Dear Ambrish,

It depends upon what c= omputer system you use. If the configuration of the system is not able hand= le the processing of your calculation, it can happen so. =A0 I have experie= nced same when I use G03W on lower end machine. try on different machine of= higher conf if you have multi-user =A0license.

thank you.

Abhinav Tathe | Research Sch= olar | Dyestuff Tech.Dept, ICT,Mumbai.
| Mobile : +91 7666110210 | goldenabhi]-[gmail.com

=A0

On Mon, Aug 27, 2012 at 4:55 PM, AMBRISH= KUMAR SRIVASTAVA ambrishphysics.:.gmail.com <owner-chemistry]-[ccl.net> wrote:<= br>

Sent to CCL by: "AMBRISH KUMAR SRIVASTAVA" [ambrishphysics(!)gmail.com]
respected all,
i am facing a problem during termination of job. i didnt get normal termina= tion at the end as expected. it shows something like this:
G03 W FROND END HAS STOPPED WORKING.
can anybody help me in this regard??
thanks to all in advance..
AMBRISH K. SRIVASTAVA
ambrishphysics=3D=3D=3Dgmail= .com

-=3D This is automatically added to each message by the mailing script =3D-=
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--f46d042dfdd9e08adb04c865e3c1-- From owner-chemistry@ccl.net Wed Aug 29 08:17:01 2012 From: "Adedapo Adeyinka u11335132:-:tuks.co.za" To: CCL Subject: CCL: Dihedral angle: DFT vs Crystal structure Message-Id: <-47496-120829024213-22075-MJHR9TE2ze2CdY2EbeVBug],[server.ccl.net> X-Original-From: Adedapo Adeyinka Content-Type: multipart/alternative; boundary=14dae9cdbf81564f8404c861db9e Date: Wed, 29 Aug 2012 08:42:04 +0200 MIME-Version: 1.0 Sent to CCL by: Adedapo Adeyinka [u11335132=tuks.co.za] --14dae9cdbf81564f8404c861db9e Content-Type: text/plain; charset=US-ASCII Dear Gopakumar, Like Cina said it would be impossible to reproduce the geometry of a molecule in the solid phase with gas phase computations. However from my experience calculations on molecules in solvent might be able to predict the geometry in solid phase. So you can try to do computations on your molecule using DFT with the PCM solvation model and the UFF force field. Adeyinka Adedapo Department of Chemistry, University of Pretoria, South Africa On 28 August 2012 16:06, G. Gopakumar gopakumar.gopinadhan]^[gmail.com < owner-chemistry^ccl.net> wrote: > Dear CCL members, > > I was calculating a molecule (71 atoms) for which the crystal > structure is > known. However, according to my calculation, one of the dihedral angles > shows > large mismatch (deviation of 12 degrees). I repeated the calculation with > both > B3LYP and BP86 functional and the values are given below: > > B3LYP/def2-TZVP ~ 21.2 > BP86/def2-TZVP ~ 20 > Experimental ~ 8.1 > > I would not worry too much if it was 2-3 degree deviation, but 12 is > something > that I should be careful with. > > I was wondering, whether there is a chance for an experimental error? Or > is it > just that DFT overestimates the dihedral angle? Does any body know any > references > where people encountered similar problem. > > I would be thankful for your comments > > with kind regards > > Gopakumar > > > -- This message and attachments are subject to a disclaimer. Please refer to http://www.it.up.ac.za/documentation/governance/disclaimer/ for full details. --14dae9cdbf81564f8404c861db9e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Dear Gopakumar,

=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0 Like Cina said it would be impossible to reproduce the geometry of a mo= lecule in the solid phase with gas phase computations. However from my expe= rience calculations on molecules in solvent might be able to predict the ge= ometry in solid phase. So you can try to do computations on your molecule u= sing DFT with=A0the PCM solvation model and the UFF force field.

=A0

Adeyinka Adedapo

Department of Chemistry,

University of Pretoria, South Africa

On 28 August 2012 16:06, G. Gopakumar gopakumar.= gopinadhan]^[gmail.com = <owner-chemistry^ccl.net> wrote:

Dear CCL members,

=A0=A0=A0=A0= I was calculating a molecule (71 atoms) for which the crystal structure is=
known. However, according to my calculation, one of the dihedral angles= shows
large mismatch (deviation of 12 degrees). I repeated the calculation with b= oth
B3LYP and BP86 functional and the values are given below:

B3L= YP/def2-TZVP=A0=A0 ~ 21.2
BP86/def2-TZVP=A0=A0=A0=A0 ~ 20
Experiment= al=A0=A0=A0=A0=A0=A0=A0=A0=A0 ~ 8.1

I would not worry too much if it was 2-3 degree deviation, but 12 is so= mething
that I should be careful with.

I was wondering, whether t= here is a chance for an experimental error? Or is it
just that DFT overe= stimates the dihedral angle? Does any body know any references
where people encountered similar problem.

I would be thankful for yo= ur comments

with kind regards

G= opakumar

This message and attachments are subject to= a disclaimer. Please refer to=20 http://www.it.u= p.ac.za/documentation/governance/disclaimer/ for full details. --14dae9cdbf81564f8404c861db9e-- From owner-chemistry@ccl.net Wed Aug 29 08:52:00 2012 From: "Can D rtbudak doech%%cup.uni-muenchen.de" To: CCL Subject: CCL: Articles about simulating short contacts Message-Id: <-47497-120829074638-9759-Bl9ALGYG3m+t8Zz/bUm/ng(-)server.ccl.net> X-Original-From: "Can D rtbudak" Date: Wed, 29 Aug 2012 07:46:36 -0400 Sent to CCL by: "Can D rtbudak" [doech^cup.uni-muenchen.de] Hi at all on the list, does someone know literature about using some small molecules in addition to the one that should be calculated to simulate cationic/anionic interactions. For example instead of calculating frequencies of H3O+ in H3O+SbF6- one uses H3O+(HF). This works well for me to get good frequency calculations. But it's hard to find articles about it. From owner-chemistry@ccl.net Wed Aug 29 11:31:00 2012 From: "rahim balgerdi balgerdi.rahim66::gmail.com" To: CCL Subject: CCL: convergence failur.........l502.exe Message-Id: <-47498-120829101421-7703-ICFS+f7TlHn7g9ojR/Otow^server.ccl.net> X-Original-From: "rahim balgerdi" Date: Wed, 29 Aug 2012 10:14:20 -0400 Sent to CCL by: "rahim balgerdi" [balgerdi.rahim66:_:gmail.com] I have used the opt b3lyp/lanl2dz geom=connectivity method to optimize qubic wo3+NO but and it always shows the following error: SCF Done: E(UB3LYP) = -1584.76084301 A.U. after 129 cycles Convg = 0.5969D-05 -V/T = 2.3148 = 0.0000 = 0.0000 = 0.5000 = 0.7980 S= 0.5237 = 0.000000000000E+00 Annihilation of the first spin contaminant: S**2 before annihilation 0.7980, after 0.7515 Convergence failure -- run terminated. Error termination via Lnk1e in C:\G09W\l502.exe at Fri Jul 13 11:15:52 2012. Job cpu time: 0 days 11 hours 23 minutes 51.0 seconds. File lengths (MBytes): RWF= 128 Int= 0 D2E= 0 Chk= 9 Scr= 1 but i am change the rute with scf=(maxcycle=9998) and it shows the same error please help me tank you very much input file: %mem=200MW %nprocshared=4 # opt b3lyp/lanl2dz geom=connectivity scf=(maxcycle=9998) CSD ENTRY isodisplace-output 0 2 W(PDBName=W,ResName=UNK,ResNum=1) -1 -0.00152947 2.66256220 0.04094268 O(PDBName=O,ResName=UNK,ResNum=1) -1 -0.00152947 2.66256220 -1.83905732 O(PDBName=O,ResName=UNK,ResNum=1) -1 1.32783153 1.33320220 0.04094268 W(PDBName=W,ResName=UNK,ResNum=1) -1 2.65719153 0.00384120 0.04094268 W(PDBName=W,ResName=UNK,ResNum=1) -1 -0.00152947 2.66256220 -3.71905732 O(PDBName=O,ResName=UNK,ResNum=1) -1 -1.33089047 1.33320220 0.04094268 W(PDBName=W,ResName=UNK,ResNum=1) -1 -2.66025047 0.00384120 0.04094268 O(PDBName=O,ResName=UNK,ResNum=1) -1 -2.66025047 0.00384120 -1.83905732 O(PDBName=O,ResName=UNK,ResNum=1) -1 -1.33089047 -1.32551980 0.04094268 W(PDBName=W,ResName=UNK,ResNum=1) -1 -0.00152947 -2.65487980 0.04094268 W(PDBName=W,ResName=UNK,ResNum=1) -1 -2.66025047 0.00384120 -3.71905732 O(PDBName=O,ResName=UNK,ResNum=1) -1 2.65719153 0.00384120 -1.83905732 W(PDBName=W,ResName=UNK,ResNum=1) -1 2.65719153 0.00384120 -3.71905732 O(PDBName=O,ResName=UNK,ResNum=1) -1 1.32783153 -1.32551980 0.04094268 O(PDBName=O,ResName=UNK,ResNum=1) -1 -0.00152947 -2.65487980 -1.83905732 W(PDBName=W,ResName=UNK,ResNum=1) -1 -0.00152947 -2.65487980 -3.71905732 O(PDBName=O,ResName=UNK,ResNum=1) -1 1.32783153 1.33320220 -3.71905732 O(PDBName=O,ResName=UNK,ResNum=1) -1 -1.33089047 1.33320220 -3.71905732 O(PDBName=O,ResName=UNK,ResNum=1) -1 -1.33089047 -1.32551980 -3.71905732 O(PDBName=O,ResName=UNK,ResNum=1) -1 1.32783153 -1.32551980 -3.71905732 H -1 -0.00152947 4.25925120 -0.06194632 H -1 -0.00152947 3.02696720 1.59889268 H -1 -4.25693947 0.00384120 -0.06194632 H -1 -3.02465547 0.00384120 1.59889268 H -1 -0.00152947 -4.25156880 -0.06194632 H -1 -0.00152947 -3.01928480 1.59889268 H -1 -0.00152947 -3.01928480 -5.27700732 H -1 -0.00152947 -4.25156880 -3.61616832 H -1 3.02159653 0.00384120 -5.27700732 H -1 4.25388053 0.00384120 -3.61616832 H -1 -0.00152947 3.02696720 -5.27700732 H -1 -0.00152947 4.25925120 -3.61616832 H -1 -3.02465547 0.00384120 -5.27700732 H -1 -4.25693947 0.00384120 -3.61616832 H -1 4.25388053 0.00384120 -0.06194632 H -1 3.02159653 0.00384120 1.59889268 N 0 0.00152947 -0.00384120 1.22678532 O 0 0.00152947 -0.00384120 2.37479532 1 2 1.0 3 1.0 6 1.0 21 1.0 22 1.0 2 5 1.0 3 4 1.0 4 12 1.0 14 1.0 35 1.0 36 1.0 5 17 1.0 18 1.0 31 1.0 32 1.0 6 7 1.0 7 8 1.0 9 1.0 23 1.0 24 1.0 8 11 1.0 9 10 1.0 10 14 1.0 15 1.0 25 1.0 26 1.0 37 1.0 11 18 1.0 19 1.0 33 1.0 34 1.0 12 13 1.0 13 17 1.0 20 1.0 29 1.0 30 1.0 14 15 16 1.0 16 19 1.0 20 1.0 27 1.0 28 1.0 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 2.0 38 From owner-chemistry@ccl.net Wed Aug 29 14:34:00 2012 From: "Sidney Ramos Santana santanasidney^-^yahoo.com.br" To: CCL Subject: CCL:G: BOMD: pure rotational and harmonic normal mode analysis. How to ? Message-Id: <-47499-120829113536-13748-t6uL18gDnaAK1vLV1zruCQ===server.ccl.net> X-Original-From: "Sidney Ramos Santana" Date: Wed, 29 Aug 2012 11:35:35 -0400 Sent to CCL by: "Sidney Ramos Santana" [santanasidney{:}yahoo.com.br] Dear CCL Users, Due the different time zones, Good day, good afternoon or good night. Please could you help me? I wanted do pure rotational and harmonic normal mode analysis for polyatomic molecules using BOMD theory. In Gaussian 2009, I try to run the BOMD example of dissociation of H2CO --> H2 + CO contained in the gaussian webpage with iop(1/79=3) and iop(1/79=2) But the calculation stops and give me the following error message: TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ Error termination in NtrErr: Please could you explain me how could I run a BOMD calculation of pure rotational and harmonic normal mode analysis for polyatomic molecules in G09 or another program ? Best regards, Sidney R. Santana From owner-chemistry@ccl.net Wed Aug 29 16:26:01 2012 From: "Amy J Austin amy_jean_austin{:}yahoo.com" To: CCL Subject: CCL: MI-QSAR Message-Id: <-47500-120829162440-30218-vRT4Udv54SHWpq/TgaEbRA__server.ccl.net> X-Original-From: "Amy J Austin" Date: Wed, 29 Aug 2012 16:24:39 -0400 Sent to CCL by: "Amy J Austin" [amy_jean_austin ~~ yahoo.com] Dear CCLer's: Does anyone where I can get MI-QSAR software? If so, please reply privately. TIA, Amy From owner-chemistry@ccl.net Wed Aug 29 17:57:01 2012 From: "Joaquin Barroso Flores joaco_barroso_-_yahoo.com" To: CCL Subject: CCL: Topological descriptor of 'molecular length' Message-Id: <-47501-120829174507-30483-bi6kzTj9cLRdb47oYRBG3w|-|server.ccl.net> X-Original-From: Joaquin Barroso Flores Content-Type: multipart/alternative; boundary="-1399187143-2122743092-1346276699=:39879" Date: Wed, 29 Aug 2012 14:44:59 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Joaquin Barroso Flores [joaco_barroso{}yahoo.com] ---1399187143-2122743092-1346276699=:39879 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCLers,=0A=0AIs anybody aware if there is a molecular descriptor of th= e molecular length/shape and the proper software to calculate it?=0AI'd lik= e to find a way to systematically treat rod-shaped or rod-like shaped molec= ules as a simple vector (with arbitrary direction imposed systematically un= der a suitable criterion) in order to have a shape-size descriptor of these= molecules.=0A=0AThanks in advanced for any help provided to this question.= =0A=0AGreetings from Mexico=0A=A0=0A=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=0AJoaquin Barroso-Fl= ores, Ph. D.=0ACentro Conjunto de Investigacion en Quimica Sustentable=0AIn= stituto de Quimica=0AUNAM=0A=0A=0A-> http://joaquinbarroso.wordpress.com=0A= =0A=0Ajoaquin.barroso''a''gmail.com =0A=0A=0A"Blogastronom=EDa": http://joa= quinbarroso.blogspot.com =0A=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 ---1399187143-2122743092-1346276699=:39879 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Dear CCLers,

I= s anybody aware if there is a molecular descriptor of the molecular length/= shape and the proper software to calculate it?
I'd like to find a way to= systematically treat rod-shaped or rod-like shaped molecules as a simple v= ector (with arbitrary direction imposed systematically under a suitable cri= terion) in order to have a shape-size descriptor of these molecules.
Thanks in advanced for any help provided to this question.

Greetin= gs from Mexico

=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
Joaquin Barroso-Flor= es, Ph. D.
Centro Conjunto de Investigacion en Quimica Sustentable
In= stituto de Quimica
UNAM

-> http://joaquinbarroso.w= ordpress.com

joaquin.barroso''a''gmail.com

"Blogastronom=EDa": http://joaquinbarroso.blogspot.com
=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

---1399187143-2122743092-1346276699=:39879--