From owner-chemistry@ccl.net Fri Nov 14 09:07:01 2014 From: "Sathish Kumar sathishk238-x-gmail.com" To: CCL Subject: CCL:G: Regarding ZINDO calculations in Gaussian 09 Message-Id: <-50744-141114085808-937-nqkkuvMI1L6HN5S86lO+2Q-#-server.ccl.net> X-Original-From: Sathish Kumar Content-Type: multipart/alternative; boundary=089e01419fc075f80a0507d20491 Date: Fri, 14 Nov 2014 05:58:02 -0800 MIME-Version: 1.0 Sent to CCL by: Sathish Kumar [sathishk238.---.gmail.com] --089e01419fc075f80a0507d20491 Content-Type: text/plain; charset=ISO-8859-1 Subject: Regarding ZINDO calculations in Gaussian 09 i am ruuning ZINDO calculation for pi-pi stacked complex, while running i am getting following error. please suggest me how to solve this. One-electron integrals computed using PRISM. Generate ZINDO/S integrals. Missing ZINDO/S parameters for atomic number 5. Error termination via Lnk1e in /lustre/applications/Gaussian/Gaussian9/g09/linda-exe/l302.exel at Fri Nov 14 01:25:01 2014. Job cpu time: 0 days 0 hours 0 minutes 9.3 seconds. File lengths (MBytes): RWF= 12 Int= 0 D2E= 0 Chk= 1 Scr= 1 failed to open execfile regards M.SathishKumar -- regards M.SathishKumar --089e01419fc075f80a0507d20491 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable


Subject: Regarding ZIND= O calculations in Gaussian 09


i am ruuning ZIND= O calculation for pi-pi stacked complex, while running i am getting followi= ng error. please suggest me how to solve this.

One-= electron integrals computed using PRISM.
=A0Generate ZINDO/S inte= grals.
=A0Missing ZINDO/S parameters for atomic number =A05.
=A0Error termination via Lnk1e in /lustre/applications/Gaussian/Gauss= ian9/g09/linda-exe/l302.exel at Fri Nov 14 01:25:01 2014.
=A0Job = cpu time: =A00 days =A00 hours =A00 minutes =A09.3 seconds.
=A0Fi= le lengths (MBytes): =A0RWF=3D =A0 =A0 12 Int=3D =A0 =A0 =A00 D2E=3D =A0 = =A0 =A00 Chk=3D =A0 =A0 =A01 Scr=3D =A0 =A0 =A01
failed to open e= xecfile



<= div dir=3D"ltr">
regards
M.SathishKumar=A0



--
regards
M.SathishKumar=A0
--089e01419fc075f80a0507d20491-- From owner-chemistry@ccl.net Fri Nov 14 11:28:01 2014 From: "Herbert Fruchtl herbert.fruchtl**st-andrews.ac.uk" To: CCL Subject: CCL:G: Regarding ZINDO calculations in Gaussian 09 Message-Id: <-50745-141114105655-28457-7VSTKgdC2g6KL4MWrsKZ4A(0)server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 14 Nov 2014 15:56:30 +0000 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl!^!st-andrews.ac.uk] Zindo is a semiempirical method, and not parametrised for all elements. Gaussian has (I think) only Zerner's original Zindo parametrisation. Parameters for other elements were added later by different research groups. I don't remember if boron (I assume that's what "atomic number 5" refers to) is available. The most complete collection I know of is in ORCA. HTH, Herbert On 14/11/14 13:58, Sathish Kumar sathishk238-x-gmail.com wrote: > > > Subject: Regarding ZINDO calculations in Gaussian 09 > > > i am ruuning ZINDO calculation for pi-pi stacked complex, while running i am > getting following error. please suggest me how to solve this. > > One-electron integrals computed using PRISM. > Generate ZINDO/S integrals. > Missing ZINDO/S parameters for atomic number 5. > Error termination via Lnk1e in > /lustre/applications/Gaussian/Gaussian9/g09/linda-exe/l302.exel at Fri Nov 14 > 01:25:01 2014. > Job cpu time: 0 days 0 hours 0 minutes 9.3 seconds. > File lengths (MBytes): RWF= 12 Int= 0 D2E= 0 Chk= 1 Scr= > 1 > failed to open execfile > > > > regards > M.SathishKumar > > > > -- > regards > M.SathishKumar -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Fri Nov 14 14:17:01 2014 From: "John McKelvey jmmckel++gmail.com" To: CCL Subject: CCL:G: Regarding ZINDO calculations in Gaussian 09 Message-Id: <-50746-141114135545-24732-pH/YGJAQbWXcFxQLiDZ8qQ . server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=001a11c1db70b8c3a70507d62cd0 Date: Fri, 14 Nov 2014 13:55:38 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel(_)gmail.com] --001a11c1db70b8c3a70507d62cd0 Content-Type: text/plain; charset=UTF-8 ORCA is indeed a good alternative, though I'm not sure about boron. The one-center 2-electron integrals may not be exactly the same as in ZINDO, and hence where ZINDO(INDO/S) is used the results may differ slightly from those from the ZINDO program code. John McKelvey On Fri, Nov 14, 2014 at 10:56 AM, Herbert Fruchtl herbert.fruchtl** st-andrews.ac.uk wrote: > > Sent to CCL by: Herbert Fruchtl [herbert.fruchtl!^!st-andrews.ac.uk] > Zindo is a semiempirical method, and not parametrised for all elements. > Gaussian has (I think) only Zerner's original Zindo parametrisation. > Parameters for other elements were added later by different research > groups. I don't remember if boron (I assume that's what "atomic number 5" > refers to) is available. The most complete collection I know of is in ORCA. > > HTH, > > Herbert > > On 14/11/14 13:58, Sathish Kumar sathishk238-x-gmail.com wrote: > >> >> >> Subject: Regarding ZINDO calculations in Gaussian 09 >> >> >> i am ruuning ZINDO calculation for pi-pi stacked complex, while running i >> am >> getting following error. please suggest me how to solve this. >> >> One-electron integrals computed using PRISM. >> Generate ZINDO/S integrals. >> Missing ZINDO/S parameters for atomic number 5. >> Error termination via Lnk1e in >> /lustre/applications/Gaussian/Gaussian9/g09/linda-exe/l302.exel at Fri >> Nov 14 >> 01:25:01 2014. >> Job cpu time: 0 days 0 hours 0 minutes 9.3 seconds. >> File lengths (MBytes): RWF= 12 Int= 0 D2E= 0 Chk= 1 >> Scr= >> 1 >> failed to open execfile >> >> >> >> regards >> M.SathishKumar >> >> >> >> -- >> regards >> M.SathishKumar >> > > -- > Herbert Fruchtl > Senior Scientific Computing Officer > School of Chemistry, School of Mathematics and Statistics > University of St Andrews > -- > The University of St Andrews is a charity registered in Scotland: > No SC013532http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: http://server.ccl.net/ > chemistry/announcements/conferences/> > > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel|,|gmail.com --001a11c1db70b8c3a70507d62cd0 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
ORCA is indeed a good alternative, though I'm not= sure about boron.=C2=A0 The one-center 2-electron=C2=A0 integrals may not = be exactly the same as in ZINDO, and hence where ZINDO(INDO/S) is used the = results may differ slightly from those from the ZINDO program code.

=
John McKelvey

On Fri, Nov 14, 2014 at 10:56 AM, Herbert Fruchtl herbert.fruc= htl**st-andrews.ac.uk <owner= -chemistry|,|ccl.net> wrote:
=
Sent to CCL by: Herbert Fruchtl [herbert.fruchtl!^!st-andrews.ac.uk]
Zindo is a semiempirical method, and not parametrised for all elements. Gau= ssian has (I think) only Zerner's original Zindo parametrisation. Param= eters for other elements were added later by different research groups. I d= on't remember if boron (I assume that's what "atomic number 5&= quot; refers to) is available. The most complete collection I know of is in= ORCA.

HTH,

=C2=A0 Herbert

On 14/11/14 13:58, Sathish Kumar sathishk238-x-gmail.com wrote:


Subject: Regarding ZINDO calculations in Gaussian 09


i am ruuning ZINDO calculation for pi-pi stacked complex, while running i a= m
getting following error. please suggest me how to solve this.

One-electron integrals computed using PRISM.
=C2=A0 Generate ZINDO/S integrals.
=C2=A0 Missing ZINDO/S parameters for atomic number=C2=A0 5.
=C2=A0 Error termination via Lnk1e in
/lustre/applications/Gaussian/Gaussian9/g09/linda-exe/l302.ex= el at Fri Nov 14
01:25:01 2014.
=C2=A0 Job cpu time:=C2=A0 0 days=C2=A0 0 hours=C2=A0 0 minutes=C2=A0 9.3 s= econds.
=C2=A0 File lengths (MBytes):=C2=A0 RWF=3D=C2=A0 =C2=A0 =C2=A012 Int=3D=C2= =A0 =C2=A0 =C2=A0 0 D2E=3D=C2=A0 =C2=A0 =C2=A0 0 Chk=3D=C2=A0 =C2=A0 =C2=A0= 1 Scr=3D
=C2=A0 =C2=A0 1
failed to open execfile



regards
M.SathishKumar



--
regards
M.SathishKumar

--
Herbert Fruchtl
Senior Scientific Computing Officer
School of Chemistry, School of Mathematics and Statistics
University of St Andrews
--
The University of St Andrews is a charity registered in Scotland:
No SC013532



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--
John McKelvey
10819 Middleford Pl
Ft Wayne, IN 46818
260-4= 89-2160
jmmckel|,|gmail.com
--001a11c1db70b8c3a70507d62cd0-- From owner-chemistry@ccl.net Fri Nov 14 17:57:01 2014 From: "Esam Orabi esam_oraby2001::yahoo.com" To: CCL Subject: CCL: MOPAC-7 Message-Id: <-50747-141114153827-32014-kdWw+u8xlPskR7i+9T8E0g*o*server.ccl.net> X-Original-From: "Esam Orabi" Date: Fri, 14 Nov 2014 15:38:25 -0500 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 ============================================================ From owner-chemistry@ccl.net Fri Nov 14 18:53:00 2014 From: "John McKelvey jmmckel-*-gmail.com" To: CCL Subject: CCL: MOPAC-7 Message-Id: <-50748-141114185004-24788-BtDTh5VEM6DS1zO811ALQw : server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=001a11c2e7f456cecb0507da4977 Date: Fri, 14 Nov 2014 18:49:58 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel|a|gmail.com] --001a11c2e7f456cecb0507da4977 Content-Type: text/plain; charset=UTF-8 At least in more recent MOPAC codes optimization flags have to be inserted after each coordinate... Label Xcoord 1 Ycoord 1 Zcoord 1 John On Fri, Nov 14, 2014 at 3:38 PM, Esam Orabi esam_oraby2001::yahoo.com < owner-chemistry+*+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 > > ============================================================> > > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel+*+gmail.com --001a11c2e7f456cecb0507da4977 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
At least in more recent MOPAC codes optimization= flags have to be inserted after each coordinate...

Label=C2= =A0=C2=A0=C2=A0 Xcoord 1=C2=A0=C2=A0=C2=A0 Ycoord 1=C2=A0=C2=A0=C2=A0 Zcoor= d 1

John

On Fri, Nov 14, 2014 at 3:38 PM, Esam Orabi esam_oraby2001::<= a href=3D"http://yahoo.com">yahoo.com <owner-chemistry+*+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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--001a11c2e7f456cecb0507da4977-- 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--