    1.3960     .0000
     4         C        1.7295    2.2542    1.1725
     5         O        -.7098    -.5736     .7889
     6         O        -.4713     .6966   -1.0315
     7         O        2.6007    3.2390    1.3825
     8         O         .7393    2.1088    1.8450
     9         H        1.8656    -.5671     .8930
    10         H        1.8530    -.5635    -.9002
    11         H        3.2638    1.2823     .0221
    12         H        1.8879    1.9377    -.9373
    13         H       -1.4407     .6608    -.9867
    14         H        2.2575    3.7746    2.1170
    15         O         .3483    -.8896    3.9742
    16         H        -.5689    -.8834    3.7009
    17         H         .8371    -.6785    3.1788
    18         O        6.0288    1.3838    -.1820
    19         H        6.9378    1.3474     .1156
    20         H        5.6952     .4975    -.0431
    21         O        1.5170   -3.8372     .4299
    22         H        1.5988   -3.8452    1.3835
    23         H        2.2879   -4.3115     .1189
    24         O        5.2353   -1.3253     .4683
    25         H        4.7007   -1.4263    -.3192
    26         H        4.6019   -1.2840    1.1846
    27         O        1.6403    2.1812    5.3032
    28         H         .7629    1.8081    5.2197
    29         H        1.6754    2.5137    6.2000
    30         O        -.8680    4.4110    -.4432
    31         H       -1.5961    4.9967    -.6500
    32         H       -1.1950    3.5371    -.6562
    33         O        2.9558    5.5383     .5657
    34         H        3.2940    5.7513    1.4354
    35         H        2.5443    6.3478     .2633
    36         O       -2.9922    2.6297   -1.2486
    37         H       -3.5815    1.8985   -1.0638
    38         H       -3.5736    3.3766   -1.3901
    39         O         .2383   -2.1322   -1.8209
    40         H         .4950   -2.4675    -.9620
    41         H         .8133   -1.3811   -1.9670
    42         O       -1.0280   -2.8457    1.6934
    43         H        -.7699   -3.6594    1.2605
    44         H        -.7451   -2.9565    2.6009
    45         O       -1.6947     .6627   -4.2554
    46         H        -.7572     .5380   -4.4023
    47         H       -1.7985    1.6091   -4.1575
    48         O        3.4460     .1449    4.8894
    49         H        2.7789     .8100    5.0583
    50         H        3.3940    -.4438    5.6423
    51         O        5.2312    4.8429   -1.4771
    52         H        5.9878    4.3427   -1.1714
    53         H        4.6968    4.9724    -.6938
    54         O        1.5901    5.1115    4.7404
    55         H        1.7962    4.2427    4.3959
    56         H        2.0799    5.1667    5.5608
    57         O         .8650     .3502   -5.2765
    58         H        1.4579    1.1010   -5.2466
    59         H        1.3423    -.3128   -5.7752
    60         O        5.3241    3.2311    2.0352
    61         H        5.3732    2.5877    2.7421
    62         H        5.8134    2.8340    1.3149
    63         O        8.6000    1.1679     .8811
    64         H        8.3773     .5952    1.6149
    65         H        9.2719     .6877     .3973
    66         O       -4.4370     .4695    -.1675
    67         H       -3.8287    -.2544    -.3158
    68         H       -5.2882     .0476    -.0513
    69         O        3.9288    4.3487   -3.9556
    70         H        3.1643    3.8132   -3.7437
    71         H        4.2391    4.6696   -3.1089
    72         O        4.1680   -4.8760   -1.5318
    73         H        4.8494   -4.2042   -1.5124
    74         H        3.5597   -4.5813   -2.2094
    75         O        -.6338    6.3975    3.8427
    76         H         .1810    5.9384    4.0462
    77         H        -.5900    6.5576    2.9001
  H: (PM3): J. J. P. STEWART, J. COMP. CHEM.     10, 209 (1989).                
  C: (PM3): J. J. P. STEWART, J. COMP. CHEM.     10, 209 (1989).                
  O: (PM3): J. J. P. STEWART, J. COMP. CHEM.     10, 209 (1989).                

          RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =107
 CYCLE:   1 TIME:  32.02 TIME LEFT:  99968.0 GRAD.:   103.812 HEAT:-1328.219    
 CYCLE:   2 TIME:   1.26 TIME LEFT:  99966.7 GRAD.:    70.387 HEAT:-1332.740    
 CYCLE:   3 TIME:  23.84 TIME LEFT:  99942.9 GRAD.:    60.491 HEAT:-1338.494    
 CYCLE:   4 TIME:  25.10 TIME LEFT:  99917.8 GRAD.:   704.929 HEAT:-1322.461    
 CYCLE:   5 TIME:  23.84 TIME LEFT:  99893.9 GRAD.:    62.837 HEAT:-1342.587    
 CYCLE:   6 TIME:  26.14 TIME LEFT:  99867.8 GRAD.:    53.759 HEAT:-1343.964    
 CYCLE:   7 TIME:  23.84 TIME LEFT:  99844.0 GRAD.:    65.823 HEAT:-1348.068    
 CYCLE:   8 TIME:  26.20 TIME LEFT:  99817.8 GRAD.:    59.487 HEAT:-1349.552    
 CYCLE:   9 TIME:  24.94 TIME LEFT:  99792.8 GRAD.:    64.908 HEAT:-1352.783    
 CYCLE:  10 TIME:  26.09 TIME LEFT:  99766.7 GRAD.:   103.067 HEAT:-1355.826    
 CYCLE:  11 TIME:  26.14 TIME LEFT:  99740.6 GRAD.:   557.161 HEAT:-1348.422    
 CYCLE:  12 TIME:  23.73 TIME LEFT:  99716.9 GRAD.:   101.505 HEAT:-1358.549    
 CYCLE:  13 TIME:  26.09 TIME LEFT:  99690.8 GRAD.:    93.131 HEAT:-1360.423    
 CYCLE:  14 TIME:  25.92 TIME LEFT:  99664.9 GRAD.:   185.981 HEAT:-1362.931    
 CYCLE:  15 TIME:  25.82 TIME LEFT:  99639.0 GRAD.:   127.480 HEAT:-1364.204    
 CYCLE:  16 TIME:  26.03 TIME LEFT:  99613.0 GRAD.:    61.331 HEAT:-1364.843    
 CYCLE:  17 TIME:  25.76 TIME LEFT:  99587.2 GRAD.:    90.996 HEAT:-1366.433    
 CYCLE:  18 TIME:  24.88 TIME LEFT:  99562.4 GRAD.:    61.303 HEAT:-1367.380    
 CYCLE:  19 TIME:  24.78 TIME LEFT:  99537.6 GRAD.:   136.028 HEAT:-1367.620    
 CYCLE:  20 TIME:  27.68 TIME LEFT:  99509.9 GRAD.:    36.245 HEAT:-1368.923    

                     CALCULATION ABANDONED AT THIS POINT

           THREE ATOMS BEING USED TO DEFINE THE
           COORDINATES OF A FOURTH ATOM, WHOSE BOND-ANGLE IS
           NOT ZERO OR 180 DEGREEES, ARE IN AN ALMOST STRAIGHT
           LINE.  THERE IS A HIGH PROBABILITY THAT THE
           COORDINATES OF THE ATOM WILL BE INCORRECT.

                    THE FAULTY ATOM IS ATOM NUMBER  19

    ATOM   CHEMICAL  BOND LENGTH    BOND ANGLE     TWIST ANGLE
   NUMBER  SYMBOL    (ANGSTROMS)     (DEGREES)      (DEGREES)
    (I)                  NA:I          NB:NA:I      NC:NB:NA:I     NA   NB   NC

      1      C       
      2      C         1.50638  *                                  1
      3      C         1.51463  *     114.83235  *                 2    1
      4      C         1.50799  *     114.80677  *   66.27431  *   3    2    1
      5      O         1.22106  *     126.61870  * -126.11112  *   1    2    3
      6      O         1.34258  *     115.33840  *   52.32612  *   1    2    3
      7      O         1.34638  *     112.41381  *  158.96576  *   4    3    2
      8      O         1.22157  *     129.54067  *  -18.55690  *   4    3    2
      9      H         1.11269  *     109.94827  *   -2.73430  *   2    1    5
     10      H         1.11659  *     110.04760  *  110.09135  *   2    1    5
     11      H         1.11153  *     110.56052  *   62.64593  *   3    2    9
     12      H         1.11803  *     110.90599  * -179.88538  *   3    2    9
     13      H          .95651  *     111.10052  *     .22036  *   6    1    5
     14      H          .95133  *     113.68904  *  -10.14267  *   7    4    8
     15      O         3.31747  *     117.49862  * -150.22047  *   5    1    6
     16      H          .95315  *      58.61400  *  148.48645  *  15    5    1
     17      H          .95552  *      50.26027  *  -11.93460  *  15    5    1
     18      O         2.79156  *     179.25848  *   24.29837  *  11    3   12
     19      H          .96075  *     166.01581  *  140.15286  *  18   11    3
     20      H          .96408  *      62.55927  * -161.31616  *  18   11    3
     21      O         3.28597  *     121.24242  *  -32.58219  *   9    2   10
     22      H          .95228  *      81.13613  * -158.81113  *  21    9    2
     23      H          .95243  *     117.14487  *   96.02923  *  21    9    2
     24      O         1.78167  *     171.04483  *   21.56710  *  20   18   19
     25      H          .95441  *     100.47948  * -167.80342  *  24   20   18
     26      H          .96419  *     108.57826  *   80.05445  *  24   20   18
     27      O         3.51928  *     102.14969  *  -73.06171  *   8    4    7
     28      H          .95605  *      65.33805  * -166.28151  *  27    8    4
     29      H          .95190  *     153.05102  *  112.44015  *  27    8    4
     30      O         3.64262  *      93.29374  *   90.14619  *   8    4    7
     31      H          .95344  *     145.27342  * -165.91160  *  30    8    4
     32      H          .95876  *      71.06533  *  105.26409  *  30    8    4
     33      O         2.63381  *      82.12892  * -139.96102  *  14    7    4
     34      H          .95222  *      76.61925  * -125.82262  *  33   14    7
     35      H          .95153  *     135.81656  *  132.89052  *  33   14    7
     36      O         2.01113  *     145.18351  *   -7.59974  *  32   30   31
     37      H          .96185  *     132.10175  * -135.37452  *  36   32   30
     38      H          .95004  *     110.77603  *    7.47458  *  36   32   30
     39      O         2.58794  *     144.34341  *   88.35220  *  10    2    9
     40      H          .95181  *      79.83553  *  -60.65591  *  39   10    2
     41      H          .95530  *      27.92843  *  121.86826  *  39   10    2
     42      O         2.67532  *     137.36821  *  123.68018  *   5    1    6
     43      H          .95095  *     121.56386  *  -22.72341  *  42    5    1
     44      H          .95155  *     111.22576  *  106.16055  *  42    5    1
     45      O         3.26219  *      93.68824  * -153.74485  *  13    6    1
     46      H          .95822  *      93.41779  *    9.47920  *  45   13    6
     47      H          .95031  *      82.19062  *  -98.23793  *  45   13    6
     48      O         2.76189  *      78.55437  *  -56.84262  *  27    8    4
     49      H          .96322  *       5.02786  *  148.29024  *  48   27   28
     50      H          .95133  *     104.63756  *  -68.61465  *  48   27   28
     51      O         3.13424  *      92.55398  *  -13.24677  *  33   14    7
     52      H          .96584  *     117.76672  *  161.40912  *  51   33   35
     53      H          .95421  *       9.58228  *  142.12528  *  51   33   35
     54      O         3.01360  *      74.58895  * -106.26791  *  29   27   28
     55      H          .95689  *      48.04905  *  -14.03719  *  54   29   27
     56      H          .95165  *      71.62174  * -150.94971  *  54   29   27
     57      O         1.80294  *     167.76579  *  -90.93834  *  46   45   47
     58      H          .95221  *     119.81813  *  103.90612  *  57   46   45
     59      H          .95042  *     131.77689  *  -75.91051  *  57   46   45
     60      O         2.84442  *     129.76901  *  120.93714  *   7    4    8
     61      H          .94956  *      99.51013  *   78.19545  *  60    7   14
     62      H          .96449  *      95.26569  * -172.64531  *  60    7   14
     63      O         1.79261  *     170.24948  *  -45.83833  *  19   18   20
     64      H          .95284  *     107.45441  *    5.61406  *  63   19   18
     65      H          .95239  *     116.42133  *  126.30252  *  63   19   18
     66      O         1.76812  *     164.77667  * -113.59141  *  37   36   38
     67      H          .96217  *     103.09085  *  -77.49687  *  66   37   36
     68      H          .94927  *     135.60770  *  146.32524  *  66   37   36
     69      O         2.72857  *     105.37371  *  -67.34916  *  51   33   35
     70      H          .95728  *     106.40417  *  -33.08933  *  69   51   53
     71      H          .96171  *        .70924  *   50.69892  *  69   51   53
     72      O         2.50918  *     153.42112  * -149.89571  *  23   21   22
     73      H          .95165  *     110.96660  *   75.85423  *  72   23   21
     74      H          .95173  *      88.07228  *  -32.53240  *  72   23   21
     75      O         2.77892  *     119.05638  *   91.75487  *  54   29   27
     76      H          .95991  *        .98524  *  124.57973  *  75   54   55
     77      H          .95043  *     106.91467  *  -59.29885  *  75   54   55

                    CARTESIAN COORDINATES UP TO FAULTY ATOM

     I            X            Y            Z
     1          .00000       .00000       .00000
     2         1.50638       .00000       .00000
     3         2.14247      1.37459       .00000
     4         1.90833      2.18008      1.25315
     5         -.72835      -.57760       .79176
     6         -.57458       .74160      -.96042
     7         2.82065      3.15721      1.41329
     8         1.06124      2.03836      2.12181
     9         1.88599      -.57541       .87342
    10         1.88915      -.58348      -.87168
    11         3.24482      1.29461      -.11803
    12         1.78024      1.98181      -.86606
    13        -1.52814       .71873      -.88898
    14         2.62305      3.75092      2.12987
    15          .43988     -1.09137      3.85393
    16         -.48976      -.95502      3.69367
    17          .89754      -.80479      3.06562
    18         6.01320      1.12413      -.43404
    19         6.95213      1.02001      -.29694

       ATOMS 18, 11, AND  3 ARE WITHIN  .0144 ANGSTROMS OF A STRAIGHT LINE

Thanks for your help.

Kay Kreidler
Department of Inorganic and Strutural Chemistry I
Heinrich-Heine-University Duesseldorf
Universitaetsstr. 1
40225 Duesseldorf
Germany
Phone: ++49-211-81-13140
FAX:   ++49-211-81-13085
Email: [email-masked]