From owner-chemistry@ccl.net Wed Feb 13 00:57:00 2008 From: "soumya samineni soumya_samineni=rediffmail.com" To: CCL Subject: CCL: rotation of an adsorbate Message-Id: <-36276-080213004837-7925-ggSUbLwqKNnxTUQE7yTpPQ() server.ccl.net> X-Original-From: "soumya samineni" Date: Wed, 13 Feb 2008 00:48:32 -0500 Sent to CCL by: "soumya samineni" [soumya_samineni=rediffmail.com] Hi all, I am trying to generate the PES of the adsorption of methane over Pt surface for a bench mark calcualtion. Translation of methane was no problem. But I am not able to genarate input where in i can rotate the methane only and leave the surface fixed .. I hope some one will help me how to go about it thanx in advance soumya From owner-chemistry@ccl.net Wed Feb 13 09:23:01 2008 From: "richard j hart ric_hart:hotmail.com" To: CCL Subject: CCL:G: Freezing atoms in MM layer for ONIOM Message-Id: <-36277-080212172907-32426-XZqFtf6H7YXnhN6v3mL74w=server.ccl.net> X-Original-From: "richard j hart" Date: Tue, 12 Feb 2008 17:29:03 -0500 Sent to CCL by: "richard j hart" [ric_hart.:.hotmail.com] Hello, I am trying to optimize one small part of an enzyme (QM layer) while keeping the surrounding amino acids as a fixed force field (MM layer). Ultimately, I will want to get out hyperfine couplings. I have fixed the atoms in the molecule specification using -1 in place of the zero. (I also tried -2). e.g.: C-C_R -1 -3.06092 -7.01089 6.42213 M My route section: # opt=loose oniom(b3lyp/6-31g(d):uff=qeq) nosymm geom=connectivity scf =conver=6 My error message: Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.00000 RFO could not converge Lambda in 999 iterations. Linear search not attempted -- first point. Steepest descent instead of Quadratic search. Maximum step size ( 0.300) exceeded in Quadratic search. -- Step size scaled by 0.013 Iteration 1 RMS(Cart)= 0.18075693 RMS(Int)= 0.01388409 Iteration 2 RMS(Cart)= 0.14954421 RMS(Int)= 0.00504281 Iteration 3 RMS(Cart)= 0.00899985 RMS(Int)= 0.00064957 Iteration 4 RMS(Cart)= 0.00009705 RMS(Int)= 0.00064921 Iteration 5 RMS(Cart)= 0.00000000 RMS(Int)= 0.00064921 Need to have at least 3 QM atoms frozen Error termination via Lnk1e in /software/horace/applications/gaussian03/g03/l103.exe at Sun Feb 10 09:14:01 2008. Job cpu time: 0 days 0 hours 13 minutes 3.4 seconds. File lengths (MBytes): RWF= 376 Int= 0 D2E= 0 Chk= 36 Scr= 8 Thank you for your help, Regards, Richard Hart (ric_hart*|*hotmail.com) From owner-chemistry@ccl.net Wed Feb 13 09:58:01 2008 From: "Richie Wang f93548056:_:ntu.edu.tw" To: CCL Subject: CCL: How to calculate number of rotatable bonds with ligand automatically? Message-Id: <-36278-080213033931-9480-6wKlPeCehOBljORFADvong!^!server.ccl.net> X-Original-From: "Richie Wang" Date: Wed, 13 Feb 2008 03:39:27 -0500 Sent to CCL by: "Richie Wang" [f93548056]_[ntu.edu.tw] Dear all, Does somebody know what programs(free or not) could help to calculate number of rotatable bonds with ligand automatically? Or, did any pulications or aligorithms ever mention about this? Best Regards, Richie Wang From owner-chemistry@ccl.net Wed Feb 13 10:41:00 2008 From: "Maxim Kholin maxim.kholin__q-pharm.com" To: CCL Subject: CCL: How to calculate number of rotatable bonds with ligand automatically? Message-Id: <-36279-080213103534-13596-A0j8IPdtf77aatQwlCZ01w(a)server.ccl.net> X-Original-From: "Maxim Kholin" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="koi8-r"; reply-type=original Date: Wed, 13 Feb 2008 18:34:54 +0300 MIME-Version: 1.0 Sent to CCL by: "Maxim Kholin" [maxim.kholin ~~ q-pharm.com] Dear Richie, Please try q-Mol, the free demo is downloadable from http://www.q-lead.com/qmol Maxim ----- Original Message ----- > From: "Richie Wang f93548056:_:ntu.edu.tw" To: "Kholin, Maxim N " Sent: Wednesday, February 13, 2008 11:39 AM Subject: CCL: How to calculate number of rotatable bonds with ligand automatically? > > Sent to CCL by: "Richie Wang" [f93548056]_[ntu.edu.tw] > Dear all, > > Does somebody know what programs(free or not) could help to calculate > number of rotatable bonds with ligand automatically? > > Or, did any pulications or aligorithms ever mention about this? > > Best Regards, > Richie Wang> > From owner-chemistry@ccl.net Wed Feb 13 12:59:00 2008 From: "Mark Zottola mzottola]^[gmail.com" To: CCL Subject: CCL: Scaling of Raman Frequencies Message-Id: <-36280-080213124158-24533-YCv88VTjz2c3y7n2pwhYDA|,|server.ccl.net> X-Original-From: "Mark Zottola" Content-Type: multipart/alternative; boundary="----=_Part_18943_27553302.1202921078484" Date: Wed, 13 Feb 2008 11:44:38 -0500 MIME-Version: 1.0 Sent to CCL by: "Mark Zottola" [mzottola---gmail.com] ------=_Part_18943_27553302.1202921078484 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline I have a few questions concerning the calculation of raman frequencies. The first is, should one consider the IR scaling factors to be valid for Raman? Raman is essentially an emission phenomenon while IR frequencies are an abosorbance phenomenon. My second question is, if Raman frequencies should be scaled, should Raman frequencies determined by incorporation of solvent effects also be scaled? Any thoughts on this are welcome. Mark ------=_Part_18943_27553302.1202921078484 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
I have a few questions concerning the calculation of raman frequencies.  The first is, should one consider the IR scaling factors to be valid for Raman?  Raman is essentially an emission phenomenon while IR frequencies are an abosorbance phenomenon.
 
My second question is, if Raman frequencies should be scaled, should Raman frequencies determined by incorporation of solvent effects also be scaled? 
 
Any thoughts on this are welcome.
 
 
Mark
------=_Part_18943_27553302.1202921078484-- From owner-chemistry@ccl.net Wed Feb 13 14:26:00 2008 From: "=?ISO-8859-1?Q?=D6d=F6n?= Farkas farkas-x-chem.elte.hu" To: CCL Subject: CCL:G: Freezing atoms in MM layer for ONIOM Message-Id: <-36281-080213133305-11863-udWxfgeDGRMi+fPSFdCxUA]~[server.ccl.net> X-Original-From: =?ISO-8859-1?Q?=D6d=F6n?= Farkas Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Wed, 13 Feb 2008 19:32:18 +0100 Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas===chem.elte.hu] Hi Richard, Mz guess is that some (but less than 3) QM atoms are frozen in your input. This might be intentional but keep in mind that the QM/MM ONIOM calculations use microiterations for the MM part and only the QM part is treated using redundant internals. If you freeze 3 QM atoms in the Cartesian space than you freeze the rigid body motion of the QM part or if you do not freeze Cartesian coordinates of atoms in the QM part than you allow that motion. It is possible to implement the cases of freezing 1 or 2 atoms in Cartesians, but as these are usually not important but complicated enough to implement, the program just writes an error message. Best wishes, Ödön On Tue, 2008-02-12 at 17:29 -0500, richard j hart ric_hart:hotmail.com wrote: > Sent to CCL by: "richard j hart" [ric_hart.:.hotmail.com] > Hello, > > I am trying to optimize one small part of an enzyme (QM layer) while keeping the > surrounding amino acids as a fixed force field (MM layer). Ultimately, I will > want to get out hyperfine couplings. > > I have fixed the atoms in the molecule specification using -1 in place of the > zero. (I also tried -2). e.g.: > > C-C_R -1 -3.06092 -7.01089 6.42213 M > > My route section: > > # opt=loose oniom(b3lyp/6-31g(d):uff=qeq) nosymm geom=connectivity scf > =conver=6 > > My error message: > > Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 > Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 > Eigenvalues --- 1000.00000 > RFO could not converge Lambda in 999 iterations. > Linear search not attempted -- first point. > Steepest descent instead of Quadratic search. > Maximum step size ( 0.300) exceeded in Quadratic search. > -- Step size scaled by 0.013 > Iteration 1 RMS(Cart)= 0.18075693 RMS(Int)= 0.01388409 > Iteration 2 RMS(Cart)= 0.14954421 RMS(Int)= 0.00504281 > Iteration 3 RMS(Cart)= 0.00899985 RMS(Int)= 0.00064957 > Iteration 4 RMS(Cart)= 0.00009705 RMS(Int)= 0.00064921 > Iteration 5 RMS(Cart)= 0.00000000 RMS(Int)= 0.00064921 > Need to have at least 3 QM atoms frozen > Error termination via Lnk1e in > /software/horace/applications/gaussian03/g03/l103.exe at Sun Feb 10 09:14:01 > 2008. > Job cpu time: 0 days 0 hours 13 minutes 3.4 seconds. > File lengths (MBytes): RWF= 376 Int= 0 D2E= 0 Chk= 36 Scr= > 8 > > Thank you for your help, > Regards, > Richard Hart (ric_hart[A]hotmail.com)> > -- Ödön Farkas Associate professor Deparment of Organic Chemistry and Laboratory of Chemical Informatics, Institute of Chemistry, Eötvös Loránd University, Budapest Address: 1/A Pázmány Péter sétány, H-1117 Budapest, Hungary Phone: +36-1-372-2570 Cell phone: +36-30-255-3111 Fax: +36-1-372-2620 URL: http://organ.elte.hu/farkas From owner-chemistry@ccl.net Wed Feb 13 15:07:00 2008 From: "David Hose Anthrax_brothers.:.hotmail.com" To: CCL Subject: CCL: Formal charges Message-Id: <-36282-080213150545-21531-nGKUu6FoHtOlR+BXQHOw8g]~[server.ccl.net> X-Original-From: "David Hose" Date: Wed, 13 Feb 2008 15:05:42 -0500 Sent to CCL by: "David Hose" [Anthrax_brothers+/-hotmail.com] OK, I see where you are coming from. I don't know of any programs that do from the Lewis structure per say. Some of the QSAR packages out there will identify charged centers within molecules, typically at physiological pH. So a summation of these values would give you the overall molecular charge. One thought did occur to me. MDL SDF file format does allow for charges to be captured within them. See Dalby et al. Description of several chemical-structure file formats used by computer- programs developed at Molecular Design Limited. J. Chem. Inf. Comput. Sci. (1992) vol. 32 pp. 244- 255. Could you build your system in say Spartan with the appropriate formal atomic charges, export as an SDF file, and then import into MOPAC either directly or via a file convertor such as Open Babel (http://openbabel.sourceforge.net/)? Regards, Dave. ----- yea in spartan it doesnt matter but in mopac you have to assign a correct charge for the system. and the systems I use are large systems so at some points I may mistakes in assigning charges and it gets frustrating. I taught maybe there could programs displaying the formal charge of the molecules according to lewis bonding system thanks tough On Feb 12, 2008 10:34 PM, David Hose anthrax_brothers*hotmail.com wrote: Sent to CCL by: "David Hose" [anthrax_brothers|-|hotmail.com] The formal charge is what you define in the properties dialogue box when you have selected an atom in your molecule (see the dropdown table towards the lower left [the default is "unspecified"]). From what I recall, unless you define the formal charge in this way, then nothing is displayed when requested. To be honest I don't use the formal charge option when setting calculations up, I just define the molecular charge and multiplicity in the calculations dialogue box before submitting the job, then extract the appropriate partial atomic charge afterwards for further analysis. Regards, Dave ----- But when I select labels and then formal charges nothing is displayed on the screen even after I run the calculations. Other charges show though (like mulliken etc). Also there is no option for formal charges in the display menu... On Feb 11, 2008 7:49 PM, David Hose anthrax_brothers ~~ hotmail.com wrote: Sent to CCL by: "David Hose" [anthrax_brothers===hotmail.com] If you want to display the charges on the 3D structure in Spartan, try this. From the Model menu select Labels. Depending upon your preferences, you might see the atom labels appear (default of white text on a green background, so the labels may be invisible if you have charged your background to white). Then select Configure... from the Model menu and select the appropriate radio button. If you haven't already discovered this, if you click the "P" icon in the Properties dialogue (under the Display menu), the charge of the atom selected will be added to the spreadsheet. Regards, Dave. > > Sent to CCL by: "Sina T reli" [sinatureli{:}gmail.com] > Hello, > > Is there any tool that will calculate formal charges on a molecular system and display it? I have tried spartan but couldnt figure how it displays formal charges though there is an option for it in the display menu... > > Thanks From owner-chemistry@ccl.net Wed Feb 13 15:41:01 2008 From: "David Hose Anthrax_brothers~!~hotmail.com" To: CCL Subject: CCL: How to calculate number of rotatable bonds with ligand automatica Message-Id: <-36283-080213152047-31872-9HGAgNGX9ipmoLHTCIgmKw|-|server.ccl.net> X-Original-From: "David Hose" Date: Wed, 13 Feb 2008 15:20:44 -0500 Sent to CCL by: "David Hose" [Anthrax_brothers|,|hotmail.com] Many of the QSAR packages will do this. Dragon: http://www.talete.mi.it/help/dragon_help/index.html?IntroducingDRAGON For the Online version of Dragon: http://www.vcclab.org/lab/edragon/ CODESSA: http://www.semichem.com/codessa/cfeatures.php Regards, Dave. ----- Sent to CCL by: "Maxim Kholin" [maxim.kholin ~~ q-pharm.com] Dear Richie, Please try q-Mol, the free demo is downloadable from http://www.q-lead.com/qmol Maxim ----- Original Message ----- > From: "Richie Wang f93548056:_:ntu.edu.tw" To: "Kholin, Maxim N " Sent: Wednesday, February 13, 2008 11:39 AM Subject: CCL: How to calculate number of rotatable bonds with ligand automatically? > > Sent to CCL by: "Richie Wang" [f93548056]_[ntu.edu.tw] > Dear all, > > Does somebody know what programs(free or not) could help to calculate > number of rotatable bonds with ligand automatically? > > Or, did any pulications or aligorithms ever mention about this? > > Best Regards, > Richie Wang> > From owner-chemistry@ccl.net Wed Feb 13 16:17:01 2008 From: "DUy Le ttduyle * gmail.com" To: CCL Subject: CCL:G: Change Overlap in ZINDO/S calculation Message-Id: <-36284-080213152313-1493-NRYsRkm/Ng46QJeBdKGX1w###server.ccl.net> X-Original-From: "DUy Le" Date: Wed, 13 Feb 2008 15:23:09 -0500 Sent to CCL by: "DUy Le" [ttduyle**gmail.com] Dear CCLers, I am doing some ZINDO/S calculation now, by default, GAUSSIAN takes overlap to be unity. I was finding in manual but I could not find how to change this overlap, i.e. to 0.6 Any suggestion is appreciated. Regards, Duy. From owner-chemistry@ccl.net Wed Feb 13 16:51:00 2008 From: "amr hamed mahmoud dramr83+/-gmail.com" To: CCL Subject: CCL: In silico lead optimisation Message-Id: <-36285-080213154856-19254-I2y4EO06zp0fYAceLc81kg]*[server.ccl.net> X-Original-From: "amr hamed mahmoud" Date: Wed, 13 Feb 2008 15:48:52 -0500 Sent to CCL by: "amr hamed mahmoud" [dramr83:_:gmail.com] I would like to know the pros and the cons of the packages concerned with this field ....leapfrog ,Rachel and LUDI ... if anyone worked on any of the above packages ..plz share your intuition about the results obtained .... From owner-chemistry@ccl.net Wed Feb 13 18:34:01 2008 From: "Zenghui Yang zenghuiy===uci.edu" To: CCL Subject: CCL: Announcement of TDDFT workshop Message-Id: <-36286-080213171758-20025-1vdQ3j5UzuFP7IxXoX+Q5w() server.ccl.net> X-Original-From: "Zenghui Yang" Date: Wed, 13 Feb 2008 17:17:54 -0500 Sent to CCL by: "Zenghui Yang" [zenghuiy . uci.edu] THIRD Psi-k/NANOQUANTA SCHOOL + WORKSHOP on Time-Dependent Density-Functional Theory: Prospects and Applications August 31st to September 14th 2008 Benasque Center for Physics, Spain http://benasque.ecm.ub.es/2008tddft/2008tddft.htm Organizers: *) E. K. U. Gross Institut fuer Theoretische Physik Freie Universitaet Berlin Arnimallee 14, D-14195 Berlin, Germany Phone: +49-30-838-54784 Fax: +49-30-838-55258 Mail: hardy]-[physik.fu-berlin.de http://www.physik.fu-berlin.de/~ag-gross/ *) Miguel A. L. Marques Laboratoire de Physique de la Mati_re Condens_e et des Nanostructures (LPMCN), Universit_ Lyon I, UMR CNRS 5586, B_timent Brillouin, Domaine scientifique de la DOUA, Villeurbanne F-69622, France. Mail: marques]-[tddft.org *) Fernando Nogueira Dep. de F_sica, Faculdade de Ci_ncias e Tecnologia, Universidade de Coimbra and Centro de F_sica Computacional Rua Larga, 3004-516 Coimbra, Portugal Phone: +351-239410114 Fax: +351-239829158 Mail: fnog]-[teor.fis.uc.pt http://nautilus.fis.uc.pt/~fnog/ *) Angel Rubio Dpto. Fisica de Materiales, Facultad de Quimicas U. Pais Vasco, Centro Mixto CSIC-UPV/EHU and Donostia International Physics Center (DIPC) Apdo. 1072, 20018 San Sebastian/Donostia, Spain Phone: +34-943018292 Fax: +34-943015600 Mail: arubio]-[sc.ehu.es http://dipc.ehu.es/arubio/ History: -------- The "School and Workshop on Time-Dependent Density Functional Theory" was first hosted by the Benasque Center for Science, Spain from August 28th to September 12th, 2004. The aim of the school was to introduce theoretical, practical, and numerical aspects of time-dependent density-functional theory (TDDFT) to young graduate students, post-docs and even older scientists that were envisaging a project for which TDDFT would be the tool of choice. The outstanding success of this school led to the organization of a second event, held once more in Benasque, from August 27th to September 11th, 2006. This school is also part of a more general training effort conducted at the European level through the Psi-k Marie Curie Series of Events (Psi-k Training in Computational Nanoscience) and the NANOQUANTA network of Excellence. The school will be followed by an international workshop, where the new developments of TDDFT and Many-Body Techniques for the calculation of excitations will be discussed. Students attending the school will be encouraged to attend the workshop, so they can get in contact with state of the art research in the field. The purpose of the workshop is to bring together leading experts in all these fields with different backgrounds, like density functional, many-body, nuclear physics, quantum chemists, and biophysicists. This will allow the exchange of ideas between the different fields and the creation of links between the traditionally separated communities. We believe that the intense and informal discussion which is possible in this kind of workshops can contribute to the formation of a strong community in the field of TDDFT. Tentative program for the school: -------------------------------- The school will be attended by a maximum of around 40 students, and will last 9 days, with theoretical sessions (mostly) in the mornings and practical (tutorial) sessions in the afternoons. The theoretical sessions will consist of four lectures lasting for 45m each (including discussions). The practical sessions will last for 3 hours and a computer will be allocated for every two students. This will allow the students to have some time every day for studying and talking to the teachers. The program of the school starts with basic TDDFT, then continues with more complex theoretical and numerical aspects of TDDFT, and will end with an outline of some of its many applications. Basic knowledge on ground state DFT calculations is required. Also during the school we will address other approaches to describe excite state properties based on either many-body perturbation theory or quantum-chemistry schemes. The preliminary program is: 31/8 a: Registration 1/9 m: TDDFT (2 x 45m, T) Overview of spectroscopies (45m, T) Many-Body - GW (45m, T) a: Introduction to the practical classes Introduction to the codes 2/9 m: Overview of spectroscopies (45m, T) TDDFT (45m, T) Many-Body - GW (45m, T) Many-Body - BSE (45m, T) a: Quantum Dots I (3h, P) 3/9 m: TDDFT (45m, T) Overview of spectroscopies (45m, T) Propagation schemes (45m, T) Many-Body - BSE (45m, T) a: Quantum Dots II (3h, P) 4/9 m: Advanced TDDFT (45m, T) Models for time-dependent phenomena (45m, T) Overview of spectroscopies (45m, T) TDDFT as a tool in chemistry (45m, T) a: Quantum Dots III (3h, T) 5/9 : Free day 6/9 m: TDDFT as a tool in chemistry (45m, T) Models for time-dependent phenomena (45m, T) Advanced TDDFT (45m, T) Current DFT (45m, T) a: OCTOPUS I (3h, P) 7/9 m: TDDFT as a tool in chemistry (45m, T) Optimal control theory (45m, T) Current DFT (45m, T) Models for time-dependent phenomena (45m, T) a: OCTOPUS II (3h, P) 8/9 m: TDDFT vs. Many-Body (45m, T) TDDFT as a tool in chemistry (45m, T) TDDFT as a tool in biophysics (45m, T) Advanced TDDFT (45m, T) a: ABINIT+SELF I (3h, P) 9/9 m: TDDFT vs. Many-Body (45m, T) Models for time-dependent phenomena (45m, T) TDDFT as a tool in biophysics (45m, T) Current DFT (45m, T) a: ABINIT+SELF II (3h, P) Final Remarks 10/9 : Free day During the school we will incentive a close and informal contact between the students and the teachers. Furthermore, the students will be stimulated to talk about their current research activities and future interests. We feel that this is an important point, since young scientists should be involved in the building up of a strong community. The preliminary program of the workshop is: ------------------------------------------- The 4 day workshop will start September 10, 2008 in the afternoon and will end September 14 in the morning. It will include both invited talks on key aspects of TDDFT (45m each), contributed talks (30m) and a poster session. The tentative We plan an informal workshop with sufficient time for discussions. The informal character of the talks will be encouraged and presentations which are partly tutorial, given the mixed character of the audience, are most welcome. The time for each talk will be divided into 75% for the presentation plus 25% discussion of discussion. Speakers will be encouraged to divide their available time into two separate parts if their topic falls under more than one heading. We will select some posters from the young researchers participating in the workshop to be presented as oral communications. The update list of invited speakers and teachers can be found at http://benasque.ecm.ub.es/2008tddft/2008tddft.htm Location/Timing --------------- We plan to organize this event at the ``Benasque Center for Science'', Benasque, Spain, from August 31, 2008 to September 14, 2008. Benasque is a beautiful town in the heart of the Pyrenees. The school will take place from August 31 (Day 0 - arrival of students for the school) to September 10, and the workshop will start September 10 (arrival of participants to the workshop) and finish on September 14 (departure of all participants). See http://benasque.ecm.ub.es/. Participants ------------ The call for participation will be mainly directed to students and scientists specialized on computational physics, quantum chemistry and biophysics. We will limit the number of students to the school to 40 and participants to the workshop to less than 100, in order to ensure a maximum interaction between all the scientists participating. Attendance of graduate students and postdocs will be strongly encouraged through the inclusion of short contributed talks and a poster session. Furthermore, we will award to PhD students who present an outstanding poster short oral presentations. Carsten A. Ullrich, Associate Professor Director of Graduate Studies Department of Physics & Astronomy University of Missouri Columbia, MO 65211 Phone: (573) 882-2467, Fax: (573) 882-4195 e-mail: ullrichc]-[missouri.edu http://web.missouri.edu/~ullrichc Office: 424 Physics From owner-chemistry@ccl.net Wed Feb 13 23:14:01 2008 From: "Daniela Dogaru danutzadb77^yahoo.com" To: CCL Subject: CCL:G: Freezing atoms in MM layer for ONIOM Message-Id: <-36287-080213115044-18933-lugRv80TyoU0bQf4CcEi8g%server.ccl.net> X-Original-From: Daniela Dogaru Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Wed, 13 Feb 2008 07:50:33 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Daniela Dogaru [danutzadb77]~[yahoo.com] Need to have at least 3 QM atoms frozen Error termination via Lnk1e in ...... Take care! Daniela --- "richard j hart ric_hart:hotmail.com" wrote: > > Sent to CCL by: "richard j hart" > [ric_hart.:.hotmail.com] > Hello, > > I am trying to optimize one small part of an enzyme > (QM layer) while keeping the > surrounding amino acids as a fixed force field (MM > layer). Ultimately, I will > want to get out hyperfine couplings. > > I have fixed the atoms in the molecule specification > using -1 in place of the > zero. (I also tried -2). e.g.: > > C-C_R -1 -3.06092 -7.01089 > 6.42213 M > > My route section: > > # opt=loose oniom(b3lyp/6-31g(d):uff=qeq) nosymm > geom=connectivity scf > =conver=6 > > My error message: > > Eigenvalues --- > 1000.000001000.000001000.000001000.000001000.00000 > Eigenvalues --- > 1000.000001000.000001000.000001000.000001000.00000 > Eigenvalues --- 1000.00000 > RFO could not converge Lambda in 999 iterations. > Linear search not attempted -- first point. > Steepest descent instead of Quadratic search. > Maximum step size ( 0.300) exceeded in Quadratic > search. > -- Step size scaled by 0.013 > Iteration 1 RMS(Cart)= 0.18075693 RMS(Int)= > 0.01388409 > Iteration 2 RMS(Cart)= 0.14954421 RMS(Int)= > 0.00504281 > Iteration 3 RMS(Cart)= 0.00899985 RMS(Int)= > 0.00064957 > Iteration 4 RMS(Cart)= 0.00009705 RMS(Int)= > 0.00064921 > Iteration 5 RMS(Cart)= 0.00000000 RMS(Int)= > 0.00064921 > Need to have at least 3 QM atoms frozen > Error termination via Lnk1e in > /software/horace/applications/gaussian03/g03/l103.exe > at Sun Feb 10 09:14:01 > 2008. > Job cpu time: 0 days 0 hours 13 minutes 3.4 > seconds. > File lengths (MBytes): RWF= 376 Int= 0 > D2E= 0 Chk= 36 Scr= > 8 > > Thank you for your help, > Regards, > Richard Hart (ric_hart[A]hotmail.com) > > > > -= 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 > look up the X-Original-From: line in the mail > header.> > E-mail to administrators: CHEMISTRY-REQUEST]-[ccl.net > or use> > Before posting, check wait time at: > http://www.ccl.net> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: > ccl, Password: search) > > If your mail bounces from CCL with 5.7.1 error, > check:> > RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/ > > > ____________________________________________________________________________________ Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping