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
------------------------------------------------------------------------------
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
[email protected]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
