From owner-chemistry@ccl.net Mon Feb 29 02:46:01 2016 From: "Bulumoni Kalita bulumoni-$-dibru.ac.in" To: CCL Subject: CCL: SCF convergence problem with M06L functional in Gaussian 09 Message-Id: <-52070-160229005711-5040-HQIjm3o2MBQCySLsBh1tdA#,#server.ccl.net> X-Original-From: "Bulumoni Kalita" Date: Mon, 29 Feb 2016 00:57:07 -0500 Sent to CCL by: "Bulumoni Kalita" [bulumoni-x-dibru.ac.in] Dear users, Thank you very much for your fruitful discussion. Ultimately, I could solve the problem as follows: %chk=Pd4_3.chk #p opt(maxcycle=500) scf(xqc, maxcycle=500, novaracc, noincfock) um06l/genecp nosym Pd4 0 1 Pd 1.55076100 -0.20840900 -0.52663500 Pd -0.96047300 -1.23708300 -0.51996300 Pd 0.00639500 -0.00412900 1.56159200 Pd -0.59668400 1.44962100 -0.51499300 Pd 0 LANL2DZ **** Pd 0 LANL2DZ From owner-chemistry@ccl.net Mon Feb 29 03:43:01 2016 From: "Rafael R. Pappalardo rafapa_+_us.es" To: CCL Subject: CCL: SCF convergence problem with M06L functional in Gaussian 09 Message-Id: <-52071-160229034006-6397-hZkanY+tr7kvAhKgBC5U8Q/a\server.ccl.net> X-Original-From: "Rafael R. Pappalardo" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Mon, 29 Feb 2016 09:39:54 +0100 Mime-Version: 1.0 (1.0) Sent to CCL by: "Rafael R. Pappalardo" [rafapa---us.es] A quick question, why do you use um06l if the multiplicity is 1? Rafael Rodríguez Pappalardo Depto. Química Física, Univ. de Sevilla > El 29 feb 2016, a las 6:57, Bulumoni Kalita bulumoni-$-dibru.ac.in escribió: > > > Sent to CCL by: "Bulumoni Kalita" [bulumoni-x-dibru.ac.in] > Dear users, > Thank you very much for your fruitful discussion. Ultimately, I could solve the problem as follows: > > %chk=Pd4_3.chk > #p opt(maxcycle=500) scf(xqc, maxcycle=500, novaracc, noincfock) um06l/genecp nosym > > Pd4 > > 0 1 > Pd 1.55076100 -0.20840900 -0.52663500 > Pd -0.96047300 -1.23708300 -0.51996300 > Pd 0.00639500 -0.00412900 1.56159200 > Pd -0.59668400 1.44962100 -0.51499300 > > Pd 0 > LANL2DZ > **** > > Pd 0 > LANL2DZ> > From owner-chemistry@ccl.net Mon Feb 29 07:56:01 2016 From: "RENXIAO WANG wangrx]_[mail.sioc.ac.cn" To: CCL Subject: CCL: Announce the release of the AutoT&T2 software Message-Id: <-52072-160229014726-8272-weeGOPwCfwQUt8xRq4/Ejg^server.ccl.net> X-Original-From: "RENXIAO WANG" Date: Mon, 29 Feb 2016 01:47:25 -0500 Sent to CCL by: "RENXIAO WANG" [wangrx^^mail.sioc.ac.cn] Dear friends, Here we announce the public release of the Automatic Tailoring and Transplanting software, i.e. AutoT&T version 2. This software is designed to conduct de novo ligand construction for structure-based drug design projects. The key methods of this software have been described in our recent publication (J. Chem. Inf. Model. DOI/10.1021/acs.jcim.5b00691) and a previous one (J. Chem. Inf. Model.,2011,Vol. 51 (6), pp 1474-1491). AutoT&T2 overcomes some intrinsic problems in the conventional fragment- based build-up methods. With AutoT&T2, one can perform not only structural optimization of a single lead compound, but also structural cross-over among a group of lead compounds. As demonstrated by a few test cases, it produced structurally more diverse and more reasonable designs in a more efficient manner than some standard build-up methods. AutoT&T2 is written in the ANSI C++ language and run in the command line mode. It has been tested on Linux and Windows platforms. A web portal for testing AutoT&T2 on-line is provided at http://www.sioc- ccbg.ac.cn/software/att2. Or, one can download the complete AutoT&T2 package, including the executable and source codes, user manual, and demo examples, from the same web page. Registration is needed for downloading the AutoT&T2 package, which is free for all academic and governmental users. Commercial users are subjected to a modest amount of license fee to use AutoT&T2. You may contact me directly if you have any question about AutoT&T2. We would love to hear the feedback from our users. Best regards, Renxiao --- Renxiao Wang, PhD Professor Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China, P.R. E-mail: wangrx++mail.sioc.ac.cn From owner-chemistry@ccl.net Mon Feb 29 11:37:01 2016 From: "Theophile Gaudin gaudin.theophile^gmail.com" To: CCL Subject: CCL: Generate image files from Chemdraw files: an automation Message-Id: <-52073-160229113323-5830-SvKBXgkL+JJVX8o0YDeVGg.:.server.ccl.net> X-Original-From: "Theophile Gaudin" Date: Mon, 29 Feb 2016 11:33:22 -0500 Sent to CCL by: "Theophile Gaudin" [gaudin.theophile|-|gmail.com] Dear CCL users, I wish to address here a practical problem that may occur when handling large databases of .cdx files: it can be cumbersome to generate all image files manually. So, specifically, I propose here an automated windows script to generate image files for all cdx files in a directory. The script was originally proposed by Arsimael ("https://www.cambridgesoft.com/support/DesktopSupport/KnowledgeBase/FAQ/det ails/Default.aspx?TechNote=1150"), but I modified it since on my machine it was not working. I will point all lines that could cause trouble in other machines. This script worked on a Windows 10 64 bits laptop computer with ChemDraw Ultra installed. It needs the software "AutoIT" to run. This free software enables GUI-scripting from Windows, that is, it automates keystrokes commands. It can be downloaded here: https://www.autoitscript.com/site/autoit/ I used AutoITv3 to program and run the script. The script is as follows (do not copy the lines of stars before and after the script): ************************************************************** #cs ------------------------------------------------------------------------ ---- AutoIt Version: 3.3.6.0 Author: Theophile from Arsimael initial script Script Function: Convert Chemdraw Files to .tif files. #ce ------------------------------------------------------------------------ ---- #include #include #include #include $sPfad = "C:\path\were\your\cdx\files\are\located" If StringRight($sPfad, 1) = "\" Then $sPfad = StringTrimRight($sPfad, 1) $aFiles = _FileListToArray($sPfad, "*.cdx", 1) Endif If Not -x-error Then For $i = 1 To UBound($aFiles) - 1 $sCur = $sPfad & "\" & $aFiles[$i] sleep (100) ShellExecute($sCur) sleep (100) WinWaitActive("ChemDraw Ultra") sleep (100) Send("^+s") sleep (100) WinWaitActive("[ACTIVE]") sleep (1000) Send("{TAB}") sleep(1000) Send("p") sleep (500) Send("C:\path\were\you\want\to\put\your\image\files\" & $aFiles[$i]) sleep (1000) send("{BS 4}") sleep (100) send(".png") sleep (100) Send("{ENTER}") sleep (100) Send ("^w") sleep (100) Next Else MsgBox(64, "Nichts zu tun", "Keine Daten zum konvertieren vorhanden!") Endif ********************************************************************* The lines "Send" send the indicated keystroke to the active window. ENTER is the "enter" keystroke, BS is the "backspace" keystrocke, TAB is the "tabulation" keystroke. The lines that contain the word "sleep" are instrumental. They delay the execution of the next script line, so that the computer has enough time to finish the previous instruction. Insufficient values may lead to weird bugs, so it can be a good track if when launched on your machine this script doesn't work. The lines containing "WinWaitActive" make the script wait to see the next window open before executing instructions. These also are important. In order to use this script, first download and install the free AutoIT (https://www.autoitscript.com/site/autoit/). Then, copy all the lines between the two lines of star in this post to a .au3 file (for example chemdraw_cdx_to_tif.au3). Please replace the path in the line $sPfad = "C:\path\were\your\cdx\files\are\located" by your .cdx files path, and the path in the line Send("C:\path\were\you\want\to\put\your\image\files\" & $aFiles[$i]) by your output folder path. Then, save the file, close it, right click on the file icon, and click on Run Script. It should work. If it doesn't work, the first thing to fix might be the paths that you indicated. Other things may be the times in the sleep functions or your version of ChemDraw that may need slightly different instructions. You can google AutoIT scripting language if you wish to modify this script in detail to meet the specific needs of your ChemDraw version/OS version/whatever. My Chemdraw version is exactly ChemDraw Ultra 12.0.2.1076. and this script worked well for this version. I cannot guarantee it will work for other versions, although it is likely that it will. Best regards From owner-chemistry@ccl.net Mon Feb 29 12:12:01 2016 From: "Robert Molt r.molt.chemical.physics||gmail.com" To: CCL Subject: CCL: SCF convergence problem with M06L functional in Gaussian 09 Message-Id: <-52074-160229120856-4199-SYDJ03d/5BHVm8EDcoDvKA * server.ccl.net> X-Original-From: Robert Molt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Mon, 29 Feb 2016 12:08:49 -0500 MIME-Version: 1.0 Sent to CCL by: Robert Molt [r.molt.chemical.physics:-:gmail.com] I would encourage you to be very careful. The suggestions given to have 500 cycles of optimization or SCF cycle are, IMHO, not good. In general, if you cannot converge your SCF of a small molecule in 100 steps, you need to be smarter, not more persistent. It speaks more to the idea that you have a fundamental problem in your description of the electronic structure in some regard. I have never encountered a situation in which more than 75 steps were needed for 4 atoms. Just check that your electronic state is really what you want to converge to and not some other spurious electronic state. I also echo the other comment about concern for using an unrestricted reference. On 2/29/16 12:57 AM, Bulumoni Kalita bulumoni-$-dibru.ac.in wrote: > Sent to CCL by: "Bulumoni Kalita" [bulumoni-x-dibru.ac.in] > Dear users, > Thank you very much for your fruitful discussion. Ultimately, I could solve the problem as follows: > > %chk=Pd4_3.chk > #p opt(maxcycle=500) scf(xqc, maxcycle=500, novaracc, noincfock) um06l/genecp nosym > > Pd4 > > 0 1 > Pd 1.55076100 -0.20840900 -0.52663500 > Pd -0.96047300 -1.23708300 -0.51996300 > Pd 0.00639500 -0.00412900 1.56159200 > Pd -0.59668400 1.44962100 -0.51499300 > > Pd 0 > LANL2DZ > **** > > Pd 0 > LANL2DZ> > From owner-chemistry@ccl.net Mon Feb 29 12:55:01 2016 From: "Chris John Swain swain---mac.com" To: CCL Subject: CCL: Generate image files from Chemdraw files: an automation Message-Id: <-52075-160229125351-3801-nlPpD2a6OayGFcnrLR8Enw]|[server.ccl.net> X-Original-From: "Chris John Swain" Date: Mon, 29 Feb 2016 12:53:49 -0500 Sent to CCL by: "Chris John Swain" [swain]=[mac.com] Very nice, I was asked if I could do something similar for a Mac user. the details and the droplet are here. http://www.macinchem.org/applescript/cdx2png.php Cheers Chris From owner-chemistry@ccl.net Mon Feb 29 14:37:00 2016 From: "Saied Mohammed Soliman saied1soliman%yahoo.com" To: CCL Subject: CCL: Overlay structure Message-Id: <-52076-160229143440-25678-g+PdM042ureiYVCBokd//Q]_[server.ccl.net> X-Original-From: "Saied Mohammed Soliman" Date: Mon, 29 Feb 2016 14:34:35 -0500 Sent to CCL by: "Saied Mohammed Soliman" [saied1soliman__yahoo.com] Hello colleagues, I need a free and user friendly software to overlay the optimized structure with the X-ray structure in order to compare the matching between them, anyone could help me. Thanks Saied From owner-chemistry@ccl.net Mon Feb 29 15:34:01 2016 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor::fluor.quimica.uniovi.es" To: CCL Subject: CCL: SCF convergence problem with M06L functional in Gaussian 09 Message-Id: <-52077-160229153036-17264-l9dfurI4W3mgSAt2ug0olQ{=}server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Mon, 29 Feb 2016 20:58:30 +0100 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor^fluor.quimica.uniovi.es] On Mon, Feb 29, 2016 at 12:08:49PM -0500, Robert Molt r.molt.chemical.physics||gmail.com wrote: > > Sent to CCL by: Robert Molt [r.molt.chemical.physics:-:gmail.com] > I would encourage you to be very careful. The suggestions given to have > 500 cycles of optimization or SCF cycle are, IMHO, not good. In general, > if you cannot converge your SCF of a small molecule in 100 steps, you > need to be smarter, not more persistent. It speaks more to the idea that > you have a fundamental problem in your description of the electronic > structure in some regard. I have never encountered a situation in which > more than 75 steps were needed for 4 atoms. > > Just check that your electronic state is really what you want to > converge to and not some other spurious electronic state. I also echo > the other comment about concern for using an unrestricted reference. > Bulumoni, Robert Molt words a quite wise. The case of a tetrahedral molecule like your Pd4 input is a clear candidate for Jahn-Teller efects in which the electronic state and the vibrational mode interact to produce complex phenomena. You don't even need to consider Pd4, which can be a nightmare by the participations of high-L electronic levels. Just H_4 is a good candidate to study the complexity of Jahn-Teller effects. Good Luck, Víctor Luaña -- . . "De la cuna a la tumba es una escuela, por eso lo que llamas / `' \ problemas son lecciones." -- Facundo Cabral, Cuna /(o)(o)\ "From the cradle to the grave life is a school, ..." /`. \/ .'\ "Lo mediocre es peor que lo bueno, pero también es peor / '`'` \ que lo malo, porque la mediocridad no es un grado, es una | \'`'`/ | actitud" -- Jorge Wasenberg, 2015 | |'`'`| | (Mediocre is worse than good, but it is also worse than \/`'`'`'\/ bad, because mediocrity is not a grade, it is an attitude) ===(((==)))==================================+========================= ! Dr.Víctor Luaña, in silico chemist & prof. ! ! Departamento de Química Física y Analítica ! ! Universidad de Oviedo, 33006-Oviedo, Spain ! ! e-mail: victor.:.fluor.quimica.uniovi.es ! ! phone: +34-985-103491 fax: +34-985-103125 ! +--------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) From owner-chemistry@ccl.net Mon Feb 29 16:08:01 2016 From: "Kimberley Cousins KCousins{=}csusb.edu" To: CCL Subject: CCL: Overlay structure Message-Id: <-52078-160229153739-21755-cfNunDyeOOBGX50MQad+mQ . server.ccl.net> X-Original-From: Kimberley Cousins Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 29 Feb 2016 20:36:54 +0000 MIME-Version: 1.0 Sent to CCL by: Kimberley Cousins [KCousins#csusb.edu] Try vmd. Opens many formats and you can overlay structures. http://www.ks.uiuc.edu/Research/vmd/ Kimberley R. Cousins Professor of Chemistry California State University, San Bernardino kcousins(!)csusb.edu ________________________________________ > From: owner-chemistry+kcousins==csusb.edu(!)ccl.net on behalf of Saied Mohammed Soliman saied1soliman%yahoo.com Sent: Monday, February 29, 2016 11:34 AM To: Kimberley Cousins Subject: CCL: Overlay structure Sent to CCL by: "Saied Mohammed Soliman" [saied1soliman__yahoo.com] Hello colleagues, I need a free and user friendly software to overlay the optimized structure with the X-ray structure in order to compare the matching between them, anyone could help me. Thanks Saiedhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Feb 29 20:06:00 2016 From: "David Shobe avidshobe]~[yahoo.com" To: CCL Subject: CCL:G: SCF convergence problem with M06L functional in Gaussian 09 Message-Id: <-52079-160229195908-9557-0hwcJFNQnnDCzq1NAuRpTQ##server.ccl.net> X-Original-From: David Shobe Content-Type: multipart/alternative; boundary="----=_Part_1100286_1569972547.1456793890084" Date: Tue, 1 Mar 2016 00:58:10 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: David Shobe [avidshobe=-=yahoo.com] ------=_Part_1100286_1569972547.1456793890084 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Can't one use Gaussian's stable command to check for this type of problem? And similarly, wouldn't a freq job show whether the tetrahedral Pd4 is a mi= nimum? With transition metals like Pd, I've often used up to even scf(qc,maxcyc=3D= 999), but I've always checked the wavefunction with stable or stable=3Dopt.= =C2=A0How many scf cycles it takes is mostly a function of how good the in= itial guess is, and that is done by the computer, not the user, so I don't = think it reflects on the user's intelligence. :-) =C2=A0[Although a really = bad initial guess can often be improved by guess=3D(read,alter), which does= require user input]. --David Shobe P.S. I'll have to take a look at H4 if I ever get Gaussian working again. := -(=20 On Monday, February 29, 2016 3:52 PM, V=C3=ADctor Lua=C3=B1a Cabal vict= or::fluor.quimica.uniovi.es wrote: =20 =20 Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor^flu= or.quimica.uniovi.es] On Mon, Feb 29, 2016 at 12:08:49PM -0500, Robert Molt r.molt.chemical.physi= cs||gmail.com wrote: > > Sent to CCL by: Robert Molt [r.molt.chemical.physics:-:gmail.com] > I would encourage you to be very careful. The suggestions given to have= =C2=A0=20 > 500 cycles of optimization or SCF cycle are, IMHO, not good. In general,= =C2=A0=20 > if you cannot converge your SCF of a small molecule in 100 steps, you=C2= =A0=20 > need to be smarter, not more persistent. It speaks more to the idea that= =C2=A0=20 > you have a fundamental problem in your description of the electronic=C2= =A0=20 > structure in some regard. I have never encountered a situation in which= =C2=A0=20 > more than 75 steps were needed for 4 atoms. > > Just check that your electronic state is really what you want to=C2=A0=20 > converge to and not some other spurious electronic state. I also echo=C2= =A0=20 > the other comment about concern for using an unrestricted reference. > Bulumoni, Robert Molt words a quite wise. The case of a tetrahedral molecule like your Pd4 input is a clear candidate for Jahn-Teller efects in which the electronic state and the vibrational mode interact to produce complex phenomena.=20 You don't even need to consider Pd4, which can be a nightmare by the participations of high-L electronic levels. Just H_4 is a good candidate to study the complexity of Jahn-Teller effects. Good Luck, =C2=A0 =C2=A0 =C2=A0 =C2=A0 V=C3=ADctor Lua=C3=B1a -- =C2=A0 =C2=A0 .=C2=A0 .=C2=A0 =C2=A0 "De la cuna a la tumba es una escuela,= por eso lo que llamas =C2=A0 =C2=A0 / `' \=C2=A0 =C2=A0 problemas son lecciones." -- Facundo Cabr= al, Cuna =C2=A0 /(o)(o)\=C2=A0 "From the cradle to the grave life is a school, ..." =C2=A0 /`. \/ .'\=C2=A0 "Lo mediocre es peor que lo bueno, pero tambi=C3=A9= n es peor /=C2=A0 '`'`=C2=A0 \ que lo malo, porque la mediocridad no es un grado, es= una |=C2=A0 \'`'`/=C2=A0 | actitud" -- Jorge Wasenberg, 2015 |=C2=A0 |'`'`|=C2=A0 | (Mediocre is worse than good, but it is also worse = than =C2=A0 \/`'`'`'\/=C2=A0 bad, because mediocrity is not a grade, it is an at= titude) =3D=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D ! Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist & prof. !=20 ! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica !=20 ! Universidad de Oviedo, 33006-Oviedo, Spain !=20 ! e-mail:=C2=A0 victor[A]fluor.quimica.uniovi.es=C2=A0 !=20 ! phone: +34-985-103491=C2=A0 fax: +34-985-103125 !=20 +--------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (being reworked) -=3D This is automatically added to each message by the mailing script =3D-=C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0Subscribe/Unsubscribe:=20 =C2=A0 =C2=A0 =C2=A0Job: http://www.ccl.net/jobs=20=C2=A0 =C2=A0 =C2=A0------=_Part_1100286_1569972547.1456793890084 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Can't one use Gaussian's stable co= mmand to check for this type of problem?

And similarly, w= ouldn't a freq job show whether the tetrahedral Pd4 is a minimum?

With transition metals like Pd, I've often used up to even scf(qc,= maxcyc=3D999), but I've always checked the wavefunction with stable or stab= le=3Dopt.  How many scf cycles it takes is mostly a function of how go= od the initial guess is, and that is done by the computer, not the user, so= I don't think it reflects on the user's intelligence. :-)  [Although = a really bad initial guess can often be improved by guess=3D(read,alter), w= hich does require user input].

--David Shobe
=

P.S. I'll have to take a look at H4 if I ever get Gaussian working a= gain. :-(


On Monday, February 29, = 2016 3:52 PM, V=C3=ADctor Lua=C3=B1a Cabal victor::fluor.quimica.uniovi.es = <owner-chemistry(~)ccl.net> wrote:



Sent to CC= L by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor^fluor.quimica= .uniovi.es]
On Mon, Feb 29, 2016 at 12:08:49PM -0500, Robert Molt r.molt= .chemical.physics||gmail.com wrote:
>
> Sent to CCL by: Robert = Molt [r.molt.chemical.physics:-:gmail.com]
> I would encourage you to= be very careful. The suggestions given to have 
> 500 cycles o= f optimization or SCF cycle are, IMHO, not good. In general, 
>= if you cannot converge your SCF of a small molecule in 100 steps, you = ;
> need to be smarter, not more persistent. It speaks more to the i= dea that 
> you have a fundamental problem in your description = of the electronic 
> structure in some regard. I have never enc= ountered a situation in which 
> more than 75 steps were needed= for 4 atoms.
>
> Just check that your electronic state is real= ly what you want to 
> converge to and not some other spurious = electronic state. I also echo 
> the other comment about concer= n for using an unrestricted reference.
>

Bulumoni,

Robe= rt Molt words a quite wise. The case of a tetrahedral molecule
like your= Pd4 input is a clear candidate for Jahn-Teller efects in which
the elec= tronic state and the vibrational mode interact to produce
complex phenom= ena.

You don't even need to consider Pd4, which can be a nightmare = by the
participations of high-L electronic levels. Just H_4 is a good ca= ndidate
to study the complexity of Jahn-Teller effects.

Good Luck= ,
        V=C3=ADctor Lua=C3=B1a
--
  &n= bsp; .  .    "De la cuna a la tumba es una escuela, por eso= lo que llamas
    / `' \    problemas son lecciones= ." -- Facundo Cabral, Cuna
  /(o)(o)\  "From the cradle to th= e grave life is a school, ..."
  /`. \/ .'\  "Lo mediocre es p= eor que lo bueno, pero tambi=C3=A9n es peor
/  '`'`  \ que = lo malo, porque la mediocridad no es un grado, es una
|  \'`'`/&nb= sp; | actitud" -- Jorge Wasenberg, 2015
|  |'`'`|  | (Mediocr= e is worse than good, but it is also worse than
  \/`'`'`'\/  = bad, because mediocrity is not a grade, it is an attitude)
=3D=3D=3D(((= =3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
! Dr.V=C3=ADctor Lua=C3=B1a, in = silico chemist & prof. !
! Departamento de Qu=C3=ADmica F=C3=ADsica= y Anal=C3=ADtica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
= ! e-mail:  victor[A]fluor.quimica.uniovi.es  !
! phone: +34= -985-103491  fax: +34-985-103125 !
+------------------------------= --------------+
GroupPage : http://azufre.quimica.uniovi.es/
    &= nbsp;       (being reworked)



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------=_Part_1100286_1569972547.1456793890084-- From owner-chemistry@ccl.net Mon Feb 29 22:12:01 2016 From: "andy andy---molsoft.com" To: CCL Subject: CCL: Overlay structure Message-Id: <-52080-160229211505-3679-tj+775NnS7/RvPy7U9iqNg^server.ccl.net> X-Original-From: andy Content-Type: multipart/alternative; boundary="--_com.android.email_35412498752740" Date: Mon, 29 Feb 2016 18:14:53 -0800 MIME-Version: 1.0 Sent to CCL by: andy [andy]![molsoft.com] ----_com.android.email_35412498752740 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: base64 CiAgICAKCllvdSBjYW4gb3ZlcmxheSBwcm90ZWluIHN0cnVjdHVyZXMgdXNpbmcgdGhlIEZyZWUg TW9sU29mdCBJQ00tQnJvd3Nlci4KSGVyZSBhcmUgdGhlIGluc3RydWN0aW9uczoKLSBEb3dubG9h ZCBJQ00tQnJvd3NlciBoZXJlOiBodHRwOi8vd3d3Lm1vbHNvZnQuY29tL2ljbV9icm93c2VyLmh0 bWwKLSBVc2UgdGhlIG1lbnUgb3B0aW9uIEZpbGUvT3BlbiBwZGIgZmlsZXMKLSBTdXBlcmltcG9z ZSBhcyBzaG93biBoZXJlIApodHRwOi8vd3d3Lm1vbHNvZnQuY29tL2d1aS9wcm90ZWluLXN0cnVj 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r.molt.chemical.physics##gmail.com" To: CCL Subject: CCL:G: SCF convergence problem with M06L functional in Gaussian 09 Message-Id: <-52081-160229223058-24730-HntZAFwxcmuGWKnvpTZAvQ|a|server.ccl.net> X-Original-From: Robert Molt Content-Type: multipart/alternative; boundary="------------000209040700050200010102" Date: Mon, 29 Feb 2016 22:30:49 -0500 MIME-Version: 1.0 Sent to CCL by: Robert Molt [r.molt.chemical.physics++gmail.com] This is a multi-part message in MIME format. --------------000209040700050200010102 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: quoted-printable No, in short. There are many complexities to the system. For one, choosing "stable" just checks if the single determinant=20 expression is a minimum. It's not clear that the electronic state=20 corresponding to the minimum is the target state of interest? Second, a frequency calculation specifies if the *geometry* is a local=20 minimum for that electronic state. It does not tell you about other=20 electronic state, nor does it even tell you if that is the geometric=20 minimum in which one is interested (there may be many). Three, I am stating as a matter of experience on simple molecules and=20 complex molecules, *more cycles is not better*. You're just wasting=20 computer time. Very rarely do more cycles help; the problem is=20 describing the electronic structure properly. "How many scf cycles it takes is mostly a function of how good the=20 initial guess is, and that is done by the computer, not the user, so I=20 don't think it reflects on the user's intelligence. " This is categorically untrue. You have to know what electronic state is=20 of interest so it does not go to the wrong state, you have to know what=20 geometric minimum is needed, you have to know if there is vibronic=20 coupling that negates the ability to describe the system easily. The=20 user has to know what (s)he is doing carefully, especially with a=20 metallic system loaded with degeneracies. You have to know what are the=20 limitations of the electronic structure method that may interfere with=20 the SCF process, basis set effects. It's also untrue that the user cannot change the initial guess. The=20 initial density guess is changed all the time by quantum chemists. On 2/29/16 7:58 PM, David Shobe avidshobe]~[yahoo.com wrote: > Can't one use Gaussian's stable command to check for this type of probl= em? > And similarly, wouldn't a freq job show whether the tetrahedral Pd4 is = a minimum? > With transition metals like Pd, I've often used up to even scf(qc,maxcy= c=3D999), but I've always checked the wavefunction with stable or stable=3D= opt. How many scf cycles it takes is mostly a function of how good the i= nitial guess is, and that is done by the computer, not the user, so I don= 't think it reflects on the user's intelligence. :-) [Although a really = bad initial guess can often be improved by guess=3D(read,alter), which do= es require user input]. > --David Shobe > P.S. I'll have to take a look at H4 if I ever get Gaussian working agai= n. :-( > > On Monday, February 29, 2016 3:52 PM, V=C3=ADctor Lua=C3=B1a Cabal= victor::fluor.quimica.uniovi.es wrote: > =20 > > =20 > Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor= ^fluor.quimica.uniovi.es] > On Mon, Feb 29, 2016 at 12:08:49PM -0500, Robert Molt r.molt.chemical.p= hysics||gmail.com wrote: >> Sent to CCL by: Robert Molt [r.molt.chemical.physics:-:gmail.com] >> I would encourage you to be very careful. The suggestions given to hav= e >> 500 cycles of optimization or SCF cycle are, IMHO, not good. In genera= l, >> if you cannot converge your SCF of a small molecule in 100 steps, you >> need to be smarter, not more persistent. It speaks more to the idea th= at >> you have a fundamental problem in your description of the electronic >> structure in some regard. I have never encountered a situation in whic= h >> more than 75 steps were needed for 4 atoms. >> >> Just check that your electronic state is really what you want to >> converge to and not some other spurious electronic state. I also echo >> the other comment about concern for using an unrestricted reference. >> > Bulumoni, > > Robert Molt words a quite wise. The case of a tetrahedral molecule > like your Pd4 input is a clear candidate for Jahn-Teller efects in whic= h > the electronic state and the vibrational mode interact to produce > complex phenomena. > > You don't even need to consider Pd4, which can be a nightmare by the > participations of high-L electronic levels. Just H_4 is a good candidat= e > to study the complexity of Jahn-Teller effects. > > Good Luck, > V=C3=ADctor Lua=C3=B1a > -- > . . "De la cuna a la tumba es una escuela, por eso lo que llam= as > / `' \ problemas son lecciones." -- Facundo Cabral, Cuna > /(o)(o)\ "From the cradle to the grave life is a school, ..." > /`. \/ .'\ "Lo mediocre es peor que lo bueno, pero tambi=C3=A9n es = peor > / '`'` \ que lo malo, porque la mediocridad no es un grado, es una > | \'`'`/ | actitud" -- Jorge Wasenberg, 2015 > | |'`'`| | (Mediocre is worse than good, but it is also worse than > \/`'`'`'\/ bad, because mediocrity is not a grade, it is an attitud= e) > =3D=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > ! Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist & prof. ! > ! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica ! > ! Universidad de Oviedo, 33006-Oviedo, Spain ! > ! e-mail: victor[A]fluor.quimica.uniovi.es ! > ! phone: +34-985-103491 fax: +34-985-103125 ! > +--------------------------------------------+ > GroupPage : http://azufre.quimica.uniovi.es/ > (being reworked) > > > > -=3D This is automatically added to each message by the mailing script = =3D-------=3D_Part_1100286_15699725= 47.1456793890084 > Content-Type: text/html; charset=3DUTF-8 > Content-Transfer-Encoding: quoted-printable > >
Can't one use Gaussian's= stable command to check for this type of problem?

= And similarly, wouldn't a freq job show whether the tetrahedral Pd4 is a = minimum?
With transition metals like Pd, I've often= used up to even scf(qc,maxcyc=3D999), but I've always checked the wavefu= nction with stable or stable=3Dopt.  How many scf cycles it takes is= mostly a function of how good the initial guess is, and that is done by = the computer, not the user, so I don't think it reflects on the user's in= telligence. :-)  [Although a really bad initial guess can often be i= mproved by guess=3D(read,alter), which does require user input].

--David Shobe

P.S. I'll have to take = a look at H4 if I ever get Gaussian working again. :-(


On Monday, February 29, 2016 3:52 PM, = V=C3=ADctor Lua=C3=B1a Cabal victor::fluor.quimica.uniovi.es <owner-ch= emistry.:.ccl.net> wrote:



Sent to CCL by: = =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor^fluor.quimica.uni= ovi.es]
On Mon, Feb 29, 2016 at 12:08:49PM -0500, Robert Molt r.molt.c= hemical.physics||gmail.com wrote:
>
> Sent to CCL by: Robert = Molt [r.molt.chemical.physics:-:gmail.com]
> I would encourage you = to be very careful. The suggestions given to have 
> 500 cycl= es of optimization or SCF cycle are, IMHO, not good. In general,  > if you cannot converge your SCF of a small molecule in 100 steps, = you 
> need to be smarter, not more persistent. It speaks mor= e to the idea that 
> you have a fundamental problem in your = description of the electronic 
> structure in some regard. I = have never encountered a situation in which 
> more than 75 s= teps were needed for 4 atoms.
>
> Just check that your electr= onic state is really what you want to 
> converge to and not = some other spurious electronic state. I also echo 
> the othe= r comment about concern for using an unrestricted reference.
>
<= br>Bulumoni,

Robert Molt words a quite wise. The case of a tetrahe= dral molecule
like your Pd4 input is a clear candidate for Jahn-Teller= efects in which
the electronic state and the vibrational mode interac= t to produce
complex phenomena.

You don't even need to conside= r Pd4, which can be a nightmare by the
participations of high-L electr= onic levels. Just H_4 is a good candidate
to study the complexity of J= ahn-Teller effects.

Good Luck,
        V=C3= =ADctor Lua=C3=B1a
--
    .  .    "De la = cuna a la tumba es una escuela, por eso lo que llamas
    / = `' \    problemas son lecciones." -- Facundo Cabral, Cuna
&n= bsp; /(o)(o)\  "From the cradle to the grave life is a school, ..."=
  /`. \/ .'\  "Lo mediocre es peor que lo bueno, pero tambi= =C3=A9n es peor
/  '`'`  \ que lo malo, porque la mediocr= idad no es un grado, es una
|  \'`'`/  | actitud" -- Jorge = Wasenberg, 2015
|  |'`'`|  | (Mediocre is worse than good, = but it is also worse than
  \/`'`'`'\/  bad, because mediocr= ity is not a grade, it is an attitude)
=3D=3D=3D(((=3D=3D)))=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D
! Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist &= ; prof. !
! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica= !
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail: = victor[A]fluor.quimica.uniovi.es  !
! phone: +34-985-103491&n= bsp; fax: +34-985-103125 !
+-----------------------------------------= ---+
GroupPage : http://azufre.quimica.uniovi.es/
      &nb= sp;     (being reworked)



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--------------000209040700050200010102 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit No, in short. There are many complexities to the system.

For one, choosing "stable" just checks if the single determinant expression is a minimum. It's not clear that the electronic state corresponding to the minimum is the target state of interest?

Second, a frequency calculation specifies if the geometry is a local minimum for that electronic state. It does not tell you about other electronic state, nor does it even tell you if that is the geometric minimum in which one is interested (there may be many).

Three, I am stating as a matter of experience on simple molecules and complex molecules, more cycles is not better. You're just wasting computer time. Very rarely do more cycles help; the problem is describing the electronic structure properly.

"How many scf cycles it takes is mostly a function of how good the initial guess is, and that is done by the computer, not the user, so I don't think it reflects on the user's intelligence. "

This is categorically untrue. You have to know what electronic state is of interest so it does not go to the wrong state, you have to know what geometric minimum is needed, you have to know if there is vibronic coupling that negates the ability to describe the system easily. The user has to know what (s)he is doing carefully, especially with a metallic system loaded with degeneracies. You have to know what are the limitations of the electronic structure method that may interfere with the SCF process, basis set effects.

It's also untrue that the user cannot change the initial guess. The initial density guess is changed all the time by quantum chemists.

On 2/29/16 7:58 PM, David Shobe avidshobe]~[yahoo.com wrote:
Can't one use Gaussian's stable command to check for this type of problem?
And similarly, wouldn't a freq job show whether the tetrahedral Pd4 is a minimum?
With transition metals like Pd, I've often used up to even scf(qc,maxcyc=999), but I've always checked the wavefunction with stable or stable=opt.  How many scf cycles it takes is mostly a function of how good the initial guess is, and that is done by the computer, not the user, so I don't think it reflects on the user's intelligence. :-)  [Although a really bad initial guess can often be improved by guess=(read,alter), which does require user input].
--David Shobe
P.S. I'll have to take a look at H4 if I ever get Gaussian working again. :-( 

    On Monday, February 29, 2016 3:52 PM, Víctor Luaña Cabal victor::fluor.quimica.uniovi.es <owner-chemistry.:.ccl.net> wrote:
 

 
Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor^fluor.quimica.uniovi.es]
On Mon, Feb 29, 2016 at 12:08:49PM -0500, Robert Molt r.molt.chemical.physics||gmail.com wrote:

Sent to CCL by: Robert Molt [r.molt.chemical.physics:-:gmail.com]
I would encourage you to be very careful. The suggestions given to have  
500 cycles of optimization or SCF cycle are, IMHO, not good. In general,  
if you cannot converge your SCF of a small molecule in 100 steps, you  
need to be smarter, not more persistent. It speaks more to the idea that  
you have a fundamental problem in your description of the electronic  
structure in some regard. I have never encountered a situation in which  
more than 75 steps were needed for 4 atoms.

Just check that your electronic state is really what you want to  
converge to and not some other spurious electronic state. I also echo  
the other comment about concern for using an unrestricted reference.


Bulumoni,

Robert Molt words a quite wise. The case of a tetrahedral molecule
like your Pd4 input is a clear candidate for Jahn-Teller efects in which
the electronic state and the vibrational mode interact to produce
complex phenomena. 

You don't even need to consider Pd4, which can be a nightmare by the
participations of high-L electronic levels. Just H_4 is a good candidate
to study the complexity of Jahn-Teller effects.

Good Luck,
        Víctor Luaña
--
    .  .    "De la cuna a la tumba es una escuela, por eso lo que llamas
    / `' \    problemas son lecciones." -- Facundo Cabral, Cuna
  /(o)(o)\  "From the cradle to the grave life is a school, ..."
  /`. \/ .'\  "Lo mediocre es peor que lo bueno, pero también es peor
 /  '`'`  \ que lo malo, porque la mediocridad no es un grado, es una
 |  \'`'`/  | actitud" -- Jorge Wasenberg, 2015
 |  |'`'`|  | (Mediocre is worse than good, but it is also worse than
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is an attitude)
===(((==)))==================================+=========================
! Dr.Víctor Luaña, in silico chemist & prof. ! 
! Departamento de Química Física y Analítica ! 
! Universidad de Oviedo, 33006-Oviedo, Spain ! 
! e-mail:  victor[A]fluor.quimica.uniovi.es  ! 
! phone: +34-985-103491  fax: +34-985-103125 ! 
+--------------------------------------------+
 GroupPage : http://azufre.quimica.uniovi.es/
            (being reworked)               Job: http://www.ccl.net/jobs      ------=_Part_1100286_1569972547.1456793890084
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

<html><head></head><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:13px"><div id="yui_3_16_0_1_1456791461898_8236"><span id="yui_3_16_0_1_1456791461898_8353">Can't one use Gaussian's stable command to check for this type of problem?</span></div><div id="yui_3_16_0_1_1456791461898_8236"><span><br></span></div><div id="yui_3_16_0_1_1456791461898_8236"><span id="yui_3_16_0_1_1456791461898_8967">And similarly, wouldn't a freq job show whether the tetrahedral Pd4 is a minimum?</span></div><div id="yui_3_16_0_1_1456791461898_8236"><span><br></span></div><div id="yui_3_16_0_1_1456791461898_8236"><span id="yui_3_16_0_1_1456791461898_8588">With transition metals like Pd, I've often used up to even scf(qc,maxcyc=999), but I've always checked the w
avefunction with stable or stable=opt. &nbsp;How many scf cycles it takes is mostly a function of how good the initial guess is, and that is done by the computer, not the user, so I don't think it reflects on the user's intelligence. :-) &nbsp;[Although a really bad initial guess can often be improved by guess=(read,alter), which does require user input].</span></div><div id="yui_3_16_0_1_1456791461898_8236"><span><br></span></div><div id="yui_3_16_0_1_1456791461898_8236"><span id="yui_3_16_0_1_1456791461898_8449">--David Shobe</span></div><div id="yui_3_16_0_1_1456791461898_8236"><span><br></span></div><div id="yui_3_16_0_1_1456791461898_8236"><span id="yui_3_16_0_1_1456791461898_9498">P.S. I'll have to take a look at H4 if I ever get Gaussian working again. :-(</span></div> <div class="qtdSeparateBR" id="yui_3_16_0_1_1456791461898_8322"><br><
br></div><div class="yahoo_quoted" id="yui_3_16_0_1_1456791461898_8314" style="display: block;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 13px;" id="yui_3_16_0_1_1456791461898_8313"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;" id="yui_3_16_0_1_1456791461898_8312"> <div dir="ltr" id="yui_3_16_0_1_1456791461898_8321"><font size="2" face="Arial" id="yui_3_16_0_1_1456791461898_8320"> On Monday, February 29, 2016 3:52 PM, Víctor Luaña Cabal victor::fluor.quimica.uniovi.es &lt;owner-chemistry.:.ccl.net&gt; wrote:<br></font></div>  <br><br> <div class="y_msg_container" id="yui_3_16_0_1_1456791461898_8311"><br>Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor^fluor.quimica.uniovi.es]<br>On Mon, Feb 29, 2016 at 12:08:49PM -0500, Robert Molt 
r.molt.chemical.physics||gmail.com wrote:<br>&gt;<br>&gt; Sent to CCL by: Robert Molt [r.molt.chemical.physics:-:gmail.com]<br>&gt; I would encourage you to be very careful. The suggestions given to have&nbsp; <br>&gt; 500 cycles of optimization or SCF cycle are, IMHO, not good. In general,&nbsp; <br>&gt; if you cannot converge your SCF of a small molecule in 100 steps, you&nbsp; <br>&gt; need to be smarter, not more persistent. It speaks more to the idea that&nbsp; <br>&gt; you have a fundamental problem in your description of the electronic&nbsp; <br>&gt; structure in some regard. I have never encountered a situation in which&nbsp; <br>&gt; more than 75 steps were needed for 4 atoms.<br>&gt;<br>&gt; Just check that your electronic state is really what you want to&nbsp; <br>&gt; converge to and not some other spurious electronic state. I 
also echo&nbsp; <br>&gt; the other comment about concern for using an unrestricted reference.<br>&gt;<br><br>Bulumoni,<br><br>Robert Molt words a quite wise. The case of a tetrahedral molecule<br>like your Pd4 input is a clear candidate for Jahn-Teller efects in which<br>the electronic state and the vibrational mode interact to produce<br>complex phenomena. <br><br>You don't even need to consider Pd4, which can be a nightmare by the<br>participations of high-L electronic levels. Just H_4 is a good candidate<br>to study the complexity of Jahn-Teller effects.<br><br>Good Luck,<br>&nbsp; &nbsp; &nbsp; &nbsp;  Víctor Luaña<br>--<br>&nbsp; &nbsp;  .&nbsp; .&nbsp; &nbsp; "De la cuna a la tumba es una escuela, por eso lo que llamas<br>&nbsp; &nbsp; / `' \&nbsp; &nbsp; problemas son lecciones." -- Facundo Cabral, Cu
na<br>&nbsp;  /(o)(o)\&nbsp; "From the cradle to the grave life is a school, ..."<br>&nbsp; /`. \/ .'\&nbsp; "Lo mediocre es peor que lo bueno, pero también es peor<br> /&nbsp;  '`'`&nbsp;  \ que lo malo, porque la mediocridad no es un grado, es una<br> |&nbsp; \'`'`/&nbsp; | actitud" -- Jorge Wasenberg, 2015<br> |&nbsp; |'`'`|&nbsp; | (Mediocre is worse than good, but it is also worse than<br>&nbsp; \/`'`'`'\/&nbsp; bad, because mediocrity is not a grade, it is an attitude)<br>===(((==)))==================================+=========================<br>! Dr.Víctor Luaña, in silico chemist &amp; prof. ! <br>! Departamento de Química Física y Analítica ! <br>! Universidad de Oviedo, 33006-Oviedo, Spain ! <br>! e-mail:&nbsp;  victor[A]fluor.quimica.uniovi.es&nbsp;  ! <br>! phone: +34-985-103491&nbsp; fax: +34-985-103125 ! <br>+----------------
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