Creating mopac.dat with openbabel

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Creating mopac.dat with openbabel

Steffen Neumann
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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Re: Creating mopac.dat with openbabel

Mathias W.
Steffen Neumann schrieb:

> 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
>

"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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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