From owner-chemistry@ccl.net Tue Jul 28 02:45:01 2009 From: "Nicolas Staelens nicolas.staelens###fundp.ac.be" To: CCL Subject: CCL: Tinker dynamic function strange data Message-Id: <-39860-090728022409-5992-n67QbyD0vnnDcvlrLjPkSw::server.ccl.net> X-Original-From: Nicolas Staelens Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes Date: Tue, 28 Jul 2009 07:46:06 +0200 Mime-Version: 1.0 (Apple Message framework v935.3) Sent to CCL by: Nicolas Staelens [nicolas.staelens~!~fundp.ac.be] Hello, Did you try performing a quick geometry optimisation prior to running =20= the Dynamic function? Maybe there are atoms too close to each other, =20 which can result in troubles with that function. Have a nice day Nicolas Staelens Ph. D. Student PCI Laboratory University of Namur Belgium Le 28 Jul 2009 =E0 01:00, Ron Salesky rsalesky%unm.edu a =E9crit : > > Sent to CCL by: "Ron Salesky" [rsalesky:_:unm.edu] > Is anyone on this list familiar with Tinker's dynamic function? =20 > Please note that this should supersede an earlier request posted on =20= > this board as it describes more accurately and in greater detail the =20= > issue at hand. > > I get very strange results as follows: > > 1. Without using a periodic box, the Cartesian coordinates 'dump' =20 > file contains either ****** for some coordinates and outlandish =20 > coordinate values for other coordinates, e.g. 46000.0 angstroms =20 > where the largest value in the input coordinates file was 20 =20 > angstroms. The input file contains ~4600 atoms > > OR > > 2. If a periodic box is defined in the key file, it simply never =20 > runs... several text output lines were placed in the fortran source =20= > to attempt a trace and it gets "lost" upon entering the gradient =20 > subroutine. This happens both for the largish 4600 atom file and for =20= > a 158 atom file. > > The prm file in both cases is amber99. > > > Thank you for any assistance, > > Ron Salesky > > > > -=3D This is automatically added to each message by the mailing script = =20 > =3D- > To recover the email address of the author of the message, please =20 > change> Conferences: http://server.ccl.net/chemistry/announcements/=20 > conferences/> From owner-chemistry@ccl.net Tue Jul 28 03:20:00 2009 From: "Cleophas Muhavini Wawire muhavini%yahoo.com" To: CCL Subject: CCL:G: Ru-complex geometry specification problem Message-Id: <-39861-090728031335-22729-kuOn/jYh9qd8O0coJBtaaA,+,server.ccl.net> X-Original-From: "Cleophas Muhavini Wawire" Date: Tue, 28 Jul 2009 03:13:31 -0400 Sent to CCL by: "Cleophas Muhavini Wawire" [muhavini:-:yahoo.com] Hello. Could someone kindly help me to (1) understand why the following input file yields the following output using g03 and also to (2) help me understand the steps (softwares if any) necessary in converting the given molecular specification into Z-matrix format from the cartesian coordinates format used here. OUTPUT FILE =================================================================================================================================== Pseudopotential Parameters =================================================================================================================================== Center Atomic Valence Angular Power Coordinates Number Number Electrons Momentum of R Exponent Coefficient X Y Z =================================================================================================================================== WANTED AN INTEGER AS INPUT. FOUND AN END-OF-LINE FOR INPUT. DZQ ? Error termination via Lnk1e in /home/gauss3/g03/l301.exe at Mon Jul 20 16:01:47 2009. Job cpu time: 0 days 0 hours 0 minutes .8 seconds. File lengths (MBytes): RWF= 13 Int= 0 D2E= 0 Chk= 12 Scr= 1 INPUT FILE IS AS FOLLOWS: %chk=ruthenium.chk #P B3LYP/Gen pseudo=read geom=coord gfinput iop(6/7=3) scf=tight Opt Freq Ru(bpy)3-2+ Opt+Freq Ru=DZQ 2 1 Ru 0.000000 0.000000 0.000000 N 1.637655 0.788035 1.046540 N 1.637655 -0.788035 -1.046540 C 2.859124 0.449484 0.571137 C 1.548271 1.609776 2.097857 C 2.662250 2.124769 2.727798 C 3.919291 1.790734 2.248252 C 4.014758 0.948118 1.158544 C 2.859124 -0.449484 -0.571137 C 1.548271 -1.609776 -2.097857 C 2.662250 -2.124769 -2.727798 C 3.919291 -1.790734 -2.248252 C 4.014758 -0.948118 -1.158544 H 0.535711 1.851838 2.435586 H 2.538391 2.789686 3.587166 H 4.821855 2.189017 2.721122 H 4.993359 0.671879 0.757350 H 0.535711 -1.851838 -2.435586 H 2.538391 -2.789686 -3.587166 H 4.821855 -2.189017 -2.721122 H 4.993359 -0.671879 -0.757350 N -0.136369 -1.812268 1.046540 N -1.501286 -1.024233 -1.046540 C -1.040298 -2.700816 0.571137 C 0.619971 -2.145730 2.097857 C 0.508979 -3.367961 2.727798 C -0.408825 -4.289573 2.248252 C -1.186285 -3.950941 1.158544 C -1.818826 -2.251332 -0.571137 C -2.168242 -0.535954 -2.097857 C -3.171229 -1.243192 -2.727798 C -3.510466 -2.498839 -2.248252 C -2.828473 -3.002823 -1.158544 H 1.335883 -1.389858 2.435586 H 1.146743 -3.593154 3.587166 H -0.515183 -5.270357 2.721122 H -1.914815 -4.660315 0.757350 H -1.871594 0.461980 -2.435586 H -3.685134 -0.803468 -3.587166 H -4.306672 -3.081340 -2.721122 H -3.078544 -3.988437 -0.757350 N -1.501286 1.024233 1.046540 N -0.136369 1.812268 -1.046540 C -1.818826 2.251332 0.571137 C -2.168242 0.535954 2.097857 C -3.171229 1.243192 2.727798 C -3.510466 2.498839 2.248252 C -2.828473 3.002823 1.158544 C -1.040298 2.700816 -0.571137 C 0.619971 2.145730 -2.097857 C 0.508979 3.367961 -2.727798 C -0.408825 4.289573 -2.248252 C -1.186285 3.950941 -1.158544 H -1.871594 -0.461980 2.435586 H -3.685134 0.803468 3.587166 H -4.306672 3.081340 2.721122 H -3.078544 3.988437 0.757350 H 1.335883 1.389858 -2.435586 H 1.146743 3.593154 -3.587166 H -0.515183 5.270357 -2.721122 H -1.914815 4.660315 -0.757350 Ru 0 SP 4 1.00 0.5600000000D+02 -0.2836999440D-02 -0.3198001447D-02 0.4625000000D+01 0.1891660626D+01 -0.1037660470D+00 0.3793000000D+01 -0.3431010322D+01 -0.1275940577D+00 0.1367000000D+01 0.2074445590D+01 0.1146533519D+01 SP 2 1.00 0.1528000000D+01 -0.6903497953D-01 -0.7298999210D-01 0.9673000000D-01 0.1020342697D+01 0.1008641891D+01 SP 1 1.00 0.3636000000D-01 0.1000000000D+01 0.1000000000D+01 SP 1 1.00 0.5183000000D+00 0.1000000000D+01 0.1000000000D+01 D 3 1.00 0.1030000000D+02 0.1196100946D-01 0.2044000000D+01 0.3645752884D+00 0.8988000000D+00 0.6943165493D+00 D 1 1.00 0.3443000000D+00 1.0000000 D 1 1.00 0.1108000000D+00 1.0000000 D 1 1.00 0.7280000000D-01 1.0000000 F 2 1.00 0.2692440000D+01 0.2446125669D+00 0.9655700000D+00 0.8407833859D+00 F 1 1.00 0.4134700000D+00 1.0000000 F 1 1.00 0.1770500000D+00 1.0000000 **** C N H 0 6-31G **** Ru 0 DZQ Ru-ECP 3 28 f-ul potential 1 1 6.9830400 -7.9844800 s-ul potential 3 0 1.2939300 4.8238400 2 3.0487100 -81.3193600 2 3.8716300 124.3691700 p-ul potential 3 0 1.2027300 3.8659000 2 2.8230300 -72.1504800 2 3.4839100 103.6700600 d-ul potential 2 0 14.3374300 3.2108300 2 4.9000300 42.0732100 From owner-chemistry@ccl.net Tue Jul 28 03:56:01 2009 From: "Jerome Kieffer jerome.Kieffer]^[terre-adelie.org" To: CCL Subject: CCL:G: IR or optical spectra plotting software for Mac 10.5.7 Message-Id: <-39862-090728015514-2928-x/DI9dy06er9F1Z7VOcGag]=[server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-15 Date: Tue, 28 Jul 2009 07:54:59 +0200 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [jerome.Kieffer*o*terre-adelie.org] On Mon, 27 Jul 2009 15:41:16 -0400 "Gennady L. Gutsev gennady.gutsev-,-famu.edu" wrote: > Could you please advise me (free or non-expensive) software > for Mac (Leopard) for transformation of bar spectra into=20 > Gaussian/Lorentzian broadened spectra and plotting them=20 > desirably one on the top another in the same figure. > Thanks, Have a look on Gabedit and GaussSum, both are free software --=20 J=E9r=F4me KIEFFER =20 http://www.terre-adelie.org From owner-chemistry@ccl.net Tue Jul 28 05:33:01 2009 From: "Rajagopalan S. r.subramanian*o*ipc.uni-stuttgart.de" To: CCL Subject: CCL:G: Ru-complex geometry specification problem Message-Id: <-39863-090728053120-17720-6KbbKG065RsW1lMxhy2UxQ(a)server.ccl.net> X-Original-From: "Rajagopalan S." Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 28 Jul 2009 10:53:20 +0200 MIME-Version: 1.0 Sent to CCL by: "Rajagopalan S." [r.subramanian]~[ipc.uni-stuttgart.de] hi, make a blank line after the last atom. see below H -0.515183 5.270357 -2.721122 H -1.914815 4.660315 -0.757350 BLANK LINE Ru 0 SP 4 1.00 0.5600000000D+02 -0.2836999440D-02 -0.3198001447D-02 0.4625000000D+01 0.1891660626D+01 -0.1037660470D+00 Cleophas Muhavini Wawire muhavini%yahoo.com wrote: > Sent to CCL by: "Cleophas Muhavini Wawire" [muhavini:-:yahoo.com] > Hello. > Could someone kindly help me to (1) understand why the following input file yields the following output using g03 and also to (2) help me understand the steps (softwares if any) necessary in converting the given molecular specification into Z-matrix format from the cartesian coordinates format used here. > > OUTPUT FILE =================================================================================================================================== > Pseudopotential Parameters > =================================================================================================================================== > Center Atomic Valence Angular Power Coordinates > Number Number Electrons Momentum of R Exponent Coefficient X Y Z > =================================================================================================================================== > WANTED AN INTEGER AS INPUT. > FOUND AN END-OF-LINE FOR INPUT. > DZQ > > > > ? > Error termination via Lnk1e in /home/gauss3/g03/l301.exe at Mon Jul 20 16:01:47 2009. > Job cpu time: 0 days 0 hours 0 minutes .8 seconds. > File lengths (MBytes): RWF= 13 Int= 0 D2E= 0 Chk= 12 Scr= 1 > > > INPUT FILE IS AS FOLLOWS: > > %chk=ruthenium.chk > > #P B3LYP/Gen pseudo=read geom=coord gfinput iop(6/7=3) scf=tight Opt Freq > > Ru(bpy)3-2+ Opt+Freq Ru=DZQ > > 2 1 > Ru 0.000000 0.000000 0.000000 > N 1.637655 0.788035 1.046540 > N 1.637655 -0.788035 -1.046540 > C 2.859124 0.449484 0.571137 > C 1.548271 1.609776 2.097857 > C 2.662250 2.124769 2.727798 > C 3.919291 1.790734 2.248252 > C 4.014758 0.948118 1.158544 > C 2.859124 -0.449484 -0.571137 > C 1.548271 -1.609776 -2.097857 > C 2.662250 -2.124769 -2.727798 > C 3.919291 -1.790734 -2.248252 > C 4.014758 -0.948118 -1.158544 > H 0.535711 1.851838 2.435586 > H 2.538391 2.789686 3.587166 > H 4.821855 2.189017 2.721122 > H 4.993359 0.671879 0.757350 > H 0.535711 -1.851838 -2.435586 > H 2.538391 -2.789686 -3.587166 > H 4.821855 -2.189017 -2.721122 > H 4.993359 -0.671879 -0.757350 > N -0.136369 -1.812268 1.046540 > N -1.501286 -1.024233 -1.046540 > C -1.040298 -2.700816 0.571137 > C 0.619971 -2.145730 2.097857 > C 0.508979 -3.367961 2.727798 > C -0.408825 -4.289573 2.248252 > C -1.186285 -3.950941 1.158544 > C -1.818826 -2.251332 -0.571137 > C -2.168242 -0.535954 -2.097857 > C -3.171229 -1.243192 -2.727798 > C -3.510466 -2.498839 -2.248252 > C -2.828473 -3.002823 -1.158544 > H 1.335883 -1.389858 2.435586 > H 1.146743 -3.593154 3.587166 > H -0.515183 -5.270357 2.721122 > H -1.914815 -4.660315 0.757350 > H -1.871594 0.461980 -2.435586 > H -3.685134 -0.803468 -3.587166 > H -4.306672 -3.081340 -2.721122 > H -3.078544 -3.988437 -0.757350 > N -1.501286 1.024233 1.046540 > N -0.136369 1.812268 -1.046540 > C -1.818826 2.251332 0.571137 > C -2.168242 0.535954 2.097857 > C -3.171229 1.243192 2.727798 > C -3.510466 2.498839 2.248252 > C -2.828473 3.002823 1.158544 > C -1.040298 2.700816 -0.571137 > C 0.619971 2.145730 -2.097857 > C 0.508979 3.367961 -2.727798 > C -0.408825 4.289573 -2.248252 > C -1.186285 3.950941 -1.158544 > H -1.871594 -0.461980 2.435586 > H -3.685134 0.803468 3.587166 > H -4.306672 3.081340 2.721122 > H -3.078544 3.988437 0.757350 > H 1.335883 1.389858 -2.435586 > H 1.146743 3.593154 -3.587166 > H -0.515183 5.270357 -2.721122 > H -1.914815 4.660315 -0.757350 > Ru 0 > SP 4 1.00 > 0.5600000000D+02 -0.2836999440D-02 -0.3198001447D-02 > 0.4625000000D+01 0.1891660626D+01 -0.1037660470D+00 > 0.3793000000D+01 -0.3431010322D+01 -0.1275940577D+00 > 0.1367000000D+01 0.2074445590D+01 0.1146533519D+01 > SP 2 1.00 > 0.1528000000D+01 -0.6903497953D-01 -0.7298999210D-01 > 0.9673000000D-01 0.1020342697D+01 0.1008641891D+01 > SP 1 1.00 > 0.3636000000D-01 0.1000000000D+01 0.1000000000D+01 > SP 1 1.00 > 0.5183000000D+00 0.1000000000D+01 0.1000000000D+01 > D 3 1.00 > 0.1030000000D+02 0.1196100946D-01 > 0.2044000000D+01 0.3645752884D+00 > 0.8988000000D+00 0.6943165493D+00 > D 1 1.00 > 0.3443000000D+00 1.0000000 > D 1 1.00 > 0.1108000000D+00 1.0000000 > D 1 1.00 > 0.7280000000D-01 1.0000000 > F 2 1.00 > 0.2692440000D+01 0.2446125669D+00 > 0.9655700000D+00 0.8407833859D+00 > F 1 1.00 > 0.4134700000D+00 1.0000000 > F 1 1.00 > 0.1770500000D+00 1.0000000 > **** > C N H 0 > 6-31G > **** > > Ru 0 > DZQ > Ru-ECP 3 28 > f-ul potential > 1 > 1 6.9830400 -7.9844800 > s-ul potential > 3 > 0 1.2939300 4.8238400 > 2 3.0487100 -81.3193600 > 2 3.8716300 124.3691700 > p-ul potential > 3 > 0 1.2027300 3.8659000 > 2 2.8230300 -72.1504800 > 2 3.4839100 103.6700600 > d-ul potential > 2 > 0 14.3374300 3.2108300 > 2 4.9000300 42.0732100> > > From owner-chemistry@ccl.net Tue Jul 28 06:50:01 2009 From: "Ol Ga eurisco1,pochta.ru" To: CCL Subject: CCL:G: Ru-complex geometry specification problem Message-Id: <-39864-090728061111-4712-g+3iEiTj97mLdIi6YyzI3Q..server.ccl.net> X-Original-From: "Ol Ga" Date: Tue, 28 Jul 2009 06:11:07 -0400 Sent to CCL by: "Ol Ga" [eurisco1..pochta.ru] Dear Cleophas Muhavini Wawire, I corrected your input. It should be : #P B3LYP/Gen pseudo=read geom=coord gfinput iop(6/7=3) scf=tight Opt Freq Ru(bpy)3-2+ Opt+Freq Ru=DZQ 2 1 Ru 0.000000 0.000000 0.000000 N 1.637655 0.788035 1.046540 N 1.637655 -0.788035 -1.046540 C 2.859124 0.449484 0.571137 C 1.548271 1.609776 2.097857 C 2.662250 2.124769 2.727798 C 3.919291 1.790734 2.248252 C 4.014758 0.948118 1.158544 C 2.859124 -0.449484 -0.571137 C 1.548271 -1.609776 -2.097857 C 2.662250 -2.124769 -2.727798 C 3.919291 -1.790734 -2.248252 C 4.014758 -0.948118 -1.158544 H 0.535711 1.851838 2.435586 H 2.538391 2.789686 3.587166 H 4.821855 2.189017 2.721122 H 4.993359 0.671879 0.757350 H 0.535711 -1.851838 -2.435586 H 2.538391 -2.789686 -3.587166 H 4.821855 -2.189017 -2.721122 H 4.993359 -0.671879 -0.757350 N -0.136369 -1.812268 1.046540 N -1.501286 -1.024233 -1.046540 C -1.040298 -2.700816 0.571137 C 0.619971 -2.145730 2.097857 C 0.508979 -3.367961 2.727798 C -0.408825 -4.289573 2.248252 C -1.186285 -3.950941 1.158544 C -1.818826 -2.251332 -0.571137 C -2.168242 -0.535954 -2.097857 C -3.171229 -1.243192 -2.727798 C -3.510466 -2.498839 -2.248252 C -2.828473 -3.002823 -1.158544 H 1.335883 -1.389858 2.435586 H 1.146743 -3.593154 3.587166 H -0.515183 -5.270357 2.721122 H -1.914815 -4.660315 0.757350 H -1.871594 0.461980 -2.435586 H -3.685134 -0.803468 -3.587166 H -4.306672 -3.081340 -2.721122 H -3.078544 -3.988437 -0.757350 N -1.501286 1.024233 1.046540 N -0.136369 1.812268 -1.046540 C -1.818826 2.251332 0.571137 C -2.168242 0.535954 2.097857 C -3.171229 1.243192 2.727798 C -3.510466 2.498839 2.248252 C -2.828473 3.002823 1.158544 C -1.040298 2.700816 -0.571137 C 0.619971 2.145730 -2.097857 C 0.508979 3.367961 -2.727798 C -0.408825 4.289573 -2.248252 C -1.186285 3.950941 -1.158544 H -1.871594 -0.461980 2.435586 H -3.685134 0.803468 3.587166 H -4.306672 3.081340 2.721122 H -3.078544 3.988437 0.757350 H 1.335883 1.389858 -2.435586 H 1.146743 3.593154 -3.587166 H -0.515183 5.270357 -2.721122 H -1.914815 4.660315 -0.757350 Ru 0 SP 4 1.00 0.5600000000D+02 -0.2836999440D-02 -0.3198001447D-02 0.4625000000D+01 0.1891660626D+01 -0.1037660470D+00 0.3793000000D+01 -0.3431010322D+01 -0.1275940577D+00 0.1367000000D+01 0.2074445590D+01 0.1146533519D+01 SP 2 1.00 0.1528000000D+01 -0.6903497953D-01 -0.7298999210D-01 0.9673000000D-01 0.1020342697D+01 0.1008641891D+01 SP 1 1.00 0.3636000000D-01 0.1000000000D+01 0.1000000000D+01 SP 1 1.00 0.5183000000D+00 0.1000000000D+01 0.1000000000D+01 D 3 1.00 0.1030000000D+02 0.1196100946D-01 0.2044000000D+01 0.3645752884D+00 0.8988000000D+00 0.6943165493D+00 D 1 1.00 0.3443000000D+00 1.0000000 D 1 1.00 0.1108000000D+00 1.0000000 D 1 1.00 0.7280000000D-01 1.0000000 F 2 1.00 0.2692440000D+01 0.2446125669D+00 0.9655700000D+00 0.8407833859D+00 F 1 1.00 0.4134700000D+00 1.0000000 F 1 1.00 0.1770500000D+00 1.0000000 **** C N H 0 6-31G **** Ru 0 Ru-ECP 3 28 f-ul potential 1 1 6.9830400 -7.9844800 s-ul potential 3 0 1.2939300 4.8238400 2 3.0487100 -81.3193600 2 3.8716300 124.3691700 p-ul potential 3 0 1.2027300 3.8659000 2 2.8230300 -72.1504800 2 3.4839100 103.6700600 d-ul potential 2 0 14.3374300 3.2108300 2 4.9000300 42.0732100 Second : You may use GaussView (it costs $$$) or/and free or not expensive editors/viewers like ChemCraft, Avogadro, WxMacMolplot etc Sincerely, Ol Ga > Sent to CCL by: "Cleophas Muhavini Wawire" [muhavini:-:yahoo.com] > Hello. > Could someone kindly help me to (1) understand why the following > input file yields the following output using g03 and also to (2) > help me understand the steps (softwares if any) necessary in > converting the given molecular specification into Z-matrix format > from the cartesian coordinates format used here. > OUTPUT FILE > =================================================================================================================================== > Pseudopotential Parameters > > =================================================================================================================================== > Center Atomic Valence Angular Power Coordinates > Number Number Electrons Momentum of R > Exponent Coefficient X Y Z > > =================================================================================================================================== > WANTED AN INTEGER AS INPUT. > FOUND AN END-OF-LINE FOR INPUT. > DZQ From owner-chemistry@ccl.net Tue Jul 28 08:14:00 2009 From: "Gennady L. Gutsev gennady.gutsev##famu.edu" To: CCL Subject: CCL:G: Ru-complex geometry specification problem Message-Id: <-39865-090728074642-15031-9leE147ZEA1VAcqv1OleYg^^^server.ccl.net> X-Original-From: "Gennady L. Gutsev" Content-class: urn:content-classes:message Content-Type: multipart/mixed; boundary="----_=_NextPart_001_01CA0F7A.3350A480" Date: Tue, 28 Jul 2009 07:53:34 -0400 MIME-Version: 1.0 Sent to CCL by: "Gennady L. Gutsev" [gennady.gutsev,+,famu.edu] This is a multi-part message in MIME format. ------_=_NextPart_001_01CA0F7A.3350A480 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable there is no empty line between " H -1.914815 4.660315 -0.757350" and "Ru 0" -----Original Message----- > From: owner-chemistry+gennady.gutsev=3D=3Dfamu.edu%%ccl.net on behalf of = Cleophas Muhavini Wawire muhavini%yahoo.com Sent: Tue 7/28/2009 3:13 AM To: Gennady L. Gutsev Subject: CCL:G: Ru-complex geometry specification problem =20 Sent to CCL by: "Cleophas Muhavini Wawire" [muhavini:-:yahoo.com] Hello. Could someone kindly help me to (1) understand why the following input = file yields the following output using g03 and also to (2) help me = understand the steps (softwares if any) necessary in converting the = given molecular specification into Z-matrix format from the cartesian = coordinates format used here. OUTPUT FILE = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D Pseudopotential Parameters = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D Center Atomic Valence Angular Power = Coordinates Number Number Electrons Momentum of R Exponent = Coefficient X Y Z = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D WANTED AN INTEGER AS INPUT. FOUND AN END-OF-LINE FOR INPUT. DZQ ? Error termination via Lnk1e in /home/gauss3/g03/l301.exe at Mon Jul 20 = 16:01:47 2009. Job cpu time: 0 days 0 hours 0 minutes .8 seconds. File lengths (MBytes): RWF=3D 13 Int=3D 0 D2E=3D 0 = Chk=3D 12 Scr=3D 1 INPUT FILE IS AS FOLLOWS: =20 %chk=3Druthenium.chk #P B3LYP/Gen pseudo=3Dread geom=3Dcoord gfinput iop(6/7=3D3) = scf=3Dtight Opt Freq Ru(bpy)3-2+ Opt+Freq Ru=3DDZQ 2 1 Ru 0.000000 0.000000 0.000000 N 1.637655 0.788035 1.046540 N 1.637655 -0.788035 -1.046540 C 2.859124 0.449484 0.571137 C 1.548271 1.609776 2.097857 C 2.662250 2.124769 2.727798 C 3.919291 1.790734 2.248252 C 4.014758 0.948118 1.158544 C 2.859124 -0.449484 -0.571137 C 1.548271 -1.609776 -2.097857 C 2.662250 -2.124769 -2.727798 C 3.919291 -1.790734 -2.248252 C 4.014758 -0.948118 -1.158544 H 0.535711 1.851838 2.435586 H 2.538391 2.789686 3.587166 H 4.821855 2.189017 2.721122 H 4.993359 0.671879 0.757350 H 0.535711 -1.851838 -2.435586 H 2.538391 -2.789686 -3.587166 H 4.821855 -2.189017 -2.721122 H 4.993359 -0.671879 -0.757350 N -0.136369 -1.812268 1.046540 N -1.501286 -1.024233 -1.046540 C -1.040298 -2.700816 0.571137 C 0.619971 -2.145730 2.097857 C 0.508979 -3.367961 2.727798 C -0.408825 -4.289573 2.248252 C -1.186285 -3.950941 1.158544 C -1.818826 -2.251332 -0.571137 C -2.168242 -0.535954 -2.097857 C -3.171229 -1.243192 -2.727798 C -3.510466 -2.498839 -2.248252 C -2.828473 -3.002823 -1.158544 H 1.335883 -1.389858 2.435586 H 1.146743 -3.593154 3.587166 H -0.515183 -5.270357 2.721122 H -1.914815 -4.660315 0.757350 H -1.871594 0.461980 -2.435586 H -3.685134 -0.803468 -3.587166 H -4.306672 -3.081340 -2.721122 H -3.078544 -3.988437 -0.757350 N -1.501286 1.024233 1.046540 N -0.136369 1.812268 -1.046540 C -1.818826 2.251332 0.571137 C -2.168242 0.535954 2.097857 C -3.171229 1.243192 2.727798 C -3.510466 2.498839 2.248252 C -2.828473 3.002823 1.158544 C -1.040298 2.700816 -0.571137 C 0.619971 2.145730 -2.097857 C 0.508979 3.367961 -2.727798 C -0.408825 4.289573 -2.248252 C -1.186285 3.950941 -1.158544 H -1.871594 -0.461980 2.435586 H -3.685134 0.803468 3.587166 H -4.306672 3.081340 2.721122 H -3.078544 3.988437 0.757350 H 1.335883 1.389858 -2.435586 H 1.146743 3.593154 -3.587166 H -0.515183 5.270357 -2.721122 H -1.914815 4.660315 -0.757350 Ru 0 SP 4 1.00 0.5600000000D+02 -0.2836999440D-02 -0.3198001447D-02 0.4625000000D+01 0.1891660626D+01 -0.1037660470D+00 0.3793000000D+01 -0.3431010322D+01 -0.1275940577D+00 0.1367000000D+01 0.2074445590D+01 0.1146533519D+01 SP 2 1.00 0.1528000000D+01 -0.6903497953D-01 -0.7298999210D-01 0.9673000000D-01 0.1020342697D+01 0.1008641891D+01 SP 1 1.00 0.3636000000D-01 0.1000000000D+01 0.1000000000D+01 SP 1 1.00 0.5183000000D+00 0.1000000000D+01 0.1000000000D+01 D 3 1.00 0.1030000000D+02 0.1196100946D-01 0.2044000000D+01 0.3645752884D+00 0.8988000000D+00 0.6943165493D+00 D 1 1.00 0.3443000000D+00 1.0000000 D 1 1.00 0.1108000000D+00 1.0000000 D 1 1.00 0.7280000000D-01 1.0000000 F 2 1.00 0.2692440000D+01 0.2446125669D+00 0.9655700000D+00 0.8407833859D+00 F 1 1.00 0.4134700000D+00 1.0000000 F 1 1.00 0.1770500000D+00 1.0000000 **** C N H 0 6-31G **** Ru 0 DZQ Ru-ECP 3 28 f-ul potential 1 1 6.9830400 -7.9844800 s-ul potential 3 0 1.2939300 4.8238400 2 3.0487100 -81.3193600 2 3.8716300 124.3691700 p-ul potential 3 0 1.2027300 3.8659000 2 2.8230300 -72.1504800 2 3.4839100 103.6700600 d-ul potential 2 0 14.3374300 3.2108300 2 4.9000300 42.0732100 -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt------_=_NextPart_001_01CA0F7A.3350A480-- From owner-chemistry@ccl.net Tue Jul 28 08:51:00 2009 From: "=?iso-8859-1?Q?Jos=E9?= Alberto Pires Fernandes jafernandes|*|ua.pt" To: CCL Subject: CCL:G: Ru-complex geometry specification problem Message-Id: <-39866-090728084546-18684-uUtQ0sDhHdMOb7NI6DtZKA|a|server.ccl.net> X-Original-From: "=?iso-8859-1?Q?Jos=E9?= Alberto Pires Fernandes" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1;format="flowed" Date: Tue, 28 Jul 2009 11:45:23 +0100 MIME-Version: 1.0 Sent to CCL by: "=?iso-8859-1?Q?Jos=E9?= Alberto Pires Fernandes" [jafernandes[*]ua.pt] Hello Cleophas H 1.146743 3.593154 -3.587166 H -0.515183 5.270357 -2.721122 H -1.914815 4.660315 -0.757350 You should have a space here! Ru 0 SP 4 1.00 0.5600000000D+02 -0.2836999440D-02 -0.3198001447D-02 Don't worry. I do this mistake lots of times. Best Regards Jose Em Tue, 28 Jul 2009 03:13:31 -0400 "Cleophas Muhavini Wawire muhavini%yahoo.com" escreveu: > > Sent to CCL by: "Cleophas Muhavini Wawire" >[muhavini:-:yahoo.com] > Hello. > Could someone kindly help me to (1) understand why the >following input file yields the following output using >g03 and also to (2) help me understand the steps >(softwares if any) necessary in converting the given >molecular specification into Z-matrix format from the >cartesian coordinates format used here. > > OUTPUT FILE >=================================================================================================================================== > Pseudopotential Parameters > =================================================================================================================================== > Center Atomic Valence Angular Power > Coordinates > Number Number Electrons Momentum of R > Exponent Coefficient X > Y Z > =================================================================================================================================== > WANTED AN INTEGER AS INPUT. > FOUND AN END-OF-LINE FOR INPUT. > DZQ > > > > ? > Error termination via Lnk1e in /home/gauss3/g03/l301.exe >at Mon Jul 20 16:01:47 2009. > Job cpu time: 0 days 0 hours 0 minutes .8 seconds. > File lengths (MBytes): RWF= 13 Int= 0 D2E= > 0 Chk= 12 Scr= 1 > > > INPUT FILE IS AS FOLLOWS: > > %chk=ruthenium.chk > > #P B3LYP/Gen pseudo=read geom=coord gfinput iop(6/7=3) >scf=tight Opt Freq > > Ru(bpy)3-2+ Opt+Freq Ru=DZQ > > 2 1 > Ru 0.000000 0.000000 0.000000 > N 1.637655 0.788035 1.046540 > N 1.637655 -0.788035 -1.046540 > C 2.859124 0.449484 0.571137 > C 1.548271 1.609776 2.097857 > C 2.662250 2.124769 2.727798 > C 3.919291 1.790734 2.248252 > C 4.014758 0.948118 1.158544 > C 2.859124 -0.449484 -0.571137 > C 1.548271 -1.609776 -2.097857 > C 2.662250 -2.124769 -2.727798 > C 3.919291 -1.790734 -2.248252 > C 4.014758 -0.948118 -1.158544 > H 0.535711 1.851838 2.435586 > H 2.538391 2.789686 3.587166 > H 4.821855 2.189017 2.721122 > H 4.993359 0.671879 0.757350 > H 0.535711 -1.851838 -2.435586 > H 2.538391 -2.789686 -3.587166 > H 4.821855 -2.189017 -2.721122 > H 4.993359 -0.671879 -0.757350 > N -0.136369 -1.812268 1.046540 > N -1.501286 -1.024233 -1.046540 > C -1.040298 -2.700816 0.571137 > C 0.619971 -2.145730 2.097857 > C 0.508979 -3.367961 2.727798 > C -0.408825 -4.289573 2.248252 > C -1.186285 -3.950941 1.158544 > C -1.818826 -2.251332 -0.571137 > C -2.168242 -0.535954 -2.097857 > C -3.171229 -1.243192 -2.727798 > C -3.510466 -2.498839 -2.248252 > C -2.828473 -3.002823 -1.158544 > H 1.335883 -1.389858 2.435586 > H 1.146743 -3.593154 3.587166 > H -0.515183 -5.270357 2.721122 > H -1.914815 -4.660315 0.757350 > H -1.871594 0.461980 -2.435586 > H -3.685134 -0.803468 -3.587166 > H -4.306672 -3.081340 -2.721122 > H -3.078544 -3.988437 -0.757350 > N -1.501286 1.024233 1.046540 > N -0.136369 1.812268 -1.046540 > C -1.818826 2.251332 0.571137 > C -2.168242 0.535954 2.097857 > C -3.171229 1.243192 2.727798 > C -3.510466 2.498839 2.248252 > C -2.828473 3.002823 1.158544 > C -1.040298 2.700816 -0.571137 > C 0.619971 2.145730 -2.097857 > C 0.508979 3.367961 -2.727798 > C -0.408825 4.289573 -2.248252 > C -1.186285 3.950941 -1.158544 > H -1.871594 -0.461980 2.435586 > H -3.685134 0.803468 3.587166 > H -4.306672 3.081340 2.721122 > H -3.078544 3.988437 0.757350 > H 1.335883 1.389858 -2.435586 > H 1.146743 3.593154 -3.587166 > H -0.515183 5.270357 -2.721122 > H -1.914815 4.660315 -0.757350 > Ru 0 > SP 4 1.00 > 0.5600000000D+02 -0.2836999440D-02 > -0.3198001447D-02 > 0.4625000000D+01 0.1891660626D+01 > -0.1037660470D+00 > 0.3793000000D+01 -0.3431010322D+01 > -0.1275940577D+00 > 0.1367000000D+01 0.2074445590D+01 > 0.1146533519D+01 > SP 2 1.00 > 0.1528000000D+01 -0.6903497953D-01 > -0.7298999210D-01 > 0.9673000000D-01 0.1020342697D+01 > 0.1008641891D+01 > SP 1 1.00 > 0.3636000000D-01 0.1000000000D+01 > 0.1000000000D+01 > SP 1 1.00 > 0.5183000000D+00 0.1000000000D+01 > 0.1000000000D+01 > D 3 1.00 > 0.1030000000D+02 0.1196100946D-01 > 0.2044000000D+01 0.3645752884D+00 > 0.8988000000D+00 0.6943165493D+00 > D 1 1.00 > 0.3443000000D+00 1.0000000 > D 1 1.00 > 0.1108000000D+00 1.0000000 > D 1 1.00 > 0.7280000000D-01 1.0000000 >F 2 1.00 > 0.2692440000D+01 0.2446125669D+00 > 0.9655700000D+00 0.8407833859D+00 >F 1 1.00 > 0.4134700000D+00 1.0000000 >F 1 1.00 > 0.1770500000D+00 1.0000000 > **** > C N H 0 > 6-31G > **** > > Ru 0 > DZQ > Ru-ECP 3 28 > f-ul potential > 1 > 1 6.9830400 -7.9844800 > s-ul potential > 3 > 0 1.2939300 4.8238400 > 2 3.0487100 -81.3193600 > 2 3.8716300 124.3691700 > p-ul potential > 3 > 0 1.2027300 3.8659000 > 2 2.8230300 -72.1504800 > 2 3.4839100 103.6700600 > d-ul potential > 2 > 0 14.3374300 3.2108300 > 2 4.9000300 42.0732100 > > > > -= This is automatically added to each message by the >mailing script =- > To recover the email address of the author of the >message, please change > the strange characters on the top line to the ++ sign. >You can also> > E-mail to administrators: CHEMISTRY-REQUEST++ccl.net or >use> Conferences: >http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: >http://www.ccl.net/chemistry/searchccl/index.shtml> > RTFI: >http://www.ccl.net/chemistry/aboutccl/instructions/ > > José Fernandes Departamento de Quimica Universidade de Aveiro 3810-193 Aveiro Portugal Tel: +351234370720 Fax: +351234370084 From owner-chemistry@ccl.net Tue Jul 28 09:43:00 2009 From: "Sunder Bugya sunderbugya ~ yahoo.com" To: CCL Subject: CCL: two photon exitation Message-Id: <-39867-090728045456-7140-oKVz50rHkQRry6MDf1ml2g],[server.ccl.net> X-Original-From: "Sunder Bugya" Date: Tue, 28 Jul 2009 04:54:51 -0400 Sent to CCL by: "Sunder Bugya" [sunderbugya * yahoo.com] I am looking for methodologies for calculating two photon exitation properties of small (mw: 300-700) organic molecules. I am especially intersted in finding something for calculating the two photon absorbtion spectra. Thanks for all help. sunderbugya---yahoo.com From owner-chemistry@ccl.net Tue Jul 28 10:58:01 2009 From: "Giuseppe Ermondi giuseppe.ermondi[]unito.it" To: CCL Subject: CCL:G: ONIOM method Message-Id: <-39868-090728105609-12621-VYyAPpYh18JHVmoLl/4ALA() server.ccl.net> X-Original-From: "Giuseppe Ermondi" Date: Tue, 28 Jul 2009 10:56:06 -0400 Sent to CCL by: "Giuseppe Ermondi" [giuseppe.ermondi/./unito.it] Dear all, I am planning to begin calculations with ONIOM method applied to platinum complexes and enzymes. Are there any software (preferably free for academics) that implement this method besides Gaussian? Thank you. Cheers, Giuseppe From owner-chemistry@ccl.net Tue Jul 28 11:33:01 2009 From: "Giuseppe Ermondi giuseppe.ermondi[#]unito.it" To: CCL Subject: CCL:G: Gaussian compilation Message-Id: <-39869-090728110411-15385-c2sqHY18CXdcLDgThnYs2w]_[server.ccl.net> X-Original-From: "Giuseppe Ermondi" Date: Tue, 28 Jul 2009 11:04:08 -0400 Sent to CCL by: "Giuseppe Ermondi" [giuseppe.ermondi- -unito.it] Dear All, does anyone experience about the compilation of Gaussian on Linux computers using a fortran compilator different from Portland F77 and preferably free? Thank you. Cheers, Giuseppe From owner-chemistry@ccl.net Tue Jul 28 14:38:00 2009 From: "Duy Le ttduyle/a\gmail.com" To: CCL Subject: CCL:G: two photon exitation Message-Id: <-39870-090728141932-14777-nZvo4YgxuPBLulvEAcQ1hQ]=[server.ccl.net> X-Original-From: Duy Le Content-Type: multipart/alternative; boundary=0016e68b6b2fd7a54b046fc81ba4 Date: Tue, 28 Jul 2009 11:18:58 -0700 MIME-Version: 1.0 Sent to CCL by: Duy Le [ttduyle^gmail.com] --0016e68b6b2fd7a54b046fc81ba4 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi, For TPA spectra, one of a way you can consider first is to calculate dipole moment and ... where S0 is ground state, Si, Sn are excited states. Those dipole moments can be calculated by using G09 (CIS, TD-DFT...) or G03 (CIS). Birge et al, JCP 70, 167 (1979) Good luck! On Tue, Jul 28, 2009 at 1:54 AM, Sunder Bugya sunderbugya ~ yahoo.com < owner-chemistry*o*ccl.net> wrote: > > Sent to CCL by: "Sunder Bugya" [sunderbugya * yahoo.com] > > I am looking for methodologies for calculating two photon exitation > properties of small (mw: 300-700) organic molecules. I am especially > intersted in finding something for calculating the two photon absorbtion > spectra. > Thanks for all help. > sunderbugya|*|yahoo.com> > > -- Men don't need hands to do things! --0016e68b6b2fd7a54b046fc81ba4 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,
For TPA spectra, one of a way you can consider first is to calculate= dipole moment <S0|d|Si> and <Si|d|Sn>... where S0 is ground st= ate, Si, Sn are excited states. Those dipole moments can be calculated by u= sing G09 (CIS, TD-DFT...) or G03 (CIS).

Birge et al, JCP 70, 167 (1979)

Good luck!

On Tue, Jul 28, 2009 at 1:54 AM, Sunder Bugya sunderbugya ~ yahoo.com <owner-chemistry*o*ccl.net> wrote= :

Sent to CCL by: "Sunder =A0 Bugya" [sunderbugya * yahoo.com]

I am looking for methodologies for calculating two photon exitation propert= ies of small (mw: 300-700) organic molecules. I am especially intersted in = finding something for calculating the two photon absorbtion spectra.
Thanks for all help.
sunderbugya|*|yahoo.com<= br>


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--0016e68b6b2fd7a54b046fc81ba4-- From owner-chemistry@ccl.net Tue Jul 28 17:21:00 2009 From: "gustavo()mercury.chem.pitt.edu" To: CCL Subject: CCL: two photon exitation Message-Id: <-39871-090728171950-19144-N+L5B/xwtZYyb9E0zwVpxg]-[server.ccl.net> X-Original-From: gustavo|-|mercury.chem.pitt.edu Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 28 Jul 2009 17:19:25 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: gustavo/./mercury.chem.pitt.edu Dear friend, In order to compute two-photon absorption spectra and cross sections, please take a look at the following article: "Two-photon absorption cross-sections from electronic structure methods: Mesoionic compounds" Moura, G.L.C. and Simas, A.M. Chem. Mater. 20, 4142 (2008) http://dx.doi.org/10.1021/cm070369o This article describes a procedure based on certain approximations of the complete sum over states equations to calculate two-photon absorption spectra of molecules and supramolecular systems. Gustavo ======= > > Sent to CCL by: "Sunder Bugya" [sunderbugya * yahoo.com] > > I am looking for methodologies for calculating two photon exitation > properties of small (mw: 300-700) organic molecules. I am especially > intersted in finding something for calculating the two photon absorbtion > spectra. > Thanks for all help. > sunderbugya|*|yahoo.com> > >