From owner-chemistry@ccl.net Mon Jul 9 07:10:01 2007 From: "Carlos Silva Lopez csilval^uvigo.es" To: CCL Subject: CCL:G: Nuclear repulsion energy Message-Id: <-34688-070709070403-17234-nGKUu6FoHtOlR+BXQHOw8g#server.ccl.net> X-Original-From: Carlos Silva Lopez Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 09 Jul 2007 13:02:08 +0200 MIME-Version: 1.0 Sent to CCL by: Carlos Silva Lopez [csilval^uvigo.es] Hi CCLers, Perhaps this is a dumb question, but I have come to this observation I cannot quite explain. The nuclear repulsion energy obtained for the same geometry with 3 different codes is uncomfortably different. Is there any explanation to this?: G03: 2415.9379779077 Hartrees GAMESS (US) 22Nov 2004: 2415.9381648177 ORCA 2.6: 2415.8913723108 Eh My coordinates are: C -1.434100 1.172214 -0.511956 C -2.181985 2.234035 -1.012304 C -1.608613 3.002788 -2.031486 C -0.336160 2.723942 -2.541720 C 0.402873 1.654375 -2.030463 C -0.156178 0.883949 -1.015498 H -3.170884 2.453751 -0.634807 H -2.177650 3.831553 -2.441786 H 0.073829 3.333722 -3.340039 H 1.389606 1.432155 -2.428665 C 0.413823 -0.288027 -0.270177 N -1.748668 0.223468 0.496948 C -0.827998 -0.855573 0.457720 C 1.438186 -1.252792 -0.935380 H -0.667452 -1.304760 1.432671 C -2.764062 0.203213 1.451205 O -2.851208 -0.659506 2.295058 O -3.597283 1.251026 1.317891 H -4.274510 1.152227 2.013056 C 2.455664 -0.964523 0.196581 H 1.767045 -0.902403 -1.914589 H 1.112584 -2.287982 -1.012839 C 3.858815 -0.488203 -0.132331 H 2.555493 -1.797377 0.906043 N 1.540767 0.069944 0.721565 C 1.663052 0.959016 1.683027 O 4.387641 -1.129715 -1.155770 O 4.447090 0.364143 0.523742 H 5.315743 -0.840314 -1.280866 O 0.583725 1.593349 2.067568 O 2.778375 1.241621 2.280917 H 0.817996 2.292019 2.710143 Br -1.611074 -2.443806 -0.649844 H 3.574491 0.922904 1.728071 Thanks! -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Carlos Silva Lopez IPP Researcher Universidad de Vigo Phone : (+34) 986813721 Departmento de Química Orgánica Fax : (+34) 986812262 Campus Universitario e-mail: csilval##uvigo.es 36310 Vigo, Pontevedra http://riesling.chem.umn.edu/~carlos ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-chemistry@ccl.net Mon Jul 9 09:29:00 2007 From: "Crawford, Daniel crawdad() vt.edu" To: CCL Subject: CCL:G: Nuclear repulsion energy Message-Id: <-34689-070709083900-20668-kSWujfcLvggAhShPOq37wQ^-^server.ccl.net> X-Original-From: "Crawford, Daniel" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 9 Jul 2007 08:05:43 -0400 MIME-Version: 1.0 Sent to CCL by: "Crawford, Daniel" [crawdad|vt.edu] Your coordinates appear to be in Angstroms, so this is very likely a result of differences in the Bohr <-> Angstrom conversion factor among the three codes. -TDC On 7/9/07 7:02 AM, "Carlos Silva Lopez csilval^uvigo.es" wrote: > > Sent to CCL by: Carlos Silva Lopez [csilval^uvigo.es] > Hi CCLers, > > Perhaps this is a dumb question, but I have come to this observation I > cannot quite explain. The nuclear repulsion energy obtained for the same > geometry with 3 different codes is uncomfortably different. Is there any > explanation to this?: > > G03: 2415.9379779077 Hartrees > GAMESS (US) 22Nov 2004: 2415.9381648177 > ORCA 2.6: 2415.8913723108 Eh > > My coordinates are: > > C -1.434100 1.172214 -0.511956 > C -2.181985 2.234035 -1.012304 > C -1.608613 3.002788 -2.031486 > C -0.336160 2.723942 -2.541720 > C 0.402873 1.654375 -2.030463 > C -0.156178 0.883949 -1.015498 > H -3.170884 2.453751 -0.634807 > H -2.177650 3.831553 -2.441786 > H 0.073829 3.333722 -3.340039 > H 1.389606 1.432155 -2.428665 > C 0.413823 -0.288027 -0.270177 > N -1.748668 0.223468 0.496948 > C -0.827998 -0.855573 0.457720 > C 1.438186 -1.252792 -0.935380 > H -0.667452 -1.304760 1.432671 > C -2.764062 0.203213 1.451205 > O -2.851208 -0.659506 2.295058 > O -3.597283 1.251026 1.317891 > H -4.274510 1.152227 2.013056 > C 2.455664 -0.964523 0.196581 > H 1.767045 -0.902403 -1.914589 > H 1.112584 -2.287982 -1.012839 > C 3.858815 -0.488203 -0.132331 > H 2.555493 -1.797377 0.906043 > N 1.540767 0.069944 0.721565 > C 1.663052 0.959016 1.683027 > O 4.387641 -1.129715 -1.155770 > O 4.447090 0.364143 0.523742 > H 5.315743 -0.840314 -1.280866 > O 0.583725 1.593349 2.067568 > O 2.778375 1.241621 2.280917 > H 0.817996 2.292019 2.710143 > Br -1.611074 -2.443806 -0.649844 > H 3.574491 0.922904 1.728071 > > > Thanks! -- T. Daniel Crawford Department of Chemistry crawdad(~)vt.edu Virginia Tech Voice: 540-231-7760 FAX: 540-231-3255 Blacksburg, Virginia 24061 -------------------- http://www.chem.vt.edu/chem-dept/crawford/ From owner-chemistry@ccl.net Mon Jul 9 10:04:00 2007 From: "errol lewars elewars]=[trentu.ca" To: CCL Subject: CCL: TDDFT problems with squarine molecule Message-Id: <-34690-070708101143-11337-3FGNnPUlwe5pwOlFssdnsQ^-^server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sun, 08 Jul 2007 10:11:49 -0400 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars . trentu.ca] 2007 July 8 Read this paper and see if it's of any help: Y. Zhao, D. G. Truhlar, J Phys Chem A, 2006, 110(49), 13126 E. Lewars ==== Arvydas Tamulis tamulis##mserv.itpa.lt wrote: > > Sent to CCL by: Arvydas Tamulis [tamulis^-^mserv.itpa.lt] > Dear Colleagues, > > We have TDDFT problems with intermolecular electron charge transfer > (ICT) complex containing exotic squarine molecule and other van der Waals > forces bonded electron acceptor molecule. > Which DFT potential and basis set you will recommend for squarine > molecule > which possesses four 90 valence bond angles in the center (i.e. possesses > high strains)? > > With best regards, > Arvydas Tamulishttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > From owner-chemistry@ccl.net Mon Jul 9 10:38:01 2007 From: "Shobe, David David.Shobe++sud-chemie.com" To: CCL Subject: CCL:G: Frequency symmetry problem Message-Id: <-34691-070709094731-1665-ntvk4sX+U8Gi8D2ZbVlWYw=server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C7C22F.AC1D87AD" Date: Mon, 9 Jul 2007 15:47:19 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe^sud-chemie.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C7C22F.AC1D87AD Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Mike, =20 Any symmetry label with a ? means that the orbital/vibrational mode does not neatly belong to any symmetry class. Usually this results from one or more orbitals having a small percentage of another orbital (of a different symmetry) mixed in, due to rounding errors. For example, an orbital may be 99.95% pi and 0.05% sigma. Similarly a vibrational mode may have a small amount of another vibrational mode (of different symmetry) mixed in.=20=20 =20 I always end up having to animate vibrational modes of interest anyway, and you can then see the true nature of the vibrational mode and which symmetry class it should belong to. =20 --David Shobe =20 ________________________________ > From: owner-chemistry[#]ccl.net [mailto:owner-chemistry[#]ccl.net]=20 Sent: Saturday, July 07, 2007 1:51 PM To: Shobe, David Subject: CCL:G: Frequency symmetry problem =20 Dear CCL users I have perform Opt+Freq calculation with Gaussian 03 and the frequency symmetry obtained is ?A. what does this mean and how do I formally represent this frequency symmetry. Any help will be greatly appreciated thanks mike =20=20 ________________________________ Building a website is a piece of cake.=20 Yahoo! Small Business gives you all the tools to get online. =20 This e-mail message may contain confidential and / or privileged informatio= n. If you are not an addressee or otherwise authorized to receive this mess= age, you should not use, copy, disclose or take any action based on this e-= mail or any information contained in the message. If you have received this= material in error, please advise the sender immediately by reply e-mail an= d delete this message.=20 Thank you. ------_=_NextPart_001_01C7C22F.AC1D87AD Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Mike,

Any symmetry label with a ? means that= the orbital/vibrational mode does not neatly belong to any symmetry class. = ; Usually this results from one or more orbitals having a small percentage of another orbital (of a different symmetry) mixed in, due to rounding errors. F= or example, an orbital may be 99.95% pi and 0.05% sigma. Similarly a vibrational mode may have a small amount of another vibrational mode (of different symmetry) mixed in.

I always end up having to animate vibrational modes of interest anyway, and you can then see the true nature = of the vibrational mode and which symmetry class it should belong to.

--David Shobe=

From: owner-ch= emistry[#]ccl.net [mailto:owner-chemistry[#]ccl.net]
Sent: Saturday, July 07, 200= 7 1:51 PM
To: Shobe, David
Subject: CCL:G: Frequency sy= mmetry problem

Dear CCL users

I have perform Opt+Freq calculation with Gaussian 03 and the frequency symm= etry obtained is ?A. what does this mean and how do I formally represent this frequency symmetry.
Any help will be greatly appreciated
thanks
mike

Building a website is a piece of cake.
Yahoo! Small Business gives you all the tools to get online.

This e-mail message may contain confidential and / or privileged informatio= n. If you are not an addressee or otherwise authorized to receive this mess= age, you should not use, copy, disclose or take any action based on this e-= mail or any information contained in the message. If you have received this= material in error, please advise the sender immediately by reply e-mail an= d delete this message.
Thank you.

------_=_NextPart_001_01C7C22F.AC1D87AD-- From owner-chemistry@ccl.net Mon Jul 9 11:15:00 2007 From: "bala bala:+:igib.res.in" To: CCL Subject: CCL: review/article on hydration changes Message-Id: <-34692-070709095339-6576-VFPmwo7j3vq4oXMs2HPLpw\a/server.ccl.net> X-Original-From: "bala" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C7C22F.8793DB1F" Date: Mon, 9 Jul 2007 19:16:19 +0530 MIME-Version: 1.0 Sent to CCL by: "bala" [bala__igib.res.in] This is a multi-part message in MIME format. ------_=_NextPart_001_01C7C22F.8793DB1F Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Can some please write me about any review/articles/book which covers in = detail about the energetics involved in hydration changes during a = duplex formation in solution from single nucleic acid strands. Thanks in advance, Bala ------_=_NextPart_001_01C7C22F.8793DB1F Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

=0A=

Can some please write me about any = review/articles/book =0A= which covers in detail about the energetics involved in hydration = changes during =0A= a duplex formation in solution from single nucleic acid = strands.

Thanks =0A= in advance,
Bala

------_=_NextPart_001_01C7C22F.8793DB1F-- From owner-chemistry@ccl.net Mon Jul 9 11:49:00 2007 From: "Carlos Silva Lopez csilval-$-uvigo.es" To: CCL Subject: CCL: ANSWER TO: Nuclear repulsion energy Message-Id: <-34693-070709102025-27705-ui+blySKpQ3Q1biC0HaDcQ!^!server.ccl.net> X-Original-From: Carlos Silva Lopez Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 09 Jul 2007 16:19:04 +0200 MIME-Version: 1.0 Sent to CCL by: Carlos Silva Lopez [csilval:-:uvigo.es] Thanks to Daniel Crawford, Abdul-Rahman ALLOUCHE, Jeff Hammond and perhaps others that already sent a response but I still did not received their mails. Eventually source of the energy discrepancies was the conversion factor > from Angstroms to Bohrs. Doing the calculation in bohrs provided the exact same repulsion energy for the three codes. Best regards -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Carlos Silva Lopez IPP Researcher Universidad de Vigo Phone : (+34) 986813721 Departmento de Química Orgánica Fax : (+34) 986812262 Campus Universitario e-mail: csilval#,#uvigo.es 36310 Vigo, Pontevedra http://riesling.chem.umn.edu/~carlos ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-chemistry@ccl.net Mon Jul 9 13:02:00 2007 From: "Frank Neese neese(0)thch.uni-bonn.de" To: CCL Subject: CCL:G: Nuclear repulsion energy Message-Id: <-34694-070709124040-27904-JtA0oc4p6NXAzzogeimbEw##server.ccl.net> X-Original-From: Frank Neese Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Mon, 09 Jul 2007 18:40:24 +0200 Mime-Version: 1.0 Sent to CCL by: Frank Neese [neese]*[thch.uni-bonn.de] > >Sent to CCL by: "Crawford, Daniel" [crawdad|vt.edu] >Your coordinates appear to be in Angstroms, so this is very likely a result >of differences in the Bohr <-> Angstrom conversion factor among the three >codes. ... we have checked it and this is exactly correct. The difference seems large but it is an accumulation of small differences. The present default orca value for au differs in the fifth digit from the latest value in the handbook of chemical and physics which is presumably what Gaussian uses (i don't know and i cannot check since we are banned by Gaussian). We have taken the opportunity to update our natural constants to their latest values. In any case, in order to ensure that different quantum chemical codes give the same answers one should input atomic units anyways. Best regards, FN From owner-chemistry@ccl.net Mon Jul 9 19:54:00 2007 From: "Lochana C Menikarachchi lochanac[*]yahoo.com" To: CCL Subject: CCL:G: Oniom_Calculation Message-Id: <-34695-070709162833-19272-CoDX24wEm6RT32d5Bs+cvw[#]server.ccl.net> X-Original-From: "Lochana C Menikarachchi" Date: Mon, 9 Jul 2007 16:28:29 -0400 Sent to CCL by: "Lochana C Menikarachchi" [lochanac . yahoo.com] Dear Keerthi, You may have to define additional bond stretching and angle bending parameters. These parameters should come after the connectivity section of the gaussian input file. For example if you are using link atoms when partitioning the system, parameters for those connections should appear in the gaussian input file. Hope this will help. Good luck! Lochana C. Menikarachchi UConn http://gascon.chem.uconn.edu From owner-chemistry@ccl.net Mon Jul 9 20:29:00 2007 From: "Lochana C Menikarachchi lochanac[-]yahoo.com" To: CCL Subject: CCL:G: Oniom_Calc Message-Id: <-34696-070709190120-12204-gb9EHjL0WCtMD5NZ66Sw1w^_^server.ccl.net> X-Original-From: "Lochana C Menikarachchi" Date: Mon, 9 Jul 2007 19:01:16 -0400 Sent to CCL by: "Lochana C Menikarachchi" [lochanac*yahoo.com] Dear Keerthi, You may have to define additional bond stretching and angle bending parameters. These parameters should come after the connectivity section of the gaussian input file. For example if you are using link atoms when partitioning the system, parameters for those connections should appear in the gaussian input file. Hope this will help. Good luck! Lochana C. Menikarachchi UConn From owner-chemistry@ccl.net Mon Jul 9 21:09:00 2007 From: "lochana menikarachchi lochanac_-_yahoo.com" To: CCL Subject: CCL:G: oniom calculation Message-Id: <-34697-070709171711-26991-V3d4n1TmY2r55b/z+h+w1g-,-server.ccl.net> X-Original-From: lochana menikarachchi Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-521775899-1184012211=:21858" Date: Mon, 9 Jul 2007 13:16:51 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: lochana menikarachchi [lochanac]~[yahoo.com] --0-521775899-1184012211=:21858 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Keerthi, You may have to define additional bond stretching and angle bending parameters. These parameters should come after the connectivity section of the gaussian input file. For example if you are using link atoms when partitioning the system, parameters for those connections should appear in the gaussian input file. Hope this will help. Good luck! Lochana C. Menikarachchi UConn http://gascon.chem.uconn.edu "Keerthi Jayasundera jaya0046(_)d.umn.edu" wrote: Sent to CCL by: "Keerthi Jayasundera" [jaya0046^d.umn.edu] I am a beginner to oniom I am trying an oniom calculation for a peptide chain with a triazole ring in the middle. I always get an error message in the middle of the calculation. As a start I used a 3-layer oniom as given in the gaussian tutorial. So I got a message saying that same parameter is missing to a N atom in the high layer. Anyway I found that could come with the "Amber" So I changed it to UFF in the low layer. Now I get some other error which does not give any understandable message. I think I have not used commands correctly. Please someone help me to solve the problem Here is my input file. %chk=quick.chk %mem=6MW %nproc=1 opt=rcfc oniom(rhf/6-31g:ram1:amber) geom=connectivity Title Card Required 0 1 0 1 0 1 0 1 0 1 0 1 C-CM- 0 -0.979628 -1.159218 0.000009 H C-CM- 0 0.422122 -1.159218 0.000009 H H-H4- 0 1.066495 -2.031924 0.000034 M H-H4 2 N- 0 -0.310937 1.003031 -0.000095 H N-N2- 0 0.846120 0.211578 0.000009 H N-N3--0.516300 0 -1.419355 0.161290 0.000000 H C-CT-0.039700 0 -2.859630 0.320067 0.000068 H H-H1-0.110500 0 -3.277620 -0.150672 -0.889757 M H-H1 7 C-CT-0.056000 0 -3.483217 -0.326921 1.232208 M H-H1 7 C-C-0.536600 0 -3.248651 1.791511 0.000147 M H-H1 7 H-HC--0.017300 0 -3.250175 -1.391678 1.241385 M H-HC--0.017300 0 -3.081256 0.140223 2.131266 M C-CT-0.013600 0 -4.981165 -0.140179 1.195083 M O-O--0.581900 0 -2.355867 2.678364 0.000146 M H-HC--0.042500 0 -5.215008 0.924407 1.186354 M H-HC--0.042500 0 -5.383929 -0.607494 0.296474 M C-C-0.805400 0 -5.605570 -0.788016 2.428839 M O-O2--0.818800 0 -5.734708 -0.067706 3.454547 M O-O2--0.818800 0 -5.947450 -1.997018 2.333810 M N-N--0.415700 0 -4.667286 2.176705 0.000223 M H-H-0.271900 0 -5.358580 1.538797 0.339614 M C-CT--0.087500 0 -5.063971 3.480727 -0.491479 M H-H1-0.096900 0 -4.580882 4.256153 0.103028 M C-CT-0.298500 0 -4.660558 3.663221 -1.950786 L H-H1 22 C-C-0.597300 0 -6.571867 3.665676 -0.399129 L H-H1 22 H-HC--0.029700 0 -3.578481 3.570399 -2.043492 L C-CT--0.319200 0 -5.336934 2.594335 -2.802621 L C-CT--0.319200 0 -5.094761 5.044582 -2.429256 L O-O--0.567900 0 -7.292069 2.741987 0.060956 L H-HC-0.079100 0 -6.419114 2.686824 -2.710783 L H-HC-0.079100 0 -5.048915 2.724325 -3.845812 L H-HC-0.079100 0 -5.026906 1.606779 -2.460984 L H-HC-0.079100 0 -4.611580 5.808946 -1.820665 L H-HC-0.079100 0 -4.806645 5.175545 -3.472299 L H-HC-0.079100 0 -6.176850 5.137991 -2.337278 L N-N--0.516300 0 -7.186941 4.923315 -0.847381 L H-H-0.293600 0 -6.651063 5.581231 -1.376513 L C-CT-0.039700 0 -8.569717 5.209666 -0.522518 L H-H1-0.110500 0 -9.210774 4.437288 -0.947463 L C-CT-0.056000 0 -8.783229 5.244046 0.987069 L C-C-0.536600 0 -8.996294 6.558691 -1.083453 L H-HC--0.017300 0 -8.518191 4.276855 1.414148 L H-HC--0.017300 0 -8.154675 6.018939 1.425887 L C-CT-0.013600 0 -10.233003 5.544569 1.283615 L O-O--0.581900 0 -8.175766 7.258267 -1.732221 L H-HC--0.042500 0 -10.498670 6.511888 0.857216 L H-HC--0.042500 0 -10.862188 4.769803 0.845477 L C-C-0.805400 0 -10.446796 5.578994 2.795182 L O-O2--0.818800 0 -10.298521 6.688991 3.372697 L O-O2--0.818800 0 -10.756343 4.494968 3.357912 L N-N--0.415700 0 -10.366797 7.044417 -0.867366 L H-H-0.271900 0 -10.957507 6.593282 -0.198382 L C-CT--0.002400 0 -10.861782 8.176899 -1.623723 L H-H1-0.097800 0 -10.239071 9.048695 -1.422967 L C-CT--0.034300 0 -10.832645 7.891714 -3.121536 L C-C-0.597300 0 -12.297546 8.506169 -1.240775 L H-HC-0.029500 0 -9.808555 7.685743 -3.432851 L H-HC-0.029500 0 -11.459040 7.026711 -3.339479 L C-CA-0.011800 0 -11.331632 9.017578 -3.995345 L O-O--0.567900 0 -12.888752 7.820305 -0.366912 L C-CA--0.125600 0 -11.350562 8.867789 -5.387180 L C-CA--0.125600 0 -11.775340 10.211216 -3.413663 L H-HA-0.133000 0 -11.005104 7.938457 -5.840061 L C-CA--0.170400 0 -11.813199 9.911636 -6.197334 L C-CA--0.170400 0 -12.237977 11.255063 -4.223817 L H-HA-0.133000 0 -11.760602 10.327838 -2.330020 L H-HA-0.143000 0 -11.827938 9.795014 -7.280977 L C-CA--0.107200 0 -12.256907 11.105274 -5.615652 L H-HA-0.143000 0 -12.583435 12.184395 -3.770936 L H-HA-0.129700 0 -12.617104 11.917984 -6.246414 L N-N--0.347900 0 -12.993637 9.625381 -1.891714 L H-H-0.274700 0 -12.550033 10.125419 -2.635473 L C-CT--0.263700 0 -14.322568 10.004049 -1.455647 L H-H1-0.156000 0 -15.001717 9.161287 -1.584520 L C-CT--0.000700 0 -14.323143 10.410005 0.014326 L C-C-0.734100 0 -14.849615 11.181352 -2.263524 L H-HC-0.032700 0 -13.982173 9.572662 0.623175 L H-HC-0.032700 0 -13.654477 11.258795 0.157651 L C-CT-0.039000 0 -15.736543 10.800370 0.433298 L O-O2--0.589400 0 -14.141789 11.688069 -3.172254 L H-HC-0.028500 0 -16.078044 11.638013 -0.174841 L H-HC-0.028500 0 -16.405741 9.951881 0.290683 L C-CT-0.048600 0 -15.737119 11.206327 1.903273 L H-H1-0.068700 0 -15.396149 10.368984 2.512121 L H-H1-0.068700 0 -15.068452 12.055116 2.046597 L N-N2--0.529500 0 -17.095392 11.592620 2.346300 L H-H-0.345600 0 -17.850021 11.554247 1.676106 L C-CA-0.807600 0 -17.367676 11.987984 3.586642 L N-N2--0.862700 0 -16.427662 12.064208 4.524438 L N-N2--0.862700 0 -18.624431 12.312365 3.876888 L H-H-0.447800 0 -15.474243 11.817145 4.300713 L H-H-0.447800 0 -16.671555 12.368807 5.456015 L H-H-0.447800 0 -19.335864 12.253370 3.162407 L H-H-0.447800 0 -18.861600 12.616204 4.810447 L O-OH- 0 -16.149152 11.711677 -1.989919 L H-HO- 0 -16.493627 12.138214 -2.777956 L C-CT- 0 -1.971529 -2.337238 0.000148 H H-H1- 0 -2.312409 -2.516359 0.998454 M H-H1 97 H-H1- 0 -2.807007 -2.100096 -0.624865 M H-H1 97 N-N- 0 -1.302226 -3.541423 -0.512564 H H-H- 0 -1.939344 -4.059457 -1.083284 M H-H 100 C-C-0.597300 0 -0.864453 -4.376461 0.615251 M H-H 100 C-CT--0.024900 0 -0.037047 -5.628013 0.359323 M O-O--0.567900 0 -1.173802 -4.056507 1.792326 M N-N--0.415700 0 0.287099 -6.301875 1.600469 M H-H1-0.084300 0 0.882942 -5.339427 -0.149046 M C-CT-0.211700 0 -0.840250 -6.536712 -0.565206 M H-H-0.271900 0 -0.030927 -5.926491 2.471070 M H-H1-0.035200 0 -0.257411 -7.428659 -0.795052 M H-H1-0.035200 0 -1.768812 -6.826793 -0.073551 M O-OH--0.654600 0 -1.140564 -5.838678 -1.776594 M H-HO-0.427500 0 -1.646188 -6.410710 -2.358593 L H-HO 111 C-C-0.597300 0 1.083440 -7.537316 1.579817 M C-CT--0.059700 0 1.182562 -8.399803 2.829927 L H-H2 113 O-O--0.567900 0 1.683197 -7.881810 0.528539 L H-H1 113 N-N--0.415700 0 2.011332 -9.565021 2.595383 L H-H1-0.086900 0 0.179485 -8.717971 3.114015 L C-CT-0.130300 0 1.787312 -7.563573 3.952701 L H-H-0.271900 0 2.427990 -9.709793 1.697922 L H-HC-0.018700 0 1.840278 -8.160662 4.863074 L C-CT--0.320400 0 3.190484 -7.117729 3.555261 L C-CT--0.043000 0 0.915074 -6.337240 4.199546 L H-HC-0.088200 0 3.138271 -6.520160 2.645160 L H-HC-0.088200 0 3.623208 -6.519964 4.357462 L H-HC-0.088200 0 3.814318 -7.993944 3.378686 L H-HC-0.023600 0 0.862007 -5.739377 3.289687 L H-HC-0.023600 0 -0.088004 -6.655407 4.483633 L C-CT--0.066000 0 1.519823 -5.501009 5.322319 L H-HC-0.018600 0 2.522801 -5.182068 5.038746 L H-HC-0.018600 0 0.896743 -4.624314 5.499167 L H-HC-0.018600 0 1.572790 -6.098098 6.232692 L C-C-0.536600 0 2.239625 -10.534308 3.676709 L C-CT-0.039700 0 3.284848 -11.628043 3.510163 L O-O--0.581900 0 1.570859 -10.459764 4.740083 L N-N--0.516300 0 3.349503 -12.471304 4.686740 L H-H1-0.110500 0 4.255202 -11.160138 3.344097 L C-CT-0.056000 0 2.917005 -12.439652 2.272582 L H-H-0.293600 0 2.749247 -12.289694 5.465655 L H-HC--0.017300 0 3.668607 -13.211525 2.107031 L H-HC--0.017300 0 1.943386 -12.906989 2.420098 L C-CT-0.013600 0 2.860022 -11.527101 1.070874 L H-HC--0.042500 0 2.108260 -10.755186 1.235505 L H-HC--0.042500 0 3.833481 -11.059722 0.922437 L C-C-0.805400 0 2.491696 -12.339774 -0.168330 L O-O2--0.818800 0 1.266381 -12.454522 -0.438582 L O-O2--0.818800 0 3.439166 -12.838062 -0.832867 L C-C-0.597300 0 4.297472 -13.593752 4.735361 L C-CT--0.024900 0 4.292558 -14.543002 5.925061 L O-O--0.567900 0 5.113049 -13.769784 3.793332 L N-N3--0.415700 0 5.300035 -15.573477 5.774352 L H-H1-0.084300 0 3.307903 -15.004749 5.998170 L C-CT-0.211700 0 4.537363 -13.715592 7.182473 L H-H-0.271900 0 5.883024 -15.587765 4.961997 L H-H1-0.035200 0 4.505016 -14.364945 8.057342 L H-H1-0.035200 0 5.515908 -13.239521 7.119974 L O-OH--0.654600 0 3.525587 -12.711534 7.296830 L H-HO-0.427500 0 3.679694 -12.190672 8.088381 L H-H-0.271900 0 5.412337 -16.270352 6.482698 L 1 2 2.0 6 1.0 97 1.0 2 3 1.0 5 1.0 3 4 5 2.0 6 1.0 5 6 7 1.0 7 8 1.0 9 1.0 10 1.0 8 9 11 1.0 12 1.0 13 1.0 10 14 2.0 20 1.0 11 12 13 15 1.0 16 1.0 17 1.0 14 15 16 17 18 1.5 19 1.5 18 19 20 21 1.0 22 1.0 21 22 23 1.0 24 1.0 25 1.0 23 24 26 1.0 27 1.0 28 1.0 25 29 2.0 36 1.0 26 27 30 1.0 31 1.0 32 1.0 28 33 1.0 34 1.0 35 1.0 29 30 31 32 33 34 35 36 37 1.0 38 1.0 37 38 39 1.0 40 1.0 41 1.0 39 40 42 1.0 43 1.0 44 1.0 41 45 2.0 51 1.0 42 43 44 46 1.0 47 1.0 48 1.0 45 46 47 48 49 1.5 50 1.5 49 50 51 52 1.0 53 1.0 52 53 54 1.0 55 1.0 56 1.0 54 55 57 1.0 58 1.0 59 1.0 56 60 2.0 71 1.0 57 58 59 61 1.5 62 1.5 60 61 63 1.0 64 1.5 62 65 1.5 66 1.0 63 64 67 1.0 68 1.5 65 68 1.5 69 1.0 66 67 68 70 1.0 69 70 71 72 1.0 73 1.0 72 73 74 1.0 75 1.0 76 1.0 74 75 77 1.0 78 1.0 79 1.0 76 80 2.0 95 1.0 77 78 79 81 1.0 82 1.0 83 1.0 80 81 82 83 84 1.0 85 1.0 86 1.0 84 85 86 87 1.0 88 1.5 87 88 89 1.5 90 1.5 89 91 1.0 92 1.0 90 93 1.0 94 1.0 91 92 93 94 95 96 1.0 96 97 98 1.0 99 1.0 100 1.0 98 99 100 101 1.0 102 1.0 101 102 103 1.0 104 2.0 103 105 1.0 106 1.0 107 1.0 104 105 108 1.0 113 1.0 106 107 109 1.0 110 1.0 111 1.0 108 109 110 111 112 1.0 112 113 114 1.0 115 2.0 114 116 1.0 117 1.0 118 1.0 115 116 119 1.0 132 1.0 117 118 120 1.0 121 1.0 122 1.0 119 120 121 123 1.0 124 1.0 125 1.0 122 126 1.0 127 1.0 128 1.0 123 124 125 126 127 128 129 1.0 130 1.0 131 1.0 129 130 131 132 133 1.0 134 2.0 133 135 1.0 136 1.0 137 1.0 134 135 138 1.0 147 1.0 136 137 139 1.0 140 1.0 141 1.0 138 139 140 141 142 1.0 143 1.0 144 1.0 142 143 144 145 1.5 146 1.5 145 146 147 148 1.0 149 2.0 148 150 1.0 151 1.0 152 1.0 149 150 153 1.0 158 1.0 151 152 154 1.0 155 1.0 156 1.0 153 154 155 156 157 1.0 157 158http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- Be a better Globetrotter. Get better travel answers from someone who knows. Yahoo! Answers - Check it out. --0-521775899-1184012211=:21858 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Keerthi,

You may have to define additional bond stretching and angle bending parameters. These parameters should come after the connectivity section of the gaussian input file. For example if you are using link atoms when partitioning the system, parameters for those connections should appear in the gaussian input file. Hope this will help. Good luck!

Lochana C. Menikarachchi
UConn
http://gascon.chem.uconn.edu

"Keerthi Jayasundera jaya0046(_)d.umn.edu" <owner-chemistry##ccl.net> wrote:

Sent to CCL by: "Keerthi Jayasundera" [jaya0046^d.umn.edu]
I am a beginner to oniom I am trying an oniom calculation for a peptide chain with a triazole ring in the middle. I always get an error message in the middle of the calculation.
As a start I used a 3-layer oniom as given in the gaussian tutorial. So I got a message saying that same parameter is missing to a N atom in the high layer.
Anyway I found that could come with the "Amber" So I changed it to UFF in the low layer. Now I get some other error which does not give any understandable message.

I think I have not used commands correctly. Please someone help me to solve the problem

Here is my input file.

%chk=quick.chk
%mem=6MW
%nproc=1
opt=rcfc oniom(rhf/6-31g:ram1:amber) geom=connectivity

Title Card Required

0 1 0 1 0 1 0 1 0 1 0 1
C-CM- 0 -0.979628 -1.159218 0.000009 H
C-CM- 0 0.422122 -1.159218 0.000009 H
H-H4- 0 1.066495 -2.031924 0.000034 M H-H4 2
N- 0 -0.310937 1.003031 -0.000095 H
N-N2- 0 0.846120 0.211578 0.000009 H
N-N3--0.516300 0 -1.419355 0.161290 0.000000 H
C-CT-0.039700 0 -2.859630 0.320067 0.000068 H
H-H1-0.110500 0 -3.277620 -0.150672 -0.889757 M H-H1 7
C-CT-0.056000 0 -3.483217 -0.326921 1.232208 M H-H1 7
C-C-0.536600 0 -3.248651 1.791511 0.000147 M H-H1 7
H-HC--0.017300 0 -3.250175 -1.391678 1.241385 M
H-HC--0.017300 0 -3.081256 0.140223 2.131266 M
C-CT-0.013600 0 -4.981165 -0.140179 1.195083 M
O-O--0.581900 0 -2.355867 2.678364 0.000146 M
H-HC--0.042500 0 -5.215008 0.924407 1.186354 M
H-HC--0.042500 0 -5.383929 -0.607494 0.296474 M
C-C-0.805400 0 -5.605570 -0.788016 2.428839 M
O-O2--0.818800 0 -5.734708 -0.067706 3.454547 M
O-O2--0.818800 0 -5.947450 -1.997018 2.333810 M
N-N--0.415700 0 -4.667286 2.176705 0.000223 M
H-H-0.271900 0 -5.358580 1.538797 0.339614 M
C-CT--0.087500 0 -5.063971 3.480727 -0.491479 M
H-H1-0.096900 0 -4.580882 4.256153 0.103028 M
C-CT-0.298500 0 -4.660558 3.663221 -1.950786 L H-H1 22
C-C-0.597300 0 -6.571867 3.665676 -0.399129 L H-H1 22
H-HC--0.029700 0 -3.578481 3.570399 -2.043492 L
C-CT--0.319200 0 -5.336934 2.594335 -2.802621 L
C-CT--0.319200 0 -5.094761 5.044582 -2.429256 L
O-O--0.567900 0 -7.292069 2.741987 0.060956 L
H-HC-0.079100 0 -6.419114 2.686824 -2.710783 L
H-HC-0.079100 0 -5.048915 2.724325 -3.845812 L
H-HC-0.079100 0 -5.026906 1.606779 -2.460984 L
H-HC-0.079100 0 -4.611580 5.808946 -1.820665 L
H-HC-0.079100 0 -4.806645 5.175545 -3.472299 L
H-HC-0.079100 0 -6.176850 5.137991 -2.337278 L
N-N--0.516300 0 -7.186941 4.923315 -0.847381 L
H-H-0.293600 0 -6.651063 5.581231 -1.376513 L
C-CT-0.039700 0 -8.569717 5.209666 -0.522518 L
H-H1-0.110500 0 -9.210774 4.437288 -0.947463 L
C-CT-0.056000 0 -8.783229 5.244046 0.987069 L
C-C-0.536600 0 -8.996294 6.558691 -1.083453 L
H-HC--0.017300 0 -8.518191 4.276855 1.414148 L
H-HC--0.017300 0 -8.154675 6.018939 1.425887 L
C-CT-0.013600 0 -10.233003 5.544569 1.283615 L
O-O--0.581900 0 -8.175766 7.258267 -1.732221 L
H-HC--0.042500 0 -10.498670 6.511888 0.857216 L
H-HC--0.042500 0 -10.862188 4.769803 0.845477 L
C-C-0.805400 0 -10.446796 5.578994 2.795182 L
O-O2--0.818800 0 -10.298521 6.688991 3.372697 L
O-O2--0.818800 0 -10.756343 4.494968 3.357912 L
N-N--0.415700 0 -10.366797 7.044417 -0.867366 L
H-H-0.271900 0 -10.957507 6.593282 -0.198382 L
C-CT--0.002400 0 -10.861782 8.176899 -1.623723 L
H-H1-0.097800 0 -10.239071 9.048695 -1.422967 L
C-CT--0.034300 0 -10.832645 7.891714 -3.121536 L
C-C-0.597300 0 -12.297546 8.506169 -1.240775 L
H-HC-0.029500 0 -9.808555 7.685743 -3.432851 L
H-HC-0.029500 0 -11.459040 7.026711 -3.339479 L
C-CA-0.011800 0 -11.331632 9.017578 -3.995345 L
O-O--0.567900 0 -12.888752 7.820305 -0.366912 L
C-CA--0.125600 0 -11.350562 8.867789 -5.387180 L
C-CA--0.125600 0 -11.775340 10.211216 -3.413663 L
H-HA-0.133000 0 -11.005104 7.938457 -5.840061 L
C-CA--0.170400 0 -11.813199 9.911636 -6.197334 L
C-CA--0.170400 0 -12.237977 11.255063 -4.223817 L
H-HA-0.133000 0 -11.760602 10.327838 -2.330020 L
H-HA-0.143000 0 -11.827938 9.795014 -7.280977 L
C-CA--0.107200 0 -12.256907 11.105274 -5.615652 L
H-HA-0.143000 0 -12.583435 12.184395 -3.770936 L
H-HA-0.129700 0 -12.617104 11.917984 -6.246414 L
N-N--0.347900 0 -12.993637 9.625381 -1.891714 L
H-H-0.274700 0 -12.550033 10.125419 -2.635473 L
C-CT--0.263700 0 -14.322568 10.004049 -1.455647 L
H-H1-0.156000 0 -15.001717 9.161287 -1.584520 L
C-CT--0.000700 0 -14.323143 10.410005 0.014326 L
C-C-0.734100 0 -14.849615 11.181352 -2.263524 L
H-HC-0.032700 0 -13.982173 9.572662 0.623175 L
H-HC-0.032700 0 -13.654477 11.258795 0.157651 L
C-CT-0.039000 0 -15.736543 10.800370 0.433298 L
O-O2--0.589400 0 -14.141789 11.688069 -3.172254 L
H-HC-0.028500 0 -16.078044 11.638013 -0.174841 L
H-HC-0.028500 0 -16.405741 9.951881 0.290683 L
C-CT-0.048600 0 -15.737119 11.206327 1.903273 L
H-H1-0.068700 0 -15.396149 10.368984 2.512121 L
H-H1-0.068700 0 -15.068452 12.055116 2.046597 L
N-N2--0.529500 0 -17.095392 11.592620 2.346300 L
H-H-0.345600 0 -17.850021 11.554247 1.676106 L
C-CA-0.807600 0 -17.367676 11.987984 3.586642 L
N-N2--0.862700 0 -16.427662 12.064208 4.524438 L
N-N2--0.862700 0 -18.624431 12.312365 3.876888 L
H-H-0.447800 0 -15.474243 11.817145 4.300713 L
H-H-0.447800 0 -16.671555 12.368807 5.456015 L
H-H-0.447800 0 -19.335864 12.253370 3.162407 L
H-H-0.447800 0 -18.861600 12.616204 4.810447 L
O-OH- 0 -16.149152 11.711677 -1.989919 L
H-HO- 0 -16.493627 12.138214 -2.777956 L
C-CT- 0 -1.971529 -2.337238 0.000148 H
H-H1- 0 -2.312409 -2.516359 0.998454 M H-H1 97
H-H1- 0 -2.807007 -2.100096 -0.624865 M H-H1 97
N-N- 0 -1.302226 -3.541423 -0.512564 H
H-H- 0 -1.939344 -4.059457 -1.083284 M H-H 100
C-C-0.597300 0 -0.864453 -4.376461 0.615251 M H-H 100
C-CT--0.024900 0 -0.037047 -5.628013 0.359323 M
O-O--0.567900 0 -1.173802 -4.056507 1.792326 M
N-N--0.415700 0 0.287099 -6.301875 1.600469 M
H-H1-0.084300 0 0.882942 -5.339427 -0.149046 M
C-CT-0.211700 0 -0.840250 -6.536712 -0.565206 M
H-H-0.271900 0 -0.030927 -5.926491 2.471070 M
H-H1-0.035200 0 -0.257411 -7.428659 -0.795052 M
H-H1-0.035200 0 -1.768812 -6.826793 -0.073551 M
O-OH--0.654600 0 -1.140564 -5.838678 -1.776594 M
H-HO-0.427500 0 -1.646188 -6.410710 -2.358593 L H-HO 111
C-C-0.597300 0 1.083440 -7.537316 1.579817 M
C-CT--0.059700 0 1.182562 -8.399803 2.829927 L H-H2 113
O-O--0.567900 0 1.683197 -7.881810 0.528539 L H-H1 113
N-N--0.415700 0 2.011332 -9.565021 2.595383 L
H-H1-0.086900 0 0.179485 -8.717971 3.114015 L
C-CT-0.130300 0 1.787312 -7.563573 3.952701 L
H-H-0.271900 0 2.427990 -9.709793 1.697922 L
H-HC-0.018700 0 1.840278 -8.160662 4.863074 L
C-CT--0.320400 0 3.190484 -7.117729 3.555261 L
C-CT--0.043000 0 0.915074 -6.337240 4.199546 L
H-HC-0.088200 0 3.138271 -6.520160 2.645160 L
H-HC-0.088200 0 3.623208 -6.519964 4.357462 L
H-HC-0.088200 0 3.814318 -7.993944 3.378686 L
H-HC-0.023600 0 0.862007 -5.739377 3.289687 L
H-HC-0.023600 0 -0.088004 -6.655407 4.483633 L
C-CT--0.066000 0 1.519823 -5.501009 5.322319 L
H-HC-0.018600 0 2.522801 -5.182068 5.038746 L
H-HC-0.018600 0 0.896743 -4.624314 5.499167 L
H-HC-0.018600 0 1.572790 -6.098098 6.232692 L
C-C-0.536600 0 2.239625 -10.534308 3.676709 L
C-CT-0.039700 0 3.284848 -11.628043 3.510163 L
O-O--0.581900 0 1.570859 -10.459764 4.740083 L
N-N--0.516300 0 3.349503 -12.471304 4.686740 L
H-H1-0.110500 0 4.255202 -11.160138 3.344097 L
C-CT-0.056000 0 2.917005 -12.439652 2.272582 L
H-H-0.293600 0 2.749247 -12.289694 5.465655 L
H-HC--0.017300 0 3.668607 -13.211525 2.107031 L
H-HC--0.017300 0 1.943386 -12.906989 2.420098 L
C-CT-0.013600 0 2.860022 -11.527101 1.070874 L
H-HC--0.042500 0 2.108260 -10.755186 1.235505 L
H-HC--0.042500 0 3.833481 -11.059722 0.922437 L
C-C-0.805400 0 2.491696 -12.339774 -0.168330 L
O-O2--0.818800 0 1.266381 -12.454522 -0.438582 L
O-O2--0.818800 0 3.439166 -12.838062 -0.832867 L
C-C-0.597300 0 4.297472 -13.593752 4.735361 L
C-CT--0.024900 0 4.292558 -14.543002 5.925061 L
O-O--0.567900 0 5.113049 -13.769784 3.793332 L
N-N3--0.415700 0 5.300035 -15.573477 5.774352 L
H-H1-0.084300 0 3.307903 -15.004749 5.998170 L
C-CT-0.211700 0 4.537363 -13.715592 7.182473 L
H-H-0.271900 0 5.883024 -15.587765 4.961997 L
H-H1-0.035200 0 4.505016 -14.364945 8.057342 L
H-H1-0.035200 0 5.515908 -13.239521 7.119974 L
O-OH--0.654600 0 3.525587 -12.711534 7.296830 L
H-HO-0.427500 0 3.679694 -12.190672 8.088381 L
H-H-0.271900 0 5.412337 -16.270352 6.482698 L

1 2 2.0 6 1.0 97 1.0
2 3 1.0 5 1.0
3
4 5 2.0 6 1.0
5
6 7 1.0
7 8 1.0 9 1.0 10 1.0
8
9 11 1.0 12 1.0 13 1.0
10 14 2.0 20 1.0
11
12
13 15 1.0 16 1.0 17 1.0
14
15
16
17 18 1.5 19 1.5
18
19
20 21 1.0 22 1.0
21
22 23 1.0 24 1.0 25 1.0
23
24 26 1.0 27 1.0 28 1.0
25 29 2.0 36 1.0
26
27 30 1.0 31 1.0 32 1.0
28 33 1.0 34 1.0 35 1.0
29
30
31
32
33
34
35
36 37 1.0 38 1.0
37
38 39 1.0 40 1.0 41 1.0
39
40 42 1.0 43 1.0 44 1.0
41 45 2.0 51 1.0
42
43
44 46 1.0 47 1.0 48 1.0
45
46
47
48 49 1.5 50 1.5
49
50
51 52 1.0 53 1.0
52
53 54 1.0 55 1.0 56 1.0
54
55 57 1.0 58 1.0 59 1.0
56 60 2.0 71 1.0
57
58
59 61 1.5 62 1.5
60
61 63 1.0 64 1.5
62 65 1.5 66 1.0
63
64 67 1.0 68 1.5
65 68 1.5 69 1.0
66
67
68 70 1.0
69
70
71 72 1.0 73 1.0
72
73 74 1.0 75 1.0 76 1.0
74
75 77 1.0 78 1.0 79 1.0
76 80 2.0 95 1.0
77
78
79 81 1.0 82 1.0 83 1.0
80
81
82
83 84 1.0 85 1.0 86 1.0
84
85
86 87 1.0 88 1.5
87
88 89 1.5 90 1.5
89 91 1.0 92 1.0
90 93 1.0 94 1.0
91
92
93
94
95 96 1.0
96
97 98 1.0 99 1.0 100 1.0
98
99
100 101 1.0 102 1.0
101
102 103 1.0 104 2.0
103 105 1.0 106 1.0 107 1.0
104
105 108 1.0 113 1.0
106
107 109 1.0 110 1.0 111 1.0
108
109
110
111 112 1.0
112
113 114 1.0 115 2.0
114 116 1.0 117 1.0 118 1.0
115
116 119 1.0 132 1.0
117
118 120 1.0 121 1.0 122 1.0
119
120
121 123 1.0 124 1.0 125 1.0
122 126 1.0 127 1.0 128 1.0
123
124
125
126
127
128 129 1.0 130 1.0 131 1.0
129
130
131
132 133 1.0 134 2.0
133 135 1.0 136 1.0 137 1.0
134
135 138 1.0 147 1.0
136
137 139 1.0 140 1.0 141 1.0
138
139
140
141 142 1.0 143 1.0 144 1.0
142
143
144 145 1.5 146 1.5
145
146
147 148 1.0 149 2.0
148 150 1.0 151 1.0 152 1.0
149
150 153 1.0 158 1.0
151
152 154 1.0 155 1.0 156 1.0
153
154
155
156 157 1.0
157
158

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Yahoo! Answers - Check it out. --0-521775899-1184012211=:21858-- From owner-chemistry@ccl.net Mon Jul 9 21:39:01 2007 From: "Raoul E Correa raoul##berkeley.edu" To: CCL Subject: CCL: Visualizing vibrational data Message-Id: <-34698-070709134944-27583-9PGASXBTRy3W0blhPcqplA-#-server.ccl.net> X-Original-From: "Raoul E Correa" Date: Mon, 9 Jul 2007 13:49:40 -0400 Sent to CCL by: "Raoul E Correa" [raoul+*+berkeley.edu] Hello, I was wondering if there is software which helps one visualize the motions of atoms along a vibrational mode, such as those described by a frequency calculation in any computational package. I run simulations on QChem but haven't found a program that will take the output and create animations of the actual vibrational mode. Does anyone know of such a stand-alone program? Or maybe a way to convert the output into something that another program (e.g. Molekel) could use? Thanks for the help! Raoul From owner-chemistry@ccl.net Mon Jul 9 22:41:00 2007 From: "Thomas Jospeh alabarae.:.yahoo.com" To: CCL Subject: CCL: what are nutlins 3a and 3b Message-Id: <-34699-070709223646-3923-+PuBWMeW6n3BXZDYsiUzyw:+:server.ccl.net> X-Original-From: "Thomas Jospeh" Date: Mon, 9 Jul 2007 22:36:43 -0400 Sent to CCL by: "Thomas Jospeh" [alabarae[a]yahoo.com] Hi, what are the structural differences between nutlin 3a and nutlin3b. they are enantiomers, but how to differentiate them structurally, your help is deeply appreciated.