From chemistry-request@ccl.net Tue Jul 28 08:34:43 1992 Date: Mon, 27 Jul 92 23:10:25 EDT From: m10!frisch@uunet.UU.NET (Michael Frisch) Subject: Re: CASSCF orbitals assignment. To: chemistry@ccl.net Status: R I am trying to perform CASSCF calculations on the singlet of a cyclic cation, C6NH6 (+1) using the 3-21G basis set. Gaussian 90 and/or 92 is the program of choice. The active space we want to define includes the six pi electrons in the six pi and pi* orbitals plus the empty p orbital on the nitrogen. I plan to do both single points and geometry optimizations. I have already done the RHF/3-21G optimization and an MP2/3-21G//RHF/3-21G single point calculations. Analysis of the Mulliken population at the RHF/3-21G level suggests that the occupied orbitals of interest are 20, 22, and 24(HOMO), and the virtual orbitals are 25, 26, 29, and 30. These results were confirmed visually using the AVS Chemistry Viewer. The manual for GAUSSIAN 90 suggests performing a single point calculation using the flag GUESS=ONLY in order to determine the proper pi orbitals (in this case, seven (7) orbitals, three occupied and four virtual) to be included in the calculation. This GUESS=ONLY run using CASSCF suggested that the occupied pi orbitals that should be included are 15, 18 and 23(HOMO-1); the virtual orbitals 27, 32, 36, and 41 also contained significant p or pi contributions and would complete the active space. Since I don't have any experience with these type of calculations, I would like to know if I am overlooking something that should be considered, included, omitted,...? and to know which approach is more correct for determination of the proper orbitals of the CASSCF calculation, i.e those from the RHF/3-21G optimization or the CAS(6,7)/RHF GUESS=ONLY run. Joseph Bitar Graduate Student, University of Toledo. Chemistry Dept. e-mail: jbitar@uoft02.utoledo.edu The numbers of the orbitals you want depend on which orbitals you're talking about. The orbitals from the initial guess aren't the same as the converged ones from an SCF calculation, and the order of symmetry types of the orbitals need not be the same, either. If you're going to start from the converged SCF orbitals, that is, use GUESS=(READ,ALTER), then specify the numbers of the orbitals from the previous SCF calculation. These would also be printed out if you do GUESS=(READ,ONLY) in a separate job step (good if you don't have the original output but do have the checkpoint file). If you're going to start from the orbitals generated by the initial guess -- using GUESS=ALTER without READ -- then use the numbers of the initial guess orbitals print by GUESS=ONLY. Mike Frisch ------- --- Administrivia: The rest of this message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Tue Jul 28 10:37:10 1992 Date: Tue, 28 Jul 92 07:50:21 EDT From: SC18000 To: Subject: RE:AVS CHEM Viewer Status: R Dear Netters, How does one get the AVS Chemistry Viewer? Thanx, Ken Fountain (sc18@NEMOMUS) --- Administrivia: The rest of this message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Tue Jul 28 11:36:48 1992 From: Mark Forster Date: Tue, 28 Jul 92 13:30:53 BST To: CHEMISTRY Status: R Subject: MGS Autumn meeting. Molecular Graphics Society Autumn meeting. On the subject of 'Entropy and Solvation'. Brasenose College, University of Oxford, Oxford, UK. September 17th and 18th 1992. The Molecular Graphics Society will be holding an Autumn meeting on the topic of entropy and solvation effects in molecular modelling and computational chemistry. The meeting will be held in the pleasant surroundings of Brasenose College Oxford, with lectures taking place in the physical chemistry laboratory. The invited speakers for the meeting are Bill Jorgensen (Yale University), Molecular recognition in organic and biomolecular systems. Barry Honig, (Columbia University), Electrostatic and hydrophobic contributions to solvation free energies: application to binding and macromolecular stability. Anders Wallqvist (University of Lund), Hydrophobic aggregation in aqueous systems, Mike Frisch (Lorentzian Inc), Incorporation of solvent effects into electronic structure calculations. James Caldwell (University of California, San Francisco), Non additive effects on the structure and energetics of water, methanol and N-methylacetamide. Chris Reynolds (University of Essex), A conformationally transferable electrostatic model for calculating hydration free energies. Contributed presentations will be given by Ian Hillier (University of Manchester), Tautomer equilibria in heterocycles in aqueous solution: a test of MD and continuum models of solvation. Liem Dang (Pacific Northwest Laboratories), Molecular dynamics simulations of ionic clusters and ionic solutions. Andrew Brass (University of Manchester), Computer simulations of solvation of O- and N-linked glycopeptide conformation and flexibility. Barry Hardy (National Institute of Health), Molecular modelling of the solution structure of oligosaccharides. Hagai Meirovitch (Biosym Technologies), Computer simulation of the entropy of polypeptides using the local states method: Application to cyclo-(Ala-Pro-DPhe)2 in vacuum and the crystal. Andrew Leach (University of Southampton), Conformational entropy and solvation in ligand design. Julia Goodfellow (Birkbeck College, London University), Solvent hydrogen bonding and hydrophobic hydration in proteins. Rebecca Wade (European Molecular Biology Laboratory), Prediction of water binding sites on proteins by Neural Networks. Poster contributions. Researchers wishing to present a poster may submit an abstract for consideration up until September 1st 1992 to the organisers: Mark Forster, Howard Broughton, NIBSC, Merck Sharp Dohme, Blanche Lane, South Mimms, Terlings Park, Harlow, Herts. EN6 3QG. Essex CM20 2QR. tel (0707) 55753 (0279) 440500 fax (0707) 46730 (0279) 440390 e-mail: forster@uk.ac.nibsc.comp hbro@merck.com Communications with the organisers that are likely to be received in the first 3 weeks of August should be sent to Howard Broughton. Meeting fees / Application form / Closing date. The meeting registration fee will be 70 pounds ($130 US) for MGS members, 95 pounds ($175US) for non MGS members and 35 pounds ($65US) for students. The registration closing date will be Monday September 7th. Accomodation in Brasenose College is limited and early booking is advised. College Accomodation will be allocated on a first-come first-served basis. Accomodation in the college will be a further 70 pounds ($130 US). Cheques should be made payable to the 'Molecular Graphics Society' and drawn in pounds sterling or US dollars only. The accomodation fee includes a single room in Brasenose College on the nights of Wednesday 16th and thursday 17th, all meals on Thursday as well as breakfast and lunch on Friday. A limited number of college rooms with private bathrooms can be made available at an extra charge. ------------------------------------------------------------------------ Meeting application form. Molecular Graphics Society Autumn meeting: Sept. 17&18 1992. I enclose the MGS member registration fee 70.00 pounds / $130 US [ ] I enclose the non MGS registration fee of 95.00 pounds / $175 US [ ] I enclose the student registration fee of 35.00 pounds / $65 US [ ] I enclose the accomodation fee of 70.00 pounds / $130 US [ ] Please send me a map/directions to Brasenose College, I enclose a stamped self addressed envelope. [ ] Specify any special requirements (diet etc). Name: Address: Phone: FAX: E-mail: Please provide a phone/FAX/e-mail contact in case of unforseen difficulties. --- Administrivia: The rest of this message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From jkl@ccl.net Tue Jul 28 12:19:27 1992 Date: Tue, 28 Jul 1992 12:19:21 -0400 From: jkl@ccl.net To: chemistry@ccl.net Subject: Re: Annotated PDB File List Status: R Thanks to Laura Walsh: = ---------- Begin Forwarded Message ---------- = Date: Tue, 28 Jul 92 09:59:34 -0500 = From: lwalsh@nemo.life.uiuc.edu (Laura L. Walsh) = To: jkl@ccl.net = Subject: Annotated PDB File = = A new version of the annotated file has been deposited in the pub = directory. This version includes the Apr92 release as well as = the pre-release files. It also includes homology information = obtained using BLAST (Altschul, 1990). Laura = = Laura Lynn Walsh (lwalsh@nemo.life.uiuc.edu) (217) 244-2894 = Beckman Inst., Univ. of IL * 405 N. Mathews Ave. * Urbana, IL 61801, USA ----------- End Forwarded Message ----------- As usual, you can get it by ftp or E-mail. It is circa 136 kBytes. For ftp users: %ftp www.ccl.net (or ftp 128.146.36.48) Login: anonymous Password: Your_E-mail_address ftp> cd pub/chemistry/pdbdoc ftp> ascii ftp> get pdb_file_list ftp> quit You can also get it by e-mail when you do not have ftp connection. However, since the file is larger than 100kB (many mailers do not like messages larger than 100kB), it was split in two parts. Send a two-line message: send ./pdbdoc/pdb_file_list.p1 from chemistry send ./pdbdoc/pdb_file_list.p2 from chemistry to OSCPOST@ccl.net or OSCPOST@OHSTPY.BITNET and the file will be automatically delivered to your mailbox. Thanks again to Laura Walsh for this valuable contribution. Jan jkl@ccl.net From chemistry-request@ccl.net Tue Jul 28 13:40:04 1992 Date: Tue, 28 Jul 92 12:02:29 -0400 From: jas@medinah.atc.ucarb.com (Jack Smith) To: SC18%NEMOMUS.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU, chemistry@ccl.net Subject: RE:AVS CHEM Viewer Status: R AVS ChemViewer is available from MSI (a.k.a. Polygen/Molecular Simulations, Inc)either as just the ChemViewer module or bundled with AVS. Jack Smith --- Administrivia: The rest of this message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Tue Jul 28 18:18:50 1992 Date: Tue, 28 Jul 92 12:45:45 -0600 From: ANDREW D. FANT Status: R Hello, This may seem a request for a dinosaur, but I am looking for a program that can do simple HMO calculations and that has a graphical interface. I have seen a program to do this on the Macintosh, but it isn't availible for FTP to the best of my knowledge, nor do I have access to a mac at this point. If anyone knows of where such a program for IBM or X could be obtained via anonymous FTP, I would be grateful for a pointer to the site. Thanks in Advance, Andrew Fant u5949@cray2.plk.af.mil .sig wanted to lease --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Tue Jul 28 19:07:43 1992 Date: Tue, 28 Jul 92 19:16:39 GMT From: jpj@lotus.medicine.rochester.edu (Jeffrey P. Jones) To: CHEMISTRY@ccl.net Subject: MOBOSOL Status: R Hello: We have been offering AMSOL incorporated into MOPAC via anonymous ftp. We now offer a modified version that gives you the option to perform full SCF derivatives and we have incorporated the NBO program of Glendening, Reed and Weinhold into the package. We have found NBO to be almost as useful with MOPAC as with G92. NBO appears to work with the solvation calculations except we have had some problems in very specific cases when we perform a NBO-AMSOL(fullSCF)-UHF calculation. The file is now called MOBOSOL.tar.Z and can be obtained via anonymous ftp >from crocus.rochester.medicine.edu in the jones directory. This file includes manuals for AMSOL, MOPAC and a short manual detailing how to use the modifications. ############################################################################## Surface Mail Jeffrey P. Jones U. of Rochester Department of Pharmacology 601 Elmwood Ave. Rochester, NY 14642 internet jpj@lotus.medicine.rochester.edu %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Tue Jul 28 19:16:08 1992 Date: Tue, 28 Jul 1992 16:55 EST From: CHIRLIAN@CC.BRYNMAWR.EDU Subject: MacroModel force field additions To: chemistry@ccl.net Status: R I'm trying to add MM2 parameters for oximes to the mm2 force field in MacroModel. I've been able to add the N-O bond stretch without any problem; however I have been having problems with the torsion parameters, specifically C2-N2-O3-Lp and H2-O3-N2-C2. I've been using the parameters already included as a model. I'd appreciate any pointers anyone might have as to what the problem might be. The parameters in question are (all on one line, I shortened the lines for this): 4 H2 - O3 - N2 - C2 2.0000 4.4500 -2.0000 0000 0000 0000 0000 A 3 C(sp2)=N(sp2)-O(sp3)-H1 4 C2 - N2 - O3 - Lp 0.0000 0.0000 0.0000 0000 0000 0000 0000 A d C(sp2)=N(sp2)-O(sp3)-Lp If anyone has done this and can point out my mistake I'd be most appreciative. Thanks in advance. Lisa Chirlian Bryn Mawr College (215)526-5108 --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Tue Jul 28 20:30:29 1992 Date: Tue, 28 JUL 92 15:37:21 From: br1@inel.gov To: chemistry@ccl.net Subject: MNDO metals Status: R Help. I have embarked on a study of In embrittlement of several metals including Au, Ag, Cu, Ni, Pt, and Pd. I told my customer that I could give him some interesting MNDO or MINDO3 surfaces of 13 and 19 atom clusters. It seems simple enough but as yet I have been unable to get a converged wave function. I have tried a number of tricks that have proven successful in the past for SCF wave functions, but to no avail. Seemingly everything I try gives me a divide by zero error. Does anyone out there have any suggestions. Please write to: BR1@INEL.GOV --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net ---