From owner-chemistry@ccl.net Fri Nov 14 19:35:01 2014 From: "William McDonald pchem_-_ucsc.edu" To: CCL Subject: CCL: MOPAC-7 Message-Id: <-50749-141114184046-16444-D01zSfnM0pHk4dq0iERBgw.@.server.ccl.net> X-Original-From: William McDonald Content-Type: multipart/alternative; boundary=001a11c24b3823c6800507da28cc Date: Fri, 14 Nov 2014 15:40:41 -0800 MIME-Version: 1.0 Sent to CCL by: William McDonald [pchem|,|ucsc.edu] --001a11c24b3823c6800507da28cc Content-Type: text/plain; charset=UTF-8 Hello Esam, The error you receive is because your syntax for specifying Cartesian coordinates is incorrect. In Mopac you need to specify either '0' (do *not* optimize this coordinate) or '1' (do optimize this coordinate) after each Cartesian coordinate entry. See www.openmopac.net/manual/cart_coord.html On Fri, Nov 14, 2014 at 12:38 PM, Esam Orabi esam_oraby2001::yahoo.com < owner-chemistry|a|ccl.net> wrote: > > Sent to CCL by: "Esam Orabi" [esam_oraby2001^yahoo.com] > Hello, > I am having a problem with a MOPAC calculation. > I am trying to run a geometry optimization for Acetaldehyde > The structure is specified using xyz coordinates which are coming from an > ab initio mp2 calculation. however the program stops immediately after it > reads the coordinates with an asteric (*) and plus (+) beside some atoms. > It is showing the distance between atoms to be too small (which is not > real). Have anyone came a cross such errors before?. > Thanks > Esam > > here is my input and output files > ================input================= > AM1 CHARGE=0 SINGLET MMOK GNORM=1.0 XYZ GEO-OK > > > C 0.229854 0.401384 -0.000036 > O 1.238177 -0.277134 0.000010 > H 0.302680 1.508887 0.000002 > C -1.170688 -0.150126 -0.000006 > H -1.704665 0.221037 -0.881084 > H -1.703988 0.219908 0.881979 > H -1.154443 -1.240312 -0.000723 > > =================output================= > ************************************************************************ > ******* > ** MOPAC (PUBLIC DOMAIN) > ** > ************************************************************************ > ******* > > AM1 CALCULATION RESULTS > > > ************************************************************************ > ******* > * MOPAC: VERSION 7.00 CALC'D. Fri Nov 14 > 15:33:25 2014 > * EXTERNAL - USE ATOMIC PARAMETERS FROM THE FOLLOWING FILE > PARAM-RM1 > * GEO-OK - OVERRIDE INTERATOMIC DISTANCE CHECK > * MMOK - APPLY MM CORRECTION TO CONH BARRIER > * XYZ - CARTESIAN COORDINATE SYSTEM TO BE USED > * SINGLET - SPIN STATE DEFINED AS A SINGLET > * > * > * > * CHARGE ON SYSTEM = 0 > * > * > * > * T= - A TIME OF 3600.0 SECONDS REQUESTED > * DUMP=N - RESTART FILE WRITTEN EVERY 3600.0 SECONDS > * AM1 - THE AM1 HAMILTONIAN TO BE USED > * GNORM= - EXIT WHEN GRADIENT NORM DROPS BELOW 1.00 > ***********************************************************************0 > 40BY040 > > > NO POINTS SUPPLIED FOR REACTION PATH > > > GEOMETRY AS READ IN IS AS FOLLOWS > 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 O 1.0083230010 > 1 > 3 H 0.0728260099 * 0.0272826070 > 1 2 > 4 C 1.4005420003 179.9961588482 > 0.0000000000 1 2 3 > 5 H 1.0302571905 121.2182541103 > 179.9999991365 4 3 2 > 6 H 1.0306825070 117.6224316468 > 179.9999999903 4 5 3 > 7 H 0.0162608153 + 118.6907390004 > 179.9999999903 4 5 6 > > ============================================================> > > -- William J. McDonald Postdoctoral Scholar Department of Chemistry and Biochemistry University of California, Santa Cruz --001a11c24b3823c6800507da28cc Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hello Esam,

The error you receive is be= cause your syntax for specifying Cartesian coordinates is incorrect. In Mop= ac you need to specify either '0' (do not optimize th= is coordinate) or '1' (do optimize this coordinate) after each Cart= esian coordinate entry. See www.openmopac.net/manual/cart_coord.html

On Fri, Nov 14, 2014 at= 12:38 PM, Esam Orabi esam_oraby2001::yahoo.co= m <owner-chemistry|a|ccl.net> wrote:

Sent to CCL by: "Esam=C2=A0 Orabi" [esam_oraby2001^yahoo.com]
Hello,
I am having a problem with a MOPAC calculation.
I am trying to run a geometry optimization for Acetaldehyde
The structure is specified using xyz coordinates which are coming from an ab initio mp2 calculation. however the program stops immediately after it reads the coordinates with an asteric (*) and plus (+) beside some atoms. It is showing the distance between atoms to be too small (which is not
real). Have anyone came a cross such errors before?.
Thanks
Esam

here is my input and output files
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3Dinput=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
AM1 CHARGE=3D0 SINGLET MMOK GNORM=3D1.0 XYZ GEO-OK


C=C2=A0 =C2=A0 =C2=A00.229854=C2=A0 =C2=A0 0.401384=C2=A0 =C2=A0-0.000036 O=C2=A0 =C2=A0 =C2=A01.238177=C2=A0 =C2=A0-0.277134=C2=A0 =C2=A0 0.000010 H=C2=A0 =C2=A0 =C2=A00.302680=C2=A0 =C2=A0 1.508887=C2=A0 =C2=A0 0.000002 C=C2=A0 =C2=A0 -1.170688=C2=A0 =C2=A0-0.150126=C2=A0 =C2=A0-0.000006
H=C2=A0 =C2=A0 -1.704665=C2=A0 =C2=A0 0.221037=C2=A0 =C2=A0-0.881084
H=C2=A0 =C2=A0 -1.703988=C2=A0 =C2=A0 0.219908=C2=A0 =C2=A0 0.881979
H=C2=A0 =C2=A0 -1.154443=C2=A0 =C2=A0-1.240312=C2=A0 =C2=A0-0.000723

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3Doutput=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
=C2=A0*********************************************************************= ***
*******
=C2=A0**=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 MOPAC (PUBLIC DOMAIN)
**
=C2=A0*********************************************************************= ***
*******

=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0AM1 CALCULATION RESULTS


=C2=A0*********************************************************************= ***
*******
=C2=A0*=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 MOPAC:=C2=A0 VERSION=C2=A0 7.00= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0CALC'D. Fri Nov = 14
15:33:25 2014
=C2=A0*=C2=A0 EXTERNAL - USE ATOMIC PARAMETERS FROM THE FOLLOWING FILE
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0PARAM-RM1
=C2=A0*=C2=A0 GEO-OK=C2=A0 =C2=A0- OVERRIDE INTERATOMIC DISTANCE CHECK
=C2=A0*=C2=A0 MMOK=C2=A0 =C2=A0 =C2=A0- APPLY MM CORRECTION TO CONH BARRIER=
=C2=A0*=C2=A0 =C2=A0XYZ=C2=A0 =C2=A0 =C2=A0- CARTESIAN COORDINATE SYSTEM TO= BE USED
=C2=A0*=C2=A0 SINGLET=C2=A0 - SPIN STATE DEFINED AS A SINGLET
=C2=A0*
=C2=A0*
=C2=A0*
=C2=A0*=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0CHARGE= ON SYSTEM =3D=C2=A0 0
=C2=A0*
=C2=A0*
=C2=A0*
=C2=A0*=C2=A0 =C2=A0T=3D=C2=A0 =C2=A0 =C2=A0 - A TIME OF=C2=A0 3600.0 SECON= DS REQUESTED
=C2=A0*=C2=A0 DUMP=3DN=C2=A0 =C2=A0- RESTART FILE WRITTEN EVERY=C2=A0 3600.= 0 SECONDS
=C2=A0*=C2=A0 AM1=C2=A0 =C2=A0 =C2=A0 - THE AM1 HAMILTONIAN TO BE USED
=C2=A0*=C2=A0 GNORM=3D=C2=A0 =C2=A0- EXIT WHEN GRADIENT NORM DROPS BELOW 1.= 00
=C2=A0*********************************************************************= **0
40BY040


=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0NO POINTS SUPPLIED FOR REACTION PA= TH


=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0GEOMETRY AS READ IN IS AS FOLLOWS<= br> =C2=A0 =C2=A0 ATOM=C2=A0 =C2=A0CHEMICAL=C2=A0 =C2=A0 =C2=A0 =C2=A0BOND LENG= TH=C2=A0 =C2=A0 =C2=A0 =C2=A0 BOND ANGLE=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0T= WIST
ANGLE
=C2=A0 =C2=A0NUMBER=C2=A0 SYMBOL=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(ANGSTROM= S)=C2=A0 =C2=A0 =C2=A0 =C2=A0 (DEGREES)=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (= DEGREES)
=C2=A0 =C2=A0 (I)=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0NA:I=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 NB= :NA:I
NC:NB:NA:I=C2=A0 =C2=A0 =C2=A0 NA=C2=A0 =C2=A0NB=C2=A0 =C2=A0NC

=C2=A0 =C2=A0 =C2=A0 1=C2=A0 =C2=A0 =C2=A0 C
=C2=A0 =C2=A0 =C2=A0 2=C2=A0 =C2=A0 =C2=A0 O=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A01.0083230010
1
=C2=A0 =C2=A0 =C2=A0 3=C2=A0 =C2=A0 =C2=A0 H=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A00.0728260099=C2=A0 *=C2=A0 =C2=A0 0.0272826070
1=C2=A0 =C2=A0 2
=C2=A0 =C2=A0 =C2=A0 4=C2=A0 =C2=A0 =C2=A0 C=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A01.4005420003=C2=A0 =C2=A0 =C2=A0179.9961588482
0.0000000000=C2=A0 =C2=A0 =C2=A01=C2=A0 =C2=A0 2=C2=A0 =C2=A0 3
=C2=A0 =C2=A0 =C2=A0 5=C2=A0 =C2=A0 =C2=A0 H=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A01.0302571905=C2=A0 =C2=A0 =C2=A0121.2182541103
179.9999991365=C2=A0 =C2=A0 =C2=A04=C2=A0 =C2=A0 3=C2=A0 =C2=A0 2
=C2=A0 =C2=A0 =C2=A0 6=C2=A0 =C2=A0 =C2=A0 H=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A01.0306825070=C2=A0 =C2=A0 =C2=A0117.6224316468
179.9999999903=C2=A0 =C2=A0 =C2=A04=C2=A0 =C2=A0 5=C2=A0 =C2=A0 3
=C2=A0 =C2=A0 =C2=A0 7=C2=A0 =C2=A0 =C2=A0 H=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A00.0162608153=C2=A0 +=C2=A0 118.6907390004
179.9999999903=C2=A0 =C2=A0 =C2=A04=C2=A0 =C2=A0 5=C2=A0 =C2=A0 6

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D



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--
William J. McDonald
Postdoctoral Scholar
Departm= ent of Chemistry and Biochemistry
University of California, Santa Cruz
--001a11c24b3823c6800507da28cc--