From owner-chemistry@ccl.net Wed Mar 24 02:56:01 2010 From: "Peter Khlyabich khlyabic|*|usc.edu" To: CCL Subject: CCL:G: Write error in NtrExt1 Message-Id: <-41509-100324025045-25791-+WuMetM5vo1ev41fxcB33A~~server.ccl.net> X-Original-From: "Peter Khlyabich" Date: Wed, 24 Mar 2010 02:50:35 -0400 Sent to CCL by: "Peter Khlyabich" [khlyabic(a)usc.edu] Hi, I'm running Gaussian 03 and after submitting the run file I get the following mistake: %chk=/scratch/test.chk %Save %mem=900MW %NProcShared=2 Will use up to 2 processors via shared memory. %NProcLinda=2 Will use up to 2 processors via Linda. Erroneous write during file extend. write -1 instead of 4096 Probably out of disk space. Write error in NtrExt1 I cleaned the scratch file but it didn't help. Please let me know if you have any ideas what is the problem Thank you in advance Peter From owner-chemistry@ccl.net Wed Mar 24 06:18:00 2010 From: "Andrew Voronkov drugdesign/a\yandex.ru" To: CCL Subject: CCL: No non-salts Message-Id: <-41510-100322124720-24289-BXf4oXJGMLJqud5nvITAFA(~)server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Mon, 22 Mar 2010 19:47:03 +0300 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign||yandex.ru] Dear CCL users, I have problem with set up of custom Filter for Open Eye. I get strange message "No non-salts (skipping molecule)". I don't want to use any salt or non-salt filter. Any non-salt filter is not mentioned in in OpenEye manual an the molecule is not salt at all. How to switch off this "No non-salts" filtering? Best regards, Andrew Typecheck = true pKaNormalization = true findUnique = false sdtag = false No selection MIN_MOLWT 200.000000 MAX_MOLWT 600.000000 MIN_Num_Heavy 15 MAX_Num_Heavy 35 MIN_RING_SYS 0 MAX_RING_SYS 5 MIN_RING_SIZE 0 MAX_RING_SIZE 20 MIN_CARBONS 7 MAX_CARBONS 35 MIN_HETEROATOMS 2 MAX_HETEROATOMS 20 MIN_Het_C_Ratio 0.100000 MAX_Het_C_Ratio 1.000000 MIN_ROT_BONDS 0 MAX_ROT_BONDS 20 MIN_RIGID_BONDS 0 MAX_RIGID_BONDS 35 MIN_CON_NON_RING 0 MAX_CON_NON_RING 15 MIN_UNBRANCHED_SIZE 0 MAX_UNBRANCHED_SIZE 6 MIN_FCN_GRP 0 MAX_FCN_GRP 18 MIN_COUNT_FORMAL_CRG 0 MAX_COUNT_FORMAL_CRG 3 MIN_SUM_FORMAL_CRG -2 MAX_SUM_FORMAL_CRG 2 MIN_HBOND_DONORS 0 MAX_HBOND_DONORS 6 MIN_HBOND_ACCEPTORS 0 MAX_HBOND_ACCEPTORS 8 MIN_LIPINSKI_DONORS 0 MAX_LIPINSKI_DONORS 5 MIN_LIPINSKI_ACCEPTORS 0 MAX_LIPINSKI_ACCEPTORS 10 MIN_CHIRAL_CENTERS 0 MAX_CHIRAL_CENTERS 4 MIN_XLOGP -5.000000 MAX_XLOGP 6.000000 MIN_SOLUBILITY moderately S and P false MIN_2D_PSA 0.000000 MAX_2D_PSA 150.000000 CMV_LEAD false CMV_DRUG false adjust rot for rings true GSK true LIPINSKI true MAX_LIPINSKI 1 PHARMACOPIA true MIN_ABS 0.500000 AGGREGATORS true PRED_AGG true **************************************** No non-salts (skipping molecule). From owner-chemistry@ccl.net Wed Mar 24 06:52:01 2010 From: "Ol Ga eurisco1- -pochta.ru" To: CCL Subject: CCL:G: Write error in NtrExt1 Message-Id: <-41511-100324053237-32732-0bBT1S5j/0UI39OvtaVgXQ()server.ccl.net> X-Original-From: "Ol Ga" Date: Wed, 24 Mar 2010 05:32:32 -0400 Sent to CCL by: "Ol Ga" [eurisco1]^[pochta.ru] Dear Peter Khlyabich, You should add in the route section keyword maxdisk=_your value. For instance, # hf/6-31g* maxdisk=150Gb scf(tight). Possible %RWF ans %SCR are also necessary. Sincerely, Ol Ga ***************************** Sent to CCL by: "Peter Khlyabich" [khlyabic(a)usc.edu] Hi, I'm running Gaussian 03 and after submitting the run file I get the following mistake: %chk=/scratch/test.chk %Save %mem=900MW %NProcShared=2 Will use up to 2 processors via shared memory. %NProcLinda=2 Will use up to 2 processors via Linda. Erroneous write during file extend. write -1 instead of 4096 Probably out of disk space. Write error in NtrExt1 I cleaned the scratch file but it didn't help. Please let me know if you have any ideas what is the problem Thank you in advance Peter From owner-chemistry@ccl.net Wed Mar 24 07:27:00 2010 From: "Fedor Goumans fedor.goumans]~[googlemail.com" To: CCL Subject: CCL:G: Write error in NtrExt1 Message-Id: <-41512-100324060323-3686-aH2zRFBrqiFkd9P2SSSQEg#%#server.ccl.net> X-Original-From: Fedor Goumans Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 24 Mar 2010 10:31:27 +0100 MIME-Version: 1.0 Sent to CCL by: Fedor Goumans [fedor.goumans!=!googlemail.com] Dear Peter, Perhaps you are trying to run G03 on Fedora Core, which isn't officially supported by Gaussian? With the older Fedora Core versions the solution appeared to be: echo 0 > /proc/sys/kernel/randomize_va_space but if you are trying to run on FC, you can google for Erroneous write, G03, Fedora Cora to see if there have been other solutions meanwhile. HTH, Fedor On 24 March 2010 07:50, Peter Khlyabich khlyabic|*|usc.edu wrote: > > Sent to CCL by: "Peter =A0Khlyabich" [khlyabic(a)usc.edu] > Hi, > > I'm running Gaussian 03 and after submitting the run file I get the follo= wing mistake: > > %chk=3D/scratch/test.chk > =A0%Save > =A0%mem=3D900MW > =A0%NProcShared=3D2 > =A0Will use up to =A0 =A02 processors via shared memory. > =A0%NProcLinda=3D2 > =A0Will use up to =A0 =A02 processors via Linda. > Erroneous write during file extend. write -1 instead of 4096 > Probably out of disk space. > Write error in NtrExt1 > > I cleaned the scratch file but it didn't help. > > Please let me know if you have any ideas what is the problem > > Thank you in advance > > Peter > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Wed Mar 24 09:40:01 2010 From: "rinu iyer rinuiyer|-|gmail.com" To: CCL Subject: CCL:G: Write error in NtrExt1 Message-Id: <-41513-100324074840-1702-tXCeYPT0Kimb7pujJM06SA{=}server.ccl.net> X-Original-From: rinu iyer Content-Type: multipart/alternative; boundary=0016e68f9c351453a0048289a483 Date: Wed, 24 Mar 2010 16:16:21 +0530 MIME-Version: 1.0 Sent to CCL by: rinu iyer [rinuiyer,,gmail.com] --0016e68f9c351453a0048289a483 Content-Type: text/plain; charset=ISO-8859-1 actually u check whether linda is installed in your computer. and also i will suggest you that dont use nprocshared and nproclinda together. and after that also if this probelm occurs then see whether the geometry of ur molecule. On Wed, Mar 24, 2010 at 12:20 PM, Peter Khlyabich khlyabic|*|usc.edu < owner-chemistry . ccl.net> wrote: > > Sent to CCL by: "Peter Khlyabich" [khlyabic(a)usc.edu] > Hi, > > I'm running Gaussian 03 and after submitting the run file I get the > following mistake: > > %chk=/scratch/test.chk > %Save > %mem=900MW > %NProcShared=2 > Will use up to 2 processors via shared memory. > %NProcLinda=2 > Will use up to 2 processors via Linda. > Erroneous write during file extend. write -1 instead of 4096 > Probably out of disk space. > Write error in NtrExt1 > > I cleaned the scratch file but it didn't help. > > Please let me know if you have any ideas what is the problem > > Thank you in advance > > Peter> > > -- K.R.Ramya Research fellow IIndian Institute of Science Education & Research(IISER) Central Tower, Sai Trinity Building, Sutarwadi Road, Pashan, Pune 411021, INDIA --0016e68f9c351453a0048289a483 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
actually u check whether linda is installed in your computer. and also= i will suggest you that dont use nprocshared and nproclinda together.=A0 a= nd after that also if this probelm occurs then see whether the geometry of = ur=A0 molecule.


=A0
On Wed, Mar 24, 2010 at 12:20 PM, Peter Khlyabic= h khlyabic|*|usc.edu <<= a href=3D"mailto:owner-chemistry . ccl.net">owner-chemistry . ccl.net> wrote:

Sent to CCL by: "Peter = =A0Khlyabich" [khlyabic(a)usc.edu]
Hi,

I'm running Gaussian 03 and after submitting the run file I = get the following mistake:

%chk=3D/scratch/test.chk
=A0%Save
= =A0%mem=3D900MW
=A0%NProcShared=3D2
=A0Will use up to =A0 =A02 proces= sors via shared memory.
=A0%NProcLinda=3D2
=A0Will use up to =A0 =A02 processors via Linda.
E= rroneous write during file extend. write -1 instead of 4096
Probably out= of disk space.
Write error in NtrExt1

I cleaned the scratch file= but it didn't help.

Please let me know if you have any ideas what is the problem

Tha= nk you in advance

Peter



-=3D This is automatically ad= ded to each message by the mailing script =3D-
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--
K.R.Ramya
R= esearch fellow
IIndian Institute of Science Education & Research(IISER)
Central Tow= er, Sai Trinity Building, Sutarwadi Road, Pashan,
Pune 411021, INDIA
--0016e68f9c351453a0048289a483-- From owner-chemistry@ccl.net Wed Mar 24 10:15:00 2010 From: "Alex Wang yawang . chem.ubc.ca" To: CCL Subject: CCL: Call for Abstracts for the OF-DFT Symposium at Pacifichem 2010 Message-Id: <-41514-100324055933-3000-8+4vcRJZBkwaSgsIpMiJ2Q{=}server.ccl.net> X-Original-From: Alex Wang Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII Date: Wed, 24 Mar 2010 02:27:13 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Alex Wang [yawang*chem.ubc.ca] We apologize if you receive multiple copies of this email. Please kindly forward this email to whom may be interested. =========================================================== Dear Colleagues: I am Alex Wang and am co-organizing a symposium on orbital-free density functional theory (OF-DFT) at the 2010 International Chemical Congress of Pacific Basin Societies (Pacifichem 2010), which will be held on Dec. 19 (whole day) and Dec. 20 (morning), 2010 at Honolulu, Hawaii, USA (http://www.pacifichem.org). With some remarkable recent developments in OF-DFT and large-scale simulations in complex systems, we want to use Pacifichem 2010 as a platform to bring together mathematicians, functional designers, methodology developers, and method practitioners to discuss and position OF-DFT as a major tool in simulating complex systems of thousands of atoms within a diverse chemical bonding environment. It is our great pleasure to invite you to submit abstracts of posters and contributed talks on the cutting-edge scientific advances made in your research group in any of the following areas: 1) Orbital-free density functional theory. 2) Anything related to kinetic-energy density functional: its functional design, functional properties, and its usage in orbital-free DFT and embedding/multiscale method. 3) High-quality transferrable local pseudopotentials. 4) Methodology, mathematical aspects, and challenges of large-scale simulations in complex systems. The Pacifichem 2010 website is already open for abstract submission (http://www.pacifichem.org/abstracts). Please submit your abstract before the April 5 deadline (only two weeks away). In the Technical Symposia listing (http://www.pacifichem.org/symposia/#5), our OF-DFT Symposium (http://www.pacifichem.org/symposia/c_symp_258.htm) is in * Area 5 - Physical, Theoretical & Computational under the title * Orbital-Free Density Functional Theory and Its Applications to Large-Scale Materials Simulations (#258) We sincerely hope that you will join us for a scientific discourse at the OF-DFT Symposium during Pacifichem 2010 in December. With best wishes, Alex Wang on behalf of the OF-DFT Symposium Organizers: Yan Alexander Wang (UBC, Canada) Carlos J. Garcia-Cervera (UC Santa Barbara, USA) Tomasz A. Wesolowski (Geneva, Switzerland) Julian D. Gale (Curtin, Australia) http://www.chem.ubc.ca/faculty/wang/PacChem_flyer.pdf http://www.pacifichem.org/symposia/c_symp_258.htm -- ---------------------------------------------------------------------- Yan Alexander Wang Office Rm#: Chemistry D334 Associate Professor Office Tel: (604) 822-6773 Department of Chemistry Cell Phone: (604) 816-6773 University of British Columbia Lab(s) Rm#: Chemistry D319 2036 Main Mall, Chemistry Building Lab(s) Tel: (604) 822-6549 Vancouver, BC V6T 1Z1, Canada Office Fax: (604) 822-2847 http://www.chem.ubc.ca/faculty/wang E-mail: yawang-$-chem.ubc.ca ---------------------------------------------------------------------- From owner-chemistry@ccl.net Wed Mar 24 10:49:02 2010 From: "Shirin Seifert shirin.seifert{=}gmail.com" To: CCL Subject: CCL:G: G03:Dipole Moment Calculation Message-Id: <-41515-100324101208-8068-bCaPOzjGcSYG1m6pFbl7xg],[server.ccl.net> X-Original-From: Shirin Seifert Content-Type: multipart/alternative; boundary=001636457330b76db304828c6df1 Date: Wed, 24 Mar 2010 18:35:54 +0430 MIME-Version: 1.0 Sent to CCL by: Shirin Seifert [shirin.seifert]|[gmail.com] --001636457330b76db304828c6df1 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Arash: I have also changed the point charges. When I use i.e. q1=3D2.4 and q2=3D 2= .2 then I get the following moments Moments=3D 2* 8.692740 2* 0.377945 2*8.692740 the linear change in moments is seen. But still I can not compute them using simple electrostatic formulas. Could anybody advise us? Thanks On Mon, Mar 22, 2010 at 7:15 PM, ~[yahoo.com < owner-chemistry a ccl.net> wrote: > Hello: > > Regarding this example from Gaussian03 manual I have a question. > =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 > > # RHF/STO-3G Opt=3DZ-Matrix Charge NoSymm > > > Water, STO-3G, point charges > > 0,1 > O > H 1 R1 > H 1 R2 2 > A1 > Variables: > R1=3D1.0 > R2=3D1.0 > A1=3D105. > > 2.0 2.0 2.0 1.2 > > 2.0 -2.0 2.0 1.1 > > =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 > > > In the output file I have: > Point Charges: > XYZ=3D 2.0000 2.0000 2.0000 Q=3D 1.2000 A=3D 0.0000 R=3D = 0.0000 C=3D 0.0000 > XYZ=3D 2.0000 -2.0000 2.0000 Q=3D 1.1000 A=3D 0.0000 R=3D = 0.0000 C=3D 0.0000 > Sum of input charges=3D 2.300000 > Moments=3D 8.692740 0.377945 8.692740 > Self energy of the charges =3D 0.1746284787 > MM energy of the charges =3D 0.0000000000 > Nuclear-Charge attraction =3D 3.5981154035 > > How the moments, self energy and > Nuclear-Charge attraction > have been computed and what are the units? > I used simple electrostatic formulas but my results are different than th= at of Gaussian output. > (i.e using p(r) =3D =E2=88=91 qi di results in px=3D4.6 eA py=3D0.2 pz= =3D4.6 eA converting to Debye gives px=3D23 py=3D1 pz=3D23) > > Thanks for your help in advance. > A.F. > > > --001636457330b76db304828c6df1 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Arash:
I have also changed the point charges. When I us= e i.e. q1=3D2.4 and q2=3D 2.2 then I get the following moments
Moments=3D 2* 8.692740 2* 0.377945 = 2*8.692740
the linear change in moments is seen. But still I can not compute them usin= g simple electrostatic formulas.
Could anybody advise us?

Thanks =


On Mon, Mar 22, 2010 at= 7:15 PM, ]~[yahoo.= com <ow= ner-chemistry a ccl.net> wrote:
Hello:

Regarding this example from Gaussian03 manual I have a question.
=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
# RHF/STO-3G Opt=3DZ-Matrix Charge NoSymm
 

Water, STO-3=
G, point charge=
s 


0,1 
O 
H 1 R1 
H 1 R2 2
 A1 
Variables: 
R1=3D1.0 R2=3D1.0 
A1=3D105. 

2.0  2.0 2.0 1.2
 
2.0 -2.0 2.0 1.1<=
br> 
=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

In the output file I have:
Point Charges:
 XYZ=3D    2.0000 =
   2.0000    2.0000 Q=3D    1.2000 A=3D    0.0000 R=3D 0.0000 C=3D    0.000=
0
 XYZ=3D    2.0000   -2.0000    2.0000 Q=3D    1.1000 A=3D 0.0000 R=3D =
   0.0000 C=3D    0.0000

 Sum of input charges=3D 2.300000
 Moments=3D            8.692740       =
     0.377945       8.692740
 Self energy of the charges =3D         0.<=
span>1746284787
 MM   energy  of the charges =3D         0.=
0000000000

 Nuclear-Charge attraction  =3D  3.5981154035

How the m=
oments, self energy and
 Nuclear-Charge attraction
have been computed=
 and what are the units?
I used simple electrostatic formulas but my res=
ults are different than that of Gaussian output.

(i.e using p(r) =3D =E2=88=91 qi di results in px=3D4.6 eA  py=3D0.2 pz=3D4=
.6 eA converting to Debye gives px=3D23 py=3D1 pz=3D23)

Thanks for y=
our help in advance.
A.F.


--001636457330b76db304828c6df1-- From owner-chemistry@ccl.net Wed Mar 24 11:24:00 2010 From: "Henry Martinez hmartine:-:gmail.com" To: CCL Subject: CCL:G: Electrostatic interaction Message-Id: <-41516-100324101229-8269-2IWJegrZpGzy5aXx9xU5IQ_._server.ccl.net> X-Original-From: "Henry Martinez" Date: Wed, 24 Mar 2010 10:12:25 -0400 Sent to CCL by: "Henry Martinez" [hmartine_._gmail.com] Hi, How can I know (or check, or verified) if two atoms are having an attractive electrostatic interaction by using Gaussian? More specific, I have one fluorine atom over the top of a electron deficient benzene ring (this is after the ground state calculation), I believe the fluorine is a that top position because his lone pairs are having an attractive electrostatic interaction with the electron poor benzene ring...how can I verified and attractive electrostatic interaction by using Gaussian 03. Thanks a lot From owner-chemistry@ccl.net Wed Mar 24 12:36:00 2010 From: "Neeraj Naithani neerajnaithani!^!gmail.com" To: CCL Subject: CCL: help regarding COLUMBUS Message-Id: <-41517-100324105004-18714-TlvjoS31L143hi97Y8/JiA=-=server.ccl.net> X-Original-From: "Neeraj Naithani" Date: Wed, 24 Mar 2010 10:50:00 -0400 Sent to CCL by: "Neeraj Naithani" [neerajnaithani,+,gmail.com] hi friends, Anybody using COLUMBUS. I Need Help to install it on Fedora 11. From owner-chemistry@ccl.net Wed Mar 24 13:11:00 2010 From: "Jean-Christophe Poully poully]|[galilee.univ-paris13.fr" To: CCL Subject: CCL: Error - PM6 - G09 Message-Id: <-41518-100324120246-19779-XnHnDmaKnB/kXR+85E3e3w..server.ccl.net> X-Original-From: Jean-Christophe Poully Content-Type: multipart/alternative; boundary="=====================_-1914822453==.ALT" Date: Wed, 24 Mar 2010 16:25:20 +0100 Mime-Version: 1.0 Sent to CCL by: Jean-Christophe Poully [poully*galilee.univ-paris13.fr] --=====================_-1914822453==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Dear Sanjay, It seems that your structure is far from a minimum at the PM6 level. I used to encounter such issue with AM1, I solved it by using HF/sto-3g instead of AM1, it is a bit more costly but it worked... You can also try with AM1. Hope it helps, Jean-Christophe At 21:15 22/03/2010, you wrote: >Dear CCL Folks, > >I came with a problem, which is bothering me a lot. > >I am trying to optimize a system using PM6 (Semiempirical method) >Hamiltonian. > >I gave the following keyword (just single point) ># pm6 scf(maxcycle=10000) >and i get the following error.(see below) > >However when i run the same geometry in B3lyp no error >is found. > >could you please help me to fix this. > >Best regards, >Sanjay > >---------------------- >Requested convergence on RMS density matrix=1.00D-08 within**** cycles. > Requested convergence on MAX density matrix=1.00D-06. > Requested convergence on energy=1.00D-06. > No special actions if energy rises. > Overlap will be assumed to be unity. > Keep J ints in memory in canonical form, NReq=101090637. > Rare condition: small coef for last iteration: 0.000D+00 > Rare condition: small coef for last iteration: 0.000D+00 > Rare condition: small coef for last iteration: 0.000D+00 > Rare condition: small coef for last iteration: 0.000D+00 > Matrix for removal 1 Erem= 6.57881359435214 Crem= 0.000D+00 > Matrix for removal 3 Erem= 6.34628677742421 Crem= 0.000D+00 > Matrix for removal 1 Erem= 4.94003472302734 Crem= 0.000D+00 > Matrix for removal 1 Erem= 0.897917718036979 Crem= 0.000D+00 > Matrix for removal 1 Erem=-0.631840924218750 Crem= 0.000D+00 > Matrix for removal 1 Erem=-0.726975008594081 Crem= 0.000D+00 > Matrix for removal 1 Erem=-0.752844884442311 Crem= 0.000D+00 > Matrix for removal 1 Erem=-0.771933264627023 Crem= 0.000D+00 > Matrix for removal 1 Erem=-0.833856880890608 Crem= 0.000D+00 > Matrix for removal 1 Erem=-0.911426582542163 Crem= 0.000D+00 > Matrix for removal 1 Erem=-0.960669360548991 Crem= 0.000D+00 > Matrix for removal 1 Erem= -1.01751365805558 Crem= 0.000D+00 > Matrix for removal 2 Erem= -1.04519031657037 Crem= 0.000D+00 > Matrix for removal 3 Erem= -1.05597140671966 Crem= 0.000D+00 > Rare condition: small coef for last iteration: 0.000D+00 > Matrix for removal 1 Erem= -1.06140699114485 Crem= 0.000D+00 > Rare condition: small coef for last iteration: 0.000D+00 >, >, (keeps continuing) >, >, > Rare condition: small coef for last iteration: 0.000D+00 > Matrix for removal 19 Erem= -1.09176692582855 Crem= 0.000D+00 > Matrix for removal 19 Erem= -1.09150839015138 Crem= 0.000D+00 > Rare condition: small coef for last iteration: 0.000D+00 > Matrix for removal 19 Erem= -1.09163847321452 Crem= 0.000D+00 > Matrix for removal 19 Erem= -1.09159089943432 Crem= 0.000D+00 > Rare condition: small coef for last iteration: 0.000D+00 > Matrix for removal 19 Erem= -1.09176744393312 Crem= 0.000D+00 > Matrix for removal 19 Erem= -1.09152382786283 Crem= 0.000D+00 > Rare condition: small coef for last iteration: 0.000D+00 > Matrix for removal 19 Erem= -1.09163734487561 Crem= 0.000D+00 > Matrix for removal 19 Erem= -1.09159849577782 Crem= 0.000D+00 > Rare condition: small coef for last iteration: 0.000D+00 > Matrix for removal 19 Erem= -1.09176958132935 Crem= 0.000D+00 > >>>>>>>>>> Convergence criterion not met. > SCF Done: E(UPM6) = -1.09156206308 A.U. after **** cycles > Convg = 0.2340D-03 -V/T = 0.9977 > = 0.0000 = 0.0000 = 0.5000 = 2.8076 S= 1.2486 > = 0.000000000000E+00 > Annihilation of the first spin contaminant: > S**2 before annihilation 2.8076, after 4.1082 > Convergence failure -- run terminated. > Error termination via Lnk1e in /usr/local/g09a01/g09/l502.exe at > Mon Mar 22 16:01:58 2010. > Job cpu time: 0 days 0 hours 12 minutes 38.0 seconds. > File lengths (MBytes): RWF= 19 Int= 0 D2E= 0 > Chk= 1 Scr= 1 >(END) > >--------------------------------- > > > > > >-- >Regards, >Dr. Sanjay Bharathwaj Kumar, >Dharmendra Institute of Technology, >India. --=====================_-1914822453==.ALT Content-Type: text/html; charset="us-ascii"
Dear Sanjay,

It seems that your structure is far from a minimum at the PM6 level. I used to encounter such issue with AM1, I solved it by using HF/sto-3g instead of AM1, it is a bit more costly but it worked... You can also try with AM1.

Hope it helps,

Jean-Christophe


At 21:15 22/03/2010, you wrote:
Dear CCL Folks,

I came with a problem, which is bothering me a lot.

I am trying to optimize a system using PM6 (Semiempirical method)
Hamiltonian.

I gave the following keyword (just single point)
# pm6 scf(maxcycle=10000)
and i get the following error.(see below)

However when i run the same geometry in B3lyp no error
is found.

could you please help me to fix this.

Best regards,
Sanjay

----------------------
Requested convergence on RMS density matrix=1.00D-08 within**** cycles.
 Requested convergence on MAX density matrix=1.00D-06.
 Requested convergence on             energy=1.00D-06.
 No special actions if energy rises.
 Overlap will be assumed to be unity.
 Keep J ints in memory in canonical form, NReq=101090637.
 Rare condition: small coef for last iteration:  0.000D+00
 Rare condition: small coef for last iteration:  0.000D+00
 Rare condition: small coef for last iteration:  0.000D+00
 Rare condition: small coef for last iteration:  0.000D+00
 Matrix for removal  1 Erem=  6.57881359435214     Crem= 0.000D+00
 Matrix for removal  3 Erem=  6.34628677742421     Crem= 0.000D+00
 Matrix for removal  1 Erem=  4.94003472302734     Crem= 0.000D+00
 Matrix for removal  1 Erem= 0.897917718036979     Crem= 0.000D+00
 Matrix for removal  1 Erem=-0.631840924218750     Crem= 0.000D+00
 Matrix for removal  1 Erem=-0.726975008594081     Crem= 0.000D+00
 Matrix for removal  1 Erem=-0.752844884442311     Crem= 0.000D+00
 Matrix for removal  1 Erem=-0.771933264627023     Crem= 0.000D+00
 Matrix for removal  1 Erem=-0.833856880890608     Crem= 0.000D+00
 Matrix for removal  1 Erem=-0.911426582542163     Crem= 0.000D+00
 Matrix for removal  1 Erem=-0.960669360548991     Crem= 0.000D+00
 Matrix for removal  1 Erem= -1.01751365805558     Crem= 0.000D+00
 Matrix for removal  2 Erem= -1.04519031657037     Crem= 0.000D+00
 Matrix for removal  3 Erem= -1.05597140671966     Crem= 0.000D+00
 Rare condition: small coef for last iteration:  0.000D+00
 Matrix for removal  1 Erem= -1.06140699114485     Crem= 0.000D+00
 Rare condition: small coef for last iteration:  0.000D+00
,
, (keeps continuing)
,
,
 Rare condition: small coef for last iteration:  0.000D+00
 Matrix for removal 19 Erem= -1.09176692582855     Crem= 0.000D+00
 Matrix for removal 19 Erem= -1.09150839015138     Crem= 0.000D+00
 Rare condition: small coef for last iteration:  0.000D+00
 Matrix for removal 19 Erem= -1.09163847321452     Crem= 0.000D+00
 Matrix for removal 19 Erem= -1.09159089943432     Crem= 0.000D+00
 Rare condition: small coef for last iteration:  0.000D+00
 Matrix for removal 19 Erem= -1.09176744393312     Crem= 0.000D+00
 Matrix for removal 19 Erem= -1.09152382786283     Crem= 0.000D+00
 Rare condition: small coef for last iteration:  0.000D+00
 Matrix for removal 19 Erem= -1.09163734487561     Crem= 0.000D+00
 Matrix for removal 19 Erem= -1.09159849577782     Crem= 0.000D+00
 Rare condition: small coef for last iteration:  0.000D+00
 Matrix for removal 19 Erem= -1.09176958132935     Crem= 0.000D+00
 >>>>>>>>>> Convergence criterion not met.
 SCF Done:  E(UPM6) =  -1.09156206308     A.U. after **** cycles
             Convg  =    0.2340D-03             -V/T =  0.9977
 <Sx>= 0.0000 <Sy>= 0.0000 <Sz>= 0.5000 <S**2>= 2.8076 S= 1.2486
 <L.S>= 0.000000000000E+00
 Annihilation of the first spin contaminant:
 S**2 before annihilation     2.8076,   after     4.1082
 Convergence failure -- run terminated.
 Error termination via Lnk1e in /usr/local/g09a01/g09/l502.exe at Mon Mar 22 16:01:58 2010.
 Job cpu time:  0 days  0 hours 12 minutes 38.0 seconds.
 File lengths (MBytes):  RWF=     19 Int=      0 D2E=      0 Chk=      1 Scr=      1
(END)

---------------------------------





--
Regards,
Dr. Sanjay Bharathwaj Kumar,
Dharmendra Institute of Technology,
India.
--=====================_-1914822453==.ALT-- From owner-chemistry@ccl.net Wed Mar 24 14:03:01 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim[A]compchem.net" To: CCL Subject: CCL:G: Electrostatic interaction Message-Id: <-41519-100324132320-1820-rIOMkiC5z4nv1eQeEmh0GQ/a\server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=0016e6da7ae5dfd67604828f2e6b Date: Wed, 24 Mar 2010 17:23:05 +0000 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim=-=compchem.net] --0016e6da7ae5dfd67604828f2e6b Content-Type: text/plain; charset=ISO-8859-1 Dear Herny This type of interaction between Fluorine atom and Benzene ring is returned to what is called Halogen-pi system interaction, some references call it closed shell interaction. This due to the presence of sigma-hole on the head of the halogen atom. It is not returned as you said to the lone pair. It may form a bond with a electron deficient ring with its side, where Fluorine has a negative charge around all the sigma-hole. We call it a directional bonding atom, Halogens as general can form bonds with positive and negative atoms, depending on the direction corresponding to its centre. AIM theory is the appropriate method to know if there is a bond between the halogen and pi-ring or, in general, between any two atoms. If you need more information, I would prefer to talk on privacy, where we are working on a project around this issue. Sincerely; M. Ibrahim On Wed, Mar 24, 2010 at 2:12 PM, Henry Martinez hmartine:-:gmail.com < owner-chemistry(0)ccl.net> wrote: > > Sent to CCL by: "Henry Martinez" [hmartine_._gmail.com] > Hi, > How can I know (or check, or verified) if two atoms are having an > attractive electrostatic interaction by using Gaussian? > More specific, I have one fluorine atom over the top of a electron > deficient benzene ring (this is after the ground state calculation), I > believe the fluorine is a that top position because his lone pairs are > having an attractive electrostatic interaction with the electron poor > benzene ring...how can I verified and attractive electrostatic interaction > by using Gaussian 03. Thanks a lot> > > -- Mahmoud A. A. Ibrahim Current Address 7.05, School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt. Contact Information Email: m.ibrahim(0)compchem.net Website: www.compchem.net Fax No.: +20862342601 --0016e6da7ae5dfd67604828f2e6b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Herny
This type of interaction between=A0Fluorine=A0atom and=A0Ben= zene=A0ring is returned to what is called Halogen-pi system interaction, so= me references call it closed shell interaction. This due to the presence of= sigma-hole on the head of the halogen atom. It is not returned as you said= to the lone pair. It may form a bond with a electron deficient ring with i= ts side, where Fluorine =A0has a negative charge around all the sigma-hole.= We call it a directional bonding atom, Halogens as general can form bonds = with positive and negative atoms, depending on the direction corresponding = to its centre.
AIM theory is the appropriate method to know if there is a bond betwee= n the halogen and pi-ring or, in general, between any two atoms.
= If you need more information, I would prefer to talk on privacy, where we a= re working on a project around this issue.
Sincerely;
M. Ibrahim


On Wed, Mar 24, 2010 at 2:12 PM, Henry Martinez hmartine:-:gmail.com <owner-chemistry(0)ccl.net> wrote:

Sent to CCL by: "Henry =A0Martinez" [hmartine_._gmail.com]
Hi,
How can I know (or check, or verified) if two atoms are having an attractiv= e electrostatic interaction by using Gaussian?
More specific, I have one fluorine atom over the top of a electron deficien= t benzene ring (this is after the ground state calculation), I believe the = fluorine is a that top position because his lone pairs are having an attrac= tive electrostatic interaction with the electron poor benzene ring...how ca= n I verified and attractive electrostatic interaction by using Gaussian 03.= Thanks a lot



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--0016e6da7ae5dfd67604828f2e6b-- From owner-chemistry@ccl.net Wed Mar 24 14:43:00 2010 From: "alfredo tlahuice tlahuicef^yahoo.com" To: CCL Subject: CCL:G: Write error in NtrExt1 Message-Id: <-41520-100324125043-29111-p7TKD6LgLjpi3S91RiBNdA||server.ccl.net> X-Original-From: alfredo tlahuice Content-Type: multipart/alternative; boundary="0-972946398-1269445832=:81714" Date: Wed, 24 Mar 2010 08:50:32 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: alfredo tlahuice [tlahuicef^yahoo.com] --0-972946398-1269445832=:81714 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi there. Your problem is of memory. The job you are trying to run has huge temporal = files. You need to increase the space on the corking directory. Good luck! --- On Wed, 3/24/10, rinu iyer rinuiyer|-|gmail.com wrote: > From: rinu iyer rinuiyer|-|gmail.com Subject: CCL:G: Write error in NtrExt1 To: "Tlahuice, Alfredo " Date: Wednesday, March 24, 2010, 10:46 AM actually u check whether linda is installed in your computer. and also i wi= ll suggest you that dont use nprocshared and nproclinda together.=A0 and af= ter that also if this probelm occurs then see whether the geometry of ur=A0= molecule. =0A=0A =A0=0AOn Wed, Mar 24, 2010 at 12:20 PM, Peter Khlyabich khlyabic|*|usc.edu = wrote: =0A=0A Sent to CCL by: "Peter =A0Khlyabich" [khlyabic(a)usc.edu] =0AHi, I'm running Gaussian 03 and after submitting the run file I get the followi= ng mistake: %chk=3D/scratch/test.chk =A0%Save =A0%mem=3D900MW =A0%NProcShared=3D2 =A0Will use up to =A0 =A02 processors via shared memory. =0A=A0%NProcLinda=3D2 =A0Will use up to =A0 =A02 processors via Linda. Erroneous write during file extend. write -1 instead of 4096 Probably out of disk space. Write error in NtrExt1 I cleaned the scratch file but it didn't help. =0A Please let me know if you have any ideas what is the problem Thank you in advance Peter -=3D This is automatically added to each message by the mailing script =3D-E-mail to subscribers: CHEMISTRY+/-ccl.net or use: =0A=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message E-mail to administrators: CHEMISTRY-REQUEST+/-ccl.net or use =0A=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml =0A=0A=A0 =A0 =A0http://www.ccl.net/spammers.txt =0A--=20 K.R.Ramya Research fellow =0AIIndian Institute of Science Education & Research(IISER) Central Tower, Sai Trinity Building, Sutarwadi Road, Pashan, Pune 411021, INDIA =0A=0A=0A=0A --0-972946398-1269445832=:81714 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi there.
Your problem is of memory. The j= ob you are trying to run has huge temporal files.
You need to increase t= he space on the corking directory.
Good luck!


--- On Wed, = 3/24/10, rinu iyer rinuiyer|-|gmail.com <owner-chemistry%x%ccl.net><= /i> wrote:

From: rinu iyer rinuiyer|-|g= mail.com <owner-chemistry%x%ccl.net>
Subject: CCL:G: Write error in = NtrExt1
To: "Tlahuice, Alfredo " <tlahuicef%x%yahoo.com>
= Date: Wednesday, March 24, 2010, 10:46 AM

=
actually u check whether linda is installed in your computer. and also= i will suggest you that dont use nprocshared and nproclinda together. = ; and after that also if this probelm occurs then see whether the geometry = of ur  molecule.
=0A=0A


 
=0A
On Wed, Mar 24, 2010 at 12:20 PM, Peter Khlyabich khlyabic|*|usc.edu <owner-chemistry+/-ccl.net> wrote:
=0A=0A

Sent to CCL by: "Peter &nbs= p;Khlyabich" [khlyabic(a)usc.edu]
=0AHi,

I'm running Gaussian 03 and afte= r submitting the run file I get the following mistake:

%chk=3D/scrat= ch/test.chk
 %Save
 %mem=3D900MW
 %NProcShared=3D2<= br> Will use up to    2 processors via shared memory.
=0A=  %NProcLinda=3D2
 Will use up to    2 processors via= Linda.
Erroneous write during file extend. write -1 instead of 4096
= Probably out of disk space.
Write error in NtrExt1

I cleaned the = scratch file but it didn't help.
=0A
Please let me know if you have a= ny ideas what is the problem

Thank you in advance

Peter


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=0A=0A --0-972946398-1269445832=:81714-- From owner-chemistry@ccl.net Wed Mar 24 22:31:00 2010 From: "Scott Brozell srb=-=osc.edu" To: CCL Subject: CCL: help regarding COLUMBUS Message-Id: <-41521-100324160631-5113-ba9XX8qOLg4KvgDYv6LqJw]|[server.ccl.net> X-Original-From: Scott Brozell Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 24 Mar 2010 15:04:42 -0400 MIME-Version: 1.0 Sent to CCL by: Scott Brozell [srb*osc.edu] Hi, On Wed, Mar 24, 2010 at 10:50:00AM -0400, Neeraj Naithani neerajnaithani!^!gmail.com wrote: > > Sent to CCL by: "Neeraj Naithani" [neerajnaithani,+,gmail.com] > hi friends, > Anybody using COLUMBUS. I Need Help to install it on Fedora 11. Yes, please subscribe to our user support list: http://email.osc.edu/mailman/listinfo/columbus and then send verbatim and verbose details of the problem. Scott