Creating mopac.dat with openbabel

Hi,

I am trying to create input files for MOPAC7,
and there are differences between those *.dat
generated by SYBYL8.0 and babel 2.2.0-2ubuntu3.

With the babel output mopac7-bin 1.13-2 (ubuntu 9.04)
does not calculate the optimized geometry.

    wget -O CID_20097272.sdf "http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=20097272&disopt=SaveSDF"
    babel CID_20097272.sdf -o mopin CID_20097272.dat -xk "PREC AM1 T=3600 GEO-OK,GNORM=0.1,MMOK,SCFCRT=1D-9"
    run_mopac7 CID_20097272

Although both files have 10 columns,
their formatting looks very different, see below.

Maybe the openbabel documentation should
list the versions a file format has been
tested against, in case there are version specific
dialects. E.g., are the following equivalent ?

       moo -- MOPAC Output format [Read-only]
       mopout -- MOPAC Output format [Read-only]

       mop -- MOPAC Cartesian format
       mopcrt -- MOPAC Cartesian format
       mpc -- MOPAC Cartesian format

       mopin -- MOPAC Internal

I'd like to know whether I missed something obvious here,
or whether I should continue and file a feature request
including proper input file examples etc.

Yours,
Steffen


==> babel generated CID_20097272.dat <==
PREC AM1 T=3600 GEO-OK,GNORM=0.1,MMOK,SCFCRT=1D-9
20097272

O    0.000000  1    0.000000  1    0.000000  1     0   0   0
N    3.000000  1    0.000000  1    0.000000  1     1   0   0
C    0.999978  1   59.999272  1    0.000000  1     2   1   0
C    1.000000  1  120.000728  1    0.000000  1     3   2   1
C    0.999978  1  120.000728  1  180.000000  1     4   3   2
C    1.000065  1   60.002137  1  180.000000  1     2   1   3
C    1.732038  1  130.894642  1    0.000000  1     3   1   2
...

==> SYBYL 8.0 generated CID_20097272-sybyl.dat <==
PREC AM1 T=3600 GEO-OK,GNORM=0.1,MMOK,SCFCRT=1D-9
/home/swolf/mopacfile.dat
 
0008 -0.4414   0001 -0.9804   0001 -0.6036   0001 0000 0000 0000
0001 0.4332    0001 -1.3559   0001 -0.8588   0001 0000 0000 0000
0006 -0.3326   0001 0.4016    0001 -0.8356   0001 0000 0000 0000
0006 -1.5078   0001 1.2165    0001 -0.8433   0001 0000 0000 0000
0006 -2.7369   0001 0.4804    0001 -0.2144   0001 0000 0000 0000
0001 -3.4477   0001 1.1915    0001 0.1660    0001 0000 0000 0000
0006 -2.1968   0001 -0.4051   0001 0.8782    0001 0000 0000 0000
...



---------------------------------------------------------------------------------------------

starting mopac7 job CID_20097272


           AN UNOPTIMIZABLE GEOMETRIC PARAMETER HAS
           BEEN MARKED FOR OPTIMIZATION. THIS IS A NON-FATAL ERROR
 *******************************************************************************
 ** MOPAC FOR LINUX (PUBLIC DOMAIN VERSION)  MTA ATOMKI, Debrecen, 95-JUN-21  **
 *******************************************************************************

                                 AM1 CALCULATION RESULTS


 *******************************************************************************
 *          MOPAC:  VERSION  7.01               CALC'D. Tue Oct 27 14:55:24 2009
 *  GEO-OK   - OVERRIDE INTERATOMIC DISTANCE CHECK
 *   T=      - A TIME OF  3600.0 SECONDS REQUESTED
 *  DUMP=N   - RESTART FILE WRITTEN EVERY  3600.0 SECONDS
 *  AM1      - THE AM1 HAMILTONIAN TO BE USED
 *  PRECISE  - CRITERIA TO BE INCREASED BY 100 TIMES
 ***********************************************************************060BY060
 PREC AM1 T=3600 GEO-OK,GNORM=0.1,MMOK,SCFCRT=1D-9
 20097272
 

    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      O      
      2      N         3.00000  *                                  1
      3      C          .99998  *      59.99927  *                 2    1
      4      C         1.00000  *     120.00073  *     .00000  *   3    2    1
      5      C          .99998  *     120.00073  *  180.00000  *   4    3    2
      6      C         1.00006  *      60.00214  *  180.00000  *   2    1    3
      7      C         1.73204  *     130.89464  *     .00000  *   3    1    2
      8      C         1.00000  *     120.00073  *  180.00000  *   5    4    3
      9      C          .99998  *     119.99854  *     .00000  *   5    4    3
...


---------------------------------------------------------------------------------------------



starting mopac7 job CID_20097272-sybyl
 *******************************************************************************
 ** MOPAC FOR LINUX (PUBLIC DOMAIN VERSION)  MTA ATOMKI, Debrecen, 95-JUN-21  **
 *******************************************************************************

                                 AM1 CALCULATION RESULTS


 *******************************************************************************
 *          MOPAC:  VERSION  7.01               CALC'D. Tue Oct 27 14:55:49 2009
 *  GEO-OK   - OVERRIDE INTERATOMIC DISTANCE CHECK
 *   T=      - A TIME OF  3600.0 SECONDS REQUESTED
 *  DUMP=N   - RESTART FILE WRITTEN EVERY  3600.0 SECONDS
 *  AM1      - THE AM1 HAMILTONIAN TO BE USED
 *  PRECISE  - CRITERIA TO BE INCREASED BY 100 TIMES
 ***********************************************************************060BY060
 PREC AM1 T=3600 GEO-OK,GNORM=0.1,MMOK,SCFCRT=1D-9
 /home/swolf/mopacfile.dat
 

    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      O      
      2      H          .98542  *                                  1
      3      C         1.40556  *     105.26130  *                 1    2
      4      C         1.43011  *     119.83776  *  166.61406  *   3    1    2
      5      C         1.56462  *     112.04238  *   15.04898  *   4    3    1
      6      H         1.07499  *     110.51470  *  155.01148  *   5    4    3
      7      C         1.50652  *     106.64340  *   33.45627  *   5    4    3
      8      H         1.08333  *     114.20317  *  -64.42539  *   7    5    4
      9      H         1.12062  *     107.97486  *   54.98324  *   7    5    4
...

--
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409


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Steffen Neumann schrieb:
"MOPAC Internal" and "MOPAC Cartesian" are obviously not the same. First is
internal coordinates last "normal" cartesians...

so try -o mopcrt

--
Mathias Weigt

Institute of Pharmaceutical Chemistry
University of Bonn

An der Immenburg 4
53121 Bonn
Germany

Phone: +49/228/73-5240

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Come build with us! The BlackBerry(R) Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9 - 12, 2009. Register now!
http://p.sf.net/sfu/devconference
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss