From owner-chemistry@ccl.net Mon Feb 4 08:17:01 2008 From: "Jens Spanget-Larsen spanget,,ruc.dk" To: CCL Subject: CCL: ZINO/s ZINDO/1 Message-Id: <-36214-080204065837-15255-7rtQ2Gr4JTnCcVrw8RVEAg^^server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 04 Feb 2008 12:05:01 +0100 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget]^[ruc.dk] Dear Naser, you may get additional information in the HyperChem log file, such as eigenvalues and eigenvectors of the CI secular equation by setting the parameter "QuantumPrintLevel". Depending on your version of HyperChem, you may set the appropriate value of the parameter (say, QuantumPrintLevel = 6) in the chem.ini file, or select the print level in the log file menu. Look for details in the HyperChem Reference Manual. Yours, Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget/./ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ Naser Eltaher Eltayeb nasertaha90*yahoo.co.uk wrote: > Sent to CCL by: "Naser Eltaher Eltayeb" [nasertaha90-#-yahoo.co.uk] > Dear All > > I am tring to calculate UV transitions using ZINDO/S in Hyperchem, I get results have good agreement with experimental, but the problem ZINO/S in Hyperchem doesn't assign transtions with which molecular orbitals. > > Then I used ZINDO/1 in hyperchem, this time the agreement with experimental is bad, but ZINO/1 assign the transition with molecular orbitals. > > Is there anyway to get good result with assignment of molecular orbitals. > > below some of output files of ZINDO/s and ZINDO/1 > ZINDO/s > > > 1 (Transition) Excitation Energy 42119.0 nm > 237.4 1/cm > > 1 -> 2 Spin S 1.00 > State Dipole 7.9712 > Oscillator Strength 0.0000 > > State Dipole Components -6.9706 -3.6308 1.3300 > Transition Dipole Components -0.1342 -0.0842 0.1180 > > > > > ZINO/1 > 1 (Transition) Excitation Energy 321.3 nm > 31120.3 1/cm > > 1 -> 2 Spin S 1.00 > State Dipole 7.0964 > Oscillator Strength 0.0000 > > State Dipole Components -6.5340 -2.7659 0.1265 > Transition Dipole Components -0.0000 -0.0000 0.0000 > > Spin Up : Occ. MO --> Unocc. MO Coefficients > ------------------------------------------------- > 75 --> 77 -0.599987 > > Spin Down: Occ. MO --> Unocc. MO Coefficients > ------------------------------------------------- > 75 --> 77 -0.599987 > > Thank you > Naser Eltaher > Universiti Sains Malaysia > Penang 11800> > > From owner-chemistry@ccl.net Mon Feb 4 09:27:01 2008 From: "javad beheshtian computational.center],[gmail.com" To: CCL Subject: CCL:G: NMR caculation Message-Id: <-36215-080204042741-4616-0ty7gEKGZISni6/EAg+nZw-*-server.ccl.net> X-Original-From: "javad beheshtian" Date: Mon, 4 Feb 2008 04:27:37 -0500 Sent to CCL by: "javad beheshtian" [computational.center .. gmail.com] Dear CCL Subscribers, I run a set of similar Gaussian jobs (NMR calculations for system consisting of 61 atoms). All this calculations have been finished with the "Normal Termination". However, I am not able to get "Normal Termination" if I slightly change the system. I just remove some atoms and add new ones (so that the totals size of the system increases to 64 atoms). In the "problematic" case I have no error message. Gaussian just stops. In the and of the output file I find the following: **** Warning!!: The largest alpha MO coefficient is 0.12682133D+03 Differentiating once with respect to magnetic field using GIAOs. Electric field/nuclear overlap derivatives assumed to be zero. Symmetry not used in FoFDir. MinBra= 0 MaxBra= 2 Meth= 1. IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0 JSym2E=0. FoFCou: FMM=T IPFlag= 0 FMFlag= 100000 FMFlg1= 8193 NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T. Symmetry not used in FoFCou. FMM levels: 10 Number of levels for PrismC: 9 PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. There are 3 degrees of freedom in the 1st order CPHF. 3 vectors were produced by pass 0. AX will form 3 AO Fock derivatives at one time. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. 3 vectors were produced by pass 1. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. 3 vectors were produced by pass 2. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4 . . . 1 vectors were produced by pass142. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. 1 vectors were produced by pass143. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. also input file is : %mem=1800Mb %nproc=4 %chk=/root/work/w1b/50-1wBnmr.chk %rwf=/home/student/tmp/s1,245mw,/home/student/tmp/s2,245mw,/home/student/tmp/s3,245mw,/home/student/tmp/s4,245mw,/home/student/tmp/s5,245mw # b3lyp/6-31+g* prop=efg nmr pop=nbo maxdisk=50GB 0 1 N -0.820146 5.162667 0.594445 H -1.378215 5.976629 0.351741 N -0.815997 2.952748 1.757583 B -1.532634 4.157957 1.383629 N -2.992371 4.146667 1.486120 H -3.436900 5.014950 1.200732 N -2.873310 1.681326 1.102722 B -3.468464 2.962562 0.770443 N -4.218302 3.065244 -0.481126 . . . Does any body know what Gaussian try to do here and why it cannot finish that? Thank you in advance, Javad Beheshtian computational.center===gmail.com From owner-chemistry@ccl.net Mon Feb 4 10:02:01 2008 From: "Francisco Munoz dqufmi0 : uib.es" To: CCL Subject: CCL: ESPA2008 Message-Id: <-36216-080204092106-17291-RWGqdBdHrXaTstnwMvJgTQ_-_server.ccl.net> X-Original-From: "Francisco Munoz" Date: Mon, 4 Feb 2008 09:21:02 -0500 Sent to CCL by: "Francisco Munoz" [dqufmi0[a]uib.es] Sincere apologies for cross posting Please circulate the announcement to your colleagues SECOND CIRCULAR ELECTRONIC STRUCTURE: PRINCIPLES AND APPLICATIONS (ESPA 2008) Palma de Mallorca, Spain September 2-5, 2008 The ESPA2008 is pleased to announce that registration and abstract submission are now open. The deadline for abstract submission and early-bird registration is May 31 2008. The Themes of the Congress are: 1) Theoretical Chemistry: Methodology, ab initio and correlated ab initio methods. Theoretical thermochemistry. Spectroscopy. 2) Structure and Reactivity: Structure. Chemical Reactivity. Catalysis. Nanoparticles. Surfaces. Condensed phases. 3) Biological Systems: Methodology. Drug Design. Enzymes. Catalysis. QSAR. Bioinformatics. The following scientists have accepted to present a plenary lecture (in alphabetic order): - Paolo Carloni. Scuola Internazionali Superiore di Estudi Avanzati, Trieste (Italy) - Christopher J. Cramer. University of Minnesota, Minneapolis (USA). - Berta Fernndez. University of Santiago de Compostela (Spain). - Victor Guallar. Barcelona Supercomputing Center (Spain). - Marco Antonio Nascimento. University Federal do Rio de Janeiro (Brazil). - Juan J. Novoa. University of Barcelona (Spain). - Maria Joao Ramos. University of Porto (Portugal). - Manuel Ruiz-Lpez. University Henry Poincar- Nancy 1 (France). - Gustavo E. Scuseria. Rice University, Houston (USA). - Dimas Surez. University of Oviedo (Spain). - Orlando Tapia. Uppsala University (Sweden). - Iaki Tun. University of Valencia (Spain). - Antonio J.C. Varandas. University of Coimbra (Portugal). - Tom Ziegler. University of Calgary (Canada) The registration price (regular fee: 325.00 , student fee: 180.00 ) includes all documentation, coffee breaks, lunches, Welcome Reception, Closing Banquet and all social activities. Visit the conference website at http://www.espa2008.org for more information, including details for online registration and abstracts submission. We hope to see you soon in Mallorca. Best regards, The organizing committee From owner-chemistry@ccl.net Mon Feb 4 12:18:01 2008 From: "=?ISO-8859-1?Q?L=E9on_Salgado?= leon.salgado _ gmail.com" To: CCL Subject: CCL: How to perform a protein MD in Gromacs, with solvent Message-Id: <-36217-080204072846-19451-Rr2nBPXEEHweJ14IE665pQ-x-server.ccl.net> X-Original-From: =?ISO-8859-1?Q?L=E9on_Salgado?= Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 04 Feb 2008 11:33:00 +0000 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?L=E9on_Salgado?= [leon.salgado:_:gmail.com] Bruno Why don't you post your question to gmx mailing list? You have there a big community ready to help, including beginners. But hey, b4 asking something, search mailing list first for similar doubts. And above all, read the manual and available tutorials. If you are having crashes right from the beginning, then your system is not ready to be simulated ;-) Never forget that MD systems must be handled gently, starting by minimizing the solvent while restraining the protein, and later all the system without coordinate restraining. Next you need an equilibration b4 moving to the production run. Only then, you will be able to analyze solvent molecules near the protein. But that's another story. Cheers, L.s. Bruno Andrade bandradefsa/ayahoo.com.br wrote: > Sent to CCL by: "Bruno Andrade" [bandradefsa-$-yahoo.com.br] > Hi there, > > I'm currently using gromacs program (as beginer), and I had some crashes in the calculations. I am trying to perform a MD using water as solvent, but in gromacs I could not found any option to use the solvent effect directly binded to the protein target, I just found the genbox option and using it, the program retuns me a crash message (system colapses with box, or something like "your system is probably not equilibrated"). > > Ps.: The system converges on the energy minimization, using option 6 force field. > > How can I perform it better? > > Thank you for you help. > > Bruno Andrade. > > From owner-chemistry@ccl.net Mon Feb 4 12:53:01 2008 From: "Pascal Boulet pascal.boulet+/-univ-provence.fr" To: CCL Subject: CCL: ZINO/s ZINDO/1 Message-Id: <-36218-080204024517-30370-bgj50NKoteMqZ8yukoU1Tg ~~ server.ccl.net> X-Original-From: Pascal Boulet Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 04 Feb 2008 08:45:03 +0100 MIME-Version: 1.0 Sent to CCL by: Pascal Boulet [pascal.boulet||univ-provence.fr] Hello, My feeling when looking at your results is that there is probably a mistake in the units with ZINDO/s output: 42119 nm should be 42119 cm-1 (which gives 237.4 nm and not 237.4 cm-1). The difference with 31120 cm-1 is large, but perhaps that you can find some correlations. If you want both transitions and OM with the same methodology, I suggest you to try TDDFT. I hope this help, Best Regards Pascal Boulet Naser Eltaher Eltayeb nasertaha90*yahoo.co.uk wrote: > Sent to CCL by: "Naser Eltaher Eltayeb" [nasertaha90-#-yahoo.co.uk] > Dear All > > I am tring to calculate UV transitions using ZINDO/S in Hyperchem, I get results have good agreement with experimental, but the problem ZINO/S in Hyperchem doesn't assign transtions with which molecular orbitals. > > Then I used ZINDO/1 in hyperchem, this time the agreement with experimental is bad, but ZINO/1 assign the transition with molecular orbitals. > > Is there anyway to get good result with assignment of molecular orbitals. > > below some of output files of ZINDO/s and ZINDO/1 > ZINDO/s > > > 1 (Transition) Excitation Energy 42119.0 nm > 237.4 1/cm > > 1 -> 2 Spin S 1.00 > State Dipole 7.9712 > Oscillator Strength 0.0000 > > State Dipole Components -6.9706 -3.6308 1.3300 > Transition Dipole Components -0.1342 -0.0842 0.1180 > > > > > ZINO/1 > 1 (Transition) Excitation Energy 321.3 nm > 31120.3 1/cm > > 1 -> 2 Spin S 1.00 > State Dipole 7.0964 > Oscillator Strength 0.0000 > > State Dipole Components -6.5340 -2.7659 0.1265 > Transition Dipole Components -0.0000 -0.0000 0.0000 > > Spin Up : Occ. MO --> Unocc. MO Coefficients > ------------------------------------------------- > 75 --> 77 -0.599987 > > Spin Down: Occ. MO --> Unocc. MO Coefficients > ------------------------------------------------- > 75 --> 77 -0.599987 > > Thank you > Naser Eltaher > Universiti Sains Malaysia > Penang 11800> > > -- Dr. Pascal Boulet, Computational Chemist University of Aix-Marseille I, II and III, and CNRS UMR6264: Laboratoire Chimie Provence Centre Saint-Jerome, case MADIREL F-13397 MARSEILLE Cedex 20, France Tel. +33 (0) 491 63 71 17 Fax. +33 (0) 491 63 71 11 courriel: pascal.boulet-$-univ-provence.fr http://www.lc-provence.fr http://allos.up.univ-mrs.fr/boulet From owner-chemistry@ccl.net Mon Feb 4 13:28:01 2008 From: "Pascal Boulet pascal.boulet%%univ-provence.fr" To: CCL Subject: CCL:G: pb to converge wavefunction with gaussian Message-Id: <-36219-080203112453-16067-hfN7HZ/8nwubscc8pMREtA||server.ccl.net> X-Original-From: Pascal Boulet Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sun, 03 Feb 2008 16:25:13 +0100 MIME-Version: 1.0 Sent to CCL by: Pascal Boulet [pascal.boulet]~[univ-provence.fr] Dear CCL users, I am trying to optimize the structure of a cluster of zirconium oxide with gaussian. I just cut a cluster from ZrO2 surface and saturated the cluster with hydrogen atoms. I'm using the Stuttgart pseudopotential for Zr and O. The SCF is not converging. I tried first the default algorithm, then switched to Fermi, then to QC (which failed at some point, for some obscur reasons) and now I'm using the combined keywords: cdiis, novaracc and vshift. Still no convergence. Does anyone know a way to make gaussian converge? Thank you for your help, Regards Pascal -- Dr. Pascal Boulet, Computational Chemist University of Aix-Marseille I, II and III, and CNRS UMR6264: Laboratoire Chimie Provence Centre Saint-Jerome, case MADIREL F-13397 MARSEILLE Cedex 20, France Tel. +33 (0) 491 63 71 17 Fax. +33 (0) 491 63 71 11 courriel: pascal.boulet^_^univ-provence.fr http://www.lc-provence.fr http://allos.up.univ-mrs.fr/boulet From owner-chemistry@ccl.net Mon Feb 4 14:03:00 2008 From: "Lorena Romero lorena.webmaster-#-gmail.com" To: CCL Subject: CCL: Meetings in madrid - summer 2008 Message-Id: <-36220-080204122610-29344-qLfbNN4OCaxhuNP1SAf9nA ~~ server.ccl.net> X-Original-From: "Lorena Romero" Content-Type: multipart/alternative; boundary="----=_Part_5773_12367049.1202142234171" Date: Mon, 4 Feb 2008 12:23:54 -0400 MIME-Version: 1.0 Sent to CCL by: "Lorena Romero" [lorena.webmaster]*[gmail.com] ------=_Part_5773_12367049.1202142234171 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi suscribres, I would like to know any information about meetings on summer 2008 in madrid. I will be there for vacation and I wolud like to assist to a meeting in the field, I am an undergraduate student interesed on computational chemistry. Any information would be apprecciated. Thanks. ------=_Part_5773_12367049.1202142234171 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi suscribres, I would like to know any information about meetings on summer 2008 in madrid.

I will be there for vacation and I wolud like to assist to a meeting in the field, I am an undergraduate student interesed on computational chemistry.

Any information would be apprecciated.

Thanks.


------=_Part_5773_12367049.1202142234171-- From owner-chemistry@ccl.net Mon Feb 4 15:12:01 2008 From: "Debellis Anthony CE US anthony.debellis=-=ciba.com" To: CCL Subject: CCL:G: pb to converge wavefunction with gaussian Message-Id: <-36221-080204150910-14907-rzywyrICdJ8nA2TPGV8t1Q---server.ccl.net> X-Original-From: Debellis Anthony CE US Content-Class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Mon, 4 Feb 2008 14:39:18 -0500 MIME-Version: 1.0 Sent to CCL by: Debellis Anthony CE US [anthony.debellis*ciba.com] Dear Pascal, I assume you are using the SDD basis which places D95V on atoms up to Ar. I would try to converge the SCF using the minimal LanL2MB basis first, followed by guess=3Dread with the larger basis. Regards, Anthony _________________________=20 Dr. Anthony D. DeBellis Research Fellow - Coating Effects Research=20 Ciba Specialty Chemicals Corp.=20 540 White Plains Road=20 Tarrytown, NY 10591=20 USA Phone: 914 785 2949=20 Fax: 914 785 3681=20 E-mail: anthony.debellis!^!cibasc.com=20 Internet: www.ciba.com=20 Sent to CCL by: Pascal Boulet [pascal.boulet]~[univ-provence.fr] Dear CCL users, I am trying to optimize the structure of a cluster of zirconium oxide with gaussian. I just cut a cluster from ZrO2 surface and saturated the cluster with hydrogen atoms. I'm using the Stuttgart pseudopotential for Zr and O. The SCF is not converging. I tried first the default algorithm, then switched to Fermi, then to QC (which failed at some point, for some obscur reasons) and now I'm using the combined keywords: cdiis, novaracc and vshift. Still no convergence. Does anyone know a way to make gaussian converge? Thank you for your help, Regards Pascal -- Dr. Pascal Boulet, Computational Chemist University of Aix-Marseille I, II and III, and CNRS UMR6264: Laboratoire Chimie Provence Centre Saint-Jerome, case MADIREL F-13397 MARSEILLE Cedex 20, France Tel. +33 (0) 491 63 71 17 Fax. +33 (0) 491 63 71 11 courriel: pascal.boulet-,-univ-provence.fr http://www.lc-provence.fr http://allos.up.univ-mrs.fr/boulet -=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 From owner-chemistry@ccl.net Mon Feb 4 15:56:00 2008 From: "kemi oloba ooloba::uh.edu" To: CCL Subject: CCL: NBO error Message-Id: <-36222-080204155132-2575-/U4zO9Z7t+sfBGToymCDgQ.@.server.ccl.net> X-Original-From: "kemi oloba" Date: Mon, 4 Feb 2008 15:51:28 -0500 Sent to CCL by: "kemi oloba" [ooloba[]uh.edu] I am trying to run a NBO job and keep getting this error Subroutine NAOANL could not find a S-type core orbital on atom P 9. ICORE : 2 1 0 0 M : 1 LA : 1 pls can someone help me thanks From owner-chemistry@ccl.net Mon Feb 4 17:15:00 2008 From: "joerg.wegner joerg.wegner..web.de" To: CCL Subject: CCL: License what you want. Open what you want. No comparison? Message-Id: <-36223-080204160932-14749-kjJKlInnLsz39nQr1JHhWg|*|server.ccl.net> X-Original-From: "joerg.wegner" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 4 Feb 2008 21:05:48 +0100 MIME-Version: 1.0 Sent to CCL by: "joerg.wegner" [joerg.wegner a web.de] Dear all, since many other people have already discussed 'free source'/'commercial source' and 'open source'/'closed source' I am quite astonished about the number of misperceptions and the lacking knowledge on both sides. I agree completely with Warren and Egon that people should be very aware of licensing issues, since 'open source' must not mean 'for free'. And I think I have not to name companies following successfully this principle. Beside, I think that every model has its pros and cons. Especially people knowing both sides are very aware of it and should rather look on how to work together than how to separate. I seriously see no benefit in hardened lines on any side, if sides indeed exist? So, stay calm, read some of the previous arguments and discuss this topic constructively. OpenSource]*[Wikipedia http://en.wikipedia.org/wiki/Open_source Article (ej07) Ertl, P. & Jelfs, S. Designing drugs on the Internet? Free web tools and services supporting medicinal chemistry Curr Top Med Chem, 2007, 7, 1491-1501. http://dx.doi.org/10.2174/156802607782194707 D. A. Wheeler, Why Open Source Software / Free Software (OSS/FS, FLOSS, or FOSS)? Look at the Numbers!, Revised as of April 16, 2007 http://www.dwheeler.com/oss_fs_why.html Article(mun06) B. Munos, Can open-source R&D reinvigorate drug research?, Nat. Rev. Drug Dis., 2006, 5, 723-729. http://dx.doi.org/10.1038/nrd2131 Open Source book (in German, business perspective) http://www.opensourcejahrbuch.de/2006/english.html Article (ggwas06) Geldenhuys, W. J.; Gaasch, K. E.; Watson, M.; Allen, D. D. & der Schyf, C. J. V. Optimizing the use of open-source software applications in drug discovery. Drug Discov. Today, 2006, 11, 127-132. http://dx.doi.org/10.1016/S1359-6446(05)03692-5 Article (ghhmrsww06) Guha, R.; Howard, M.; Hutchison, G.; Murray--Rust, P.; Rzepa, H.; Steinbeck, C.; Wegner, J. K. & Willighagen, E. L. The Blue Obelisk--Interoperability in Chemical Informatics J. Chem. Inf. Model., 2006, 46, 991-998. http://dx.doi.org/10.1021/ci050400b CCL discussion 2006 http://server.ccl.net/cgi-bin/ccl/day-index.cgi?2006+02+26 http://server.ccl.net/cgi-bin/ccl/day-index.cgi?2006+02+27 http://server.ccl.net/cgi-bin/ccl/day-index.cgi?2006+02+28 http://server.ccl.net/cgi-bin/ccl/day-index.cgi?2006+03+01 Article (wea05) Weaver, D. C. Build vs. Buy vs. Both Pharmaceutical Discovery, 2005, 42-43. http://www.pharmadd.com/archives/Feb%201%202005/Build%20vs%20Buy%20vs%20Both .pdf Article (del05) DeLano, W. L. The case for open-source software in drug discovery Drug Discovery Today, 2005, 10, 213-217. http://dx.doi.org/10.1016/S1359-6446(04)03363-X Article (del05) DeLano, W. L. The case for open-source software in drug discovery Drug Discovery Today, 2005, 10, 213-217. http://dx.doi.org/10.1016/S1359-6446(04)03364-1 Article (dr03) Dupradeau, F. & Rochette, J. Bugs in computational chemistry software and their consequences: the importance of the source code. J. Mol. Model., 2003, 9, 271-272. http://dx.doi.org/10.1007/s00894-003-0141-1 Cheers, Joerg From owner-chemistry@ccl.net Mon Feb 4 17:49:00 2008 From: "abdeladim guermoune lguermoune!^!hotmail.com" To: CCL Subject: CCL:G: Aim calculation Message-Id: <-36224-080204173516-17550-opjUkrhhwGs+ym2cbMbhrw[a]server.ccl.net> X-Original-From: "abdeladim guermoune" Date: Mon, 4 Feb 2008 17:35:12 -0500 Sent to CCL by: "abdeladim guermoune" [lguermoune!^!hotmail.com] Dear members, Its amazing to see how AIMALL program can generate easily the wfn file from formatted check file (Fchk) without problem usually encountered with Gaussian program.So I get the following results before treating the wfn data by aim2000. Bond ellipticity rho Del**2(rho( r) G V H Fe - B1 0,294 0,069 -0,014 0,023 -0,050 -0,027 Fe - H1 0,123 0,103 0,238 0,098 -0,137 -0,039 B2 - H1 0,391 0,101 -0,018 0,073 -0,151 -0,078 B1 - H2 0,280 0,117 0,156 0,131 -0,223 -0,092 B2 - H2 0,332 0,119 0,119 0,125 -0,220 -0,095 Del**2(rho( r): Laplacian rho : density G : kinetic energy density. V : electronic potential energy H : the electronic density energy B: boron atom ; Fe : iron atom , H : hydrogen. Laplacian is calculated from formula: (-1/4 Del**2(rho( r)) as done in data file Its well known that Laplacian is related to the bond interaction energy by local expression of virial theorem. A positive value of Laplacian shows a depletion of electronic charge along the bond. This is the case in a closed-shell electrostatic interaction. A negative value of Laplacian, on the other hand, indicates that electronic charge is concentrated in the internuclear region. This is the case in an electron-sharing (or covalent) interaction. In this context, we expect to find :If the density is high , Laplacian will be negative.If the density is low , Laplacian will be positive. But as you can see above for the highest values of density correspond positive Laplacian. Can any expert in aim calculations tell me if I m wrong, or really some things is not correct with that file? Best regards; ----------------------------------- GUERMOUNE Abdeladim. University Cadi Ayyad Morocco.