Subject: Re: CCL:M:problems with MOPAC93 and "real! water molecules

From: "Andrey V. Khavryutchenko" <[email-masked]>
Date: Fri, 9 Feb 1996 16:21:45 -0200 (UKR)

>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.
>

This means that the three atoms you used to define the dihedral angle for
fourth atom are 'almost straight line' and thus dihedral angle looses its
meaning and the cartesian coords are likely to be VERY 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.
>

As far as I know Hyperchem does all intermediate input/output/calculations in
cartesian coordinates, so this problem is not encountered.

We (our CompChem Group) often meet these kind of error, so we've wrote a
simple program that allows to substitute atoms, used for internal coordinates
definition (NA,NB,NC) to any other, you want.  I have no source code avaible
now, but calculations are quite simple.

>    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

Pay attention to atoms 18, 24 and 63.  Angles, you've used are very close to
straight line (>170 degrees).

If you can't or don't want to change file with internal coordinates, you have
to change the atoms, which 18th, 24th and 63th atoms are bound to.  This will
force Hyperchem to produce different NA,NB and NC set, so the problem is
likely to disappear.

>Thanks for your help.

Asking a question certainly can't hurt ;-)

>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]

Andrey
--
Andrey Khavryutchenko
-- C++, Unix, Networking, Computational Chemistry, Nanotech --
[email-masked]