From chemistry-request@server.ccl.net Thu Nov 30 18:02:49 2000 Received: from chemsun.chem.umn.edu (chemsun.chem.umn.edu [128.101.157.2]) by server.ccl.net (8.8.7/8.8.7) with SMTP id SAA26103 for ; Thu, 30 Nov 2000 18:02:49 -0500 Received: (qmail 88825 invoked by uid 1120); 30 Nov 2000 17:02:51 -0600 Date: Thu, 30 Nov 2000 17:02:51 -0600 (CST) From: Lakshmi Devi Kesavan To: "'chemistry@ccl.net'" Subject: CCL: summarzing the responses for Sigma value of Carbon in TMS In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Thanks to all of you who responded to my question. I have enclosed the all the responses I received as a summary below: My question: > I am doing NMR calculations using gaussian98 to calculate the > chemical shift of a molecule. I am using HF/6-31G* level to do the > calculation. I was wondering if I can get the sigma value for the > carbons in TMS from any database on the net or someplace so that I > donot have to calculate them myself again. And it will also be helpful > if someone can point out the availability of any database of NMR > parameters calculated using ab-initio methods. > > I shall summarize the responses. > > Thanking you all in advance, > > Devi Kesavan > ********** Responses: ********** (1) I can tell you this from my own work: the carbon sigma value of TMS at B3LYP/6-311G*//B3LYP/6-311G* is 184.38 From: Joseph W. Bausch ---------------------------------------------------------------------------- (2) please search for NMR-SHARC in the INTERNET or go directly to http://www.quantchem.kuleuven.ac.be/sharc/supplmat/refs_index.html cheers Alk p.s. 1) contributions are welcome 2) a majour update of the NMR-SHARC pages content will be after christmas From: Alk Dransfeld ---------------------------------------------------------------------------- (3) There is virtually no possibility to determine these values experimentally. You have to calculate them (once forever) or get them from a friend, since the chemical shift calculation strongly relies on error compensation, i.e. if you try another basis set, you have to recalculate TMS with that basis set. There is then still the issue of which molecular geometry to use, but it leads to far to discuss this here. cheers, From: +---------------------------------+-------------------------------------+ | Prof. Christoph van Wullen | Tele-Phone (+49) (0)30 314 27870 | | Technische Universitat Sekr. C3 | Tele-Fax (+49) (0)30 314 23727 | | Strasse des 17. Juni 135 | eMail | | D-10623 Berlin, Germany | Christoph.vanWullen@TU-Berlin.De | +---------------------------------+-------------------------------------+ ---------------------------------------------------------------------------- (4) My copy of Exploring Chemistry with Electronic Structure Methods, Second Ed, came with an errata table that gives 199.9853, 449.7802, and 32.5976 for the absolute shielding of C, Si, and H in TMS at the HF/6-31g(d) level. Steve From: ***************************************** Steve Williams F F F Chemistry \ / \ / Appalachian State University Al Al Boone, NC 28608 / \ / \ USA F F F willsd@appstate.edu 828-262-2965 ---------------------------------------------------------------------------- (5) I highly recommend you spectral base at http://www.aist.go.jp/RIODB/SDBS/menu-e.html Best regards, From: Dr. Ilfir R. Ramazanov, Laboratory of Catalytic Synthesis Institute of Petrochemistry and Catalysis, pr. Oktyabrya, 141, Ufa, 450075, Russia. ---------------------------------------------------------------------------- Thankyou all once again. Sincerely, Devi Kesavan Graduate student University of Minnesota From chemistry-request@server.ccl.net Thu Nov 30 17:03:26 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA25845 for ; Thu, 30 Nov 2000 17:03:26 -0500 Received: from oscdesk53.ccl.net (oscdesk53.ccl.net [192.148.249.53]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id RAA09194; Thu, 30 Nov 2000 17:03:24 -0500 (EST) Date: Thu, 30 Nov 2000 17:03:24 -0500 From: Gerald Lushington To: chemistry@ccl.net cc: gerald@ccl.net Subject: Re: CCL:G98 / displacement issue with frozen coordinates In-Reply-To: <06ae01c05b0c$7fd032e0$bbc0e380@qtp.ufl.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi again! No intention of closing down this discussion so quickly if others have points to make, but I thought I'd take a moment and share the three very insightful responses I've gotten so far. Each response addressed different aspects of the problem and in each case proved very helpful. Glad to see you're all so coordinated ;) Jeremy Greenwood confirmed that convergence is slow, but also that it's generally possible to (eventually) achieve. You may wish to refer below to his response for a few constraining tips he suggests. Nicolas Ferre gave a few suggestions as to how to circumvent the strange "Delta X" and "New X" values we were getting. Turns out that using the "NOSYM" keyword straightens this glitch out nicely! Finally, as you have likely seen, Stefan Fau provided a very thoughtful and detailed discussion on the validity of frequency analysis on our constrained system. Have to sit down and think carefully about this, but his suggestions make sense to me on the first pass. Anyway, thanks all! Original question and the three responses appended below. - Gerry ---------------------------------------------------------------------- Gerald H. Lushington Ph: 614-292-6036 Research Specialist Fax: 614-292-7168 OSC / PET-CCM e-mail: gerald@ccl.net 1224 Kinnear Road http://www.arl.hpc.mil/PET/cta/ccm Columbus OH 43212-1163 http://www.asc.hpc.mil/PET/CCM == Original Question ========================================================== Dear all, In working with a colleague on large cluster optimizations of enzyme active site (via G98), I've encountered a problem that seems to be: - part philosophical - part methodological - part bug (?) Anyway, the issue has to do with doing geometry optimizations with some degrees of freedom contrained. In general it's proving necessary to freeze the coordinates for at least a couple of atoms in order to keep the cluster in some sort of shape comparable to the real biosystem. The tradeoff, of course, comes in the fact that forces and displacements will never achieve global minima. Standard protocol seems to be to run the job until these quantities level off to some reasonably converged values. When we apply this strategy we find that force and net displacement eventually level off, but the net displacement remains very high. This brings me to question number 1: 1) If we stop the geometry optimization at a structure whose force and displacement values have leveled, but whose displacement is still high, would any subsequent vibrational analysis be at all physically meaningful? Are there any effective guidelines for this? My first thought on this was that Gaussian would likely decompose both force and displacement as a sum over coordinates. Since the only freezing we do is way out on the perifery of the cluster, while the structural and vibrational information of interest is in the center of the system, maybe we can track the forces and displacements in the central region of interest and feel comfortable about the results when those central contributions are low. So, to try to follow that strategy, we've been refering to a table generated as standard G98 output during the geometry optimization that looks like: Variable Old X -DE/DX Delta X Delta X Delta X New X (Linear) (Quad) (Total) X1 -2.50100 -0.00465 0.00000 0.00000 2.50100 0.00000 Y1 8.90656 0.01749 0.00000 0.00000 -8.90656 0.00000 Z1 -8.10547 -0.01647 0.00000 0.00000 8.10547 0.00000 X11 -3.32922 0.00421 0.00000 0.00000 2.50100 -0.82822 Y11 -9.47808 -0.00542 0.00000 0.00000 -8.90656 -18.38465 Z11 -1.01768 -0.00913 0.00000 0.00000 8.10547 7.08779 X38 3.49152 0.00310 0.00000 0.00000 2.50100 5.99252 Y38 14.83066 0.00184 0.00000 0.00000 -8.90656 5.92410 Z38 -5.24649 -0.00415 0.00000 0.00000 8.10547 2.85898 X48 -1.96597 0.00535 0.00000 0.00000 2.50100 0.53502 Y48 -4.25077 -0.01552 0.00000 0.00000 -8.90656 -13.15733 Z48 9.58721 0.02164 0.00000 0.00000 8.10547 17.69267 X50 1.54048 -0.00800 0.00000 0.00000 2.50100 4.04148 Y50 -8.97461 0.00161 0.00000 0.00000 -8.90656 -17.88117 Z50 5.17857 0.00810 0.00000 0.00000 8.10547 13.28404 R1 2.84387 0.01822 0.00000 0.00000 0.00000 2.84388 R2 2.02201 0.01493 0.00000 0.00000 0.00000 2.02201 R3 2.02201 0.01403 0.00000 0.00000 0.00000 2.02201 R4 2.02201 0.01490 0.00000 0.00000 0.00000 2.02201 R5 2.81303 -0.01054 0.00000 -0.01044 -0.00995 2.80307 R6 2.10327 -0.02056 0.00000 -0.01706 -0.01706 2.08621 R7 2.10327 -0.01967 0.00000 -0.01633 -0.01633 2.08694 R8 2.60262 -0.00578 0.00000 -0.00448 -0.00457 2.59805 R9 2.55751 -0.00018 0.00000 -0.00230 -0.00185 2.55566 .. .. .. NOTE: in the above, the first bunch of coordinates (X1-R4 inclusive) are all frozen. R5 onwards (many coordinates not shown) are freely varying. Anyway, in the variable coordinates toward the bottom, it seems that the "DE/DX" is a real force, the "Delta X" are real displacements, and the "Old X" and "New X" are exactly as they sound -- initial and final values for the coordinate. However: 2) What's going on with these the "Delta X" and "New X" values for the frozen coordinates?? They're frozen (and really do not vary during the optimization) so shouldn't "New X" = "Old X" regardless of nonzero forces and predicted displacements? 3) Furthermore, the values written in "Delta X (Total)" look extremely fishy to me? They're all either "2.50100", "-8.90656", "8.10547" or "0.00000"! Is this a bug, and if so, might it be corrupting the value given for net displacement at the end of each geometry step? Anyway, this may be a complex issue, but any insight you may have would be greatly appreciated! - Gerry P.S. I did drop Gaussian Inc. a note on this several weeks ago -- I guess it's somewhere in their queue. == Response #1: Jeremy Greenwood ==================== I am doing the same kind of thing at the moment. I *have* been able to get the displacement all the way down eventually, though it gets harder the larger the system and the greater the constraints. Are you constraining cartesian co-ordinates? I suggest trying to constrain a minimal number of internal co-ordinates for key heavy atoms. Hope this helps a little, Jeremy ---------------------------------------------------------------------- Jeremy Greenwood jeremy.greenwood@i.am Department of Medicinal Chemistry bh +45 35306117 Royal Danish School of Pharmacy fx +45 35306040 Universitetsparken 2, DK-2100 Copenhagen, Denmark ah +45 32598030 ---------------------------------------------------------------------- == Response #2: Nicolas Ferre ================ Hi Gerald, I'm very surprised by the output you give. Normally the total Delta X is the sum of the 2 previous one, Linear and Quad. And when you freeze some variables, all of theses 3 quantities have to be zero. I've performed some calculations on crambin, allowing only 3 residues to move, so freezing other 43 residues (it's a QM/MM calculation) and the output looked fine. In your case, it seems to me that only R1 to R5 are really frozen, but that atoms 1, 11, 38, 48 and 50 are translated by the vector (2.501, -8.90656,8.10547) in bohrs. I don't understand why. Are you sure that these atoms don't move ? Did you check the values during optimization ? How did you freeze the coordinates of these atoms ? With a "-1" in the How did you freeze the coordinates of these atoms ? With a "-1" in the Z-Matrix or with the MODREDUNDANT keyword ? Did you use the NOSYM keyword (optimization in the input orientation or in the standard orientation) ? Nicolas == Response #3: Stefan Fau ================================= Hi, an interesting practical problem... Here are my 2 cents, comments invited. to 2) and 3) Delta X and New X are the differences and new values of the geometry descriptors. G98 allows mixed geometry specifications using internal coordinates together with cartesian coordinates. Freezing cartesian coordinates is equivalent to freezing all internal coordinates between this group of atoms (provided you have only one spatial group of frozen atoms). If you have two clusters of frozen atoms linked by a unconstrained part of the molecule, one way of optimizing the molecule is to allow movement of the two clusters with respect to each other. I don't think G98 does it this way, but you can check by tracking the distances between atoms of different frozen clusters over the optimization. Another reason for blockwise movement of the frozen atom clusters is that sometimes the standard orientation of the molecule flips from one optimization step to the next. (I think that the standard orientation is determined by the moments of inertia. Sometimes two of them are very similar and change sequence from one geometry to the next.) I think the list of geometry variables contains both the original set of geometry descriptors and the redundant internal coordinates. I am not sure if original descriptors that are NOT redundant internal coordinates enter in the computation of the displacement used as a convergence criterion. You may want to browse the CCL archives: I faintly remember a mail from Gaussian (maybe Doug Fox) on that topic a year or two ago. to 1) Vibrational frequencies are molecular properties. They all depend on all of the molecule. At the same time, some are quite specific for functional groups. Therefore the influence of other parts of the molecule must be small, probably rapidly declining with distance. The common implementation of harmonic frequencies requires the forces (=first derivatives of the energy w.r.t. nuclear positions) to be (nearly) zero. I don't know how the second derivatives change with displacements that cause nearly no forces, but the displacements must be along floppy modes with very small force constants and frequencies. I suppose that big residual displacements will mainly influence small frequencies. In the harmonic approximation you may diagonalize the matrix of mass weighted second derivatives of the energy with respect to nuclear coordinates and get the vibrational modes and vibrational energies. Like with the solution of the HF equation, you can apply unitary transformations to get a localized description (ideally only one internal coordinate varying in a mode) that is not diagonal anymore. The off-diagonal matrix elements describe how the localized modes influence each other. More to your problem: I think you can use frequencies that have NO movement of frozen atoms in the corresponding vibrations. You may try to block-diagonalize the matrix with a unitary transformation that constricts vibrations with motion of frozen atoms in one block. Since the coupling elements with the other block would be zero, the frequencies >from that block would be valid. One caveat: When you truncate a molecule, you omit interactions between the cut off parts as well as interactions between the cut off and the retained part of the molecule. If you have to freeze clusters of atoms to force the truncated molecule into the original configuration, some of the omitted interactions were important. I would like to make sure that none of the cut off parts had a significant interaction with the interesting part of the molecule. I hope it answers some of your questions, Stefan ______________________________________________________________________ Dr. Stefan Fau | fau@qtp.ufl.edu Quantum Theory Project | (352) 392-6714 University of Florida Gainesville, FL 32611-8435 =============================================================================== From chemistry-request@server.ccl.net Fri Dec 1 05:46:11 2000 Received: from nottingham.ac.uk (pat.ccc.nottingham.ac.uk [128.243.40.194]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA29325 for ; Fri, 1 Dec 2000 05:46:09 -0500 Received: from gotham.ccc.nottingham.ac.uk ([128.243.40.48] helo=unix.ccc.nottingham.ac.uk) by nottingham.ac.uk with esmtp (Exim 3.16 #1) id 141ngi-00003Z-00 for chemistry@ccl.net; Fri, 01 Dec 2000 10:45:08 +0000 Received: from granby ([128.243.40.43] helo=granby.ccc.nottingham.ac.uk) by unix.ccc.nottingham.ac.uk with esmtp (Exim 3.16 #1) id 141nhV-00023H-00 for chemistry@ccl.net; Fri, 01 Dec 2000 10:45:57 +0000 Date: Fri, 1 Dec 2000 10:45:56 +0000 (GMT) From: Simon Cross X-Sender: pcxsc@granby.ccc.nottingham.ac.uk To: ccl list Subject: Small Molecule Paramaterisation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I'm trying to parameterise a diphenylphosphonate molecule PhP(O*2)OPh for use in an MD simulation in Amber5. The phosphonate is an anion and therefore has an axis of symmetry. I've run Gaussian98 with 3-21G* basis set (due to lack of computer time) to generate a fully optimised structure and used these bond lengths and angles in my parameter file. For the dihedrals I've fixed the chosen bond (3 in total) at 0, 15, 30..180 degrees and optimised the rest of the molecule which has given me what a believe to be fairly accurate torsional information. For the charges I ran G98 with 6-31G* basis set (to be consistent with amber forcefield) and used RESP to fit the charges. I am now having problems trying to get amber to reproduce these data. Setting the new dihedral force constants to zero (to see nonbonding interactions) I've run a one step minimisation on each of the 0,15,30..180 degree dihedral structures and plotted the energies. For the P-Ph bond there is a flat line (as expected) except at 2 torsion angles, 30 and 150. These correspond to steric clashes between the hydrogen atoms on the phenyl ring, and the 2 phosphonate oxygens. I would also expect this. However, the problem seems to be this: 1) There is no gradual increase - all other points are approx. zero and 2) The magnitude of the energy is about 135 kcal/mol! I then set the newly paramaterised angle force constants to zero as there seemed to be some contribution in the amber output file, and this just reproduced the same 'curves' but at a slightly lesser energy, therefore all relative values equal to the first 'curve'. The 135 kcal/mol energy is specified as being in the VderW term in the amber output files, but there is no clash as far as Gaussian98 is concerned. I was wondering whether the charges on the two phosphonate oxygens (about -0.8 each, P is about +1, OS is about -0.5; total = -1) being relatively large are causing these problems. I should say that I have introduced a new atom type for the P, called PN and borrowed any parameters I could not get from Gaussian from the Parm98 phosphate P. If anyone can help me I would be grateful, as it seems that this forcefield does not seem to reproduce the theoretical data, which is worrying! I will gladly summarise responses. Cheers, ----------------------------------------- Simon Cross School of Chemistry University of Nottingham tel. 0115 9514193 Email: pcxsc@nottingham.ac.uk From chemistry-request@server.ccl.net Fri Dec 1 06:12:42 2000 Received: from tigris.klte.hu (tigris.klte.hu [193.6.138.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA29438 for ; Fri, 1 Dec 2000 06:12:41 -0500 Received: from anti07 (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP; Fri, 1 Dec 2000 12:09:59 +0100 Message-ID: <000601c05b88$0d20b0e0$3b8506c1@chem.klte.hu> From: "Tamas E. Gunda" To: "Clair W Cabal" , References: Subject: Re: CCL:Looking for BABEL and DRAGON users Date: Fri, 1 Dec 2000 09:32:18 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-2" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id GAA29439 Dear Clair, No wonder that the first Sybyl 2 structure does not work, as all of the coordinates are zero. As to the second one, I had no problem with it. I reformatted it with Mol2mol, the result is actually the same. I attach it below, maybe it works. Some program may sensitive to white spaces, change in line endings when moving files from/to UNIX/WINDOWS etc. Best regards Tamas Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 512 900/2472 fax: (+36-52) 512 914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm ------------------------------------------------- # Name: iodophenol # Created by Mol2Mol 3.50 # Creation time: P 1 dec 2000 9:16:23 # from CCLLOOKING FOR BABEL AND DRAGON USERS.TXT of type Sybyl 2 # @MOLECULE iodophenol 13 13 1 0 0 SMALL NO_CHARGES @ATOM 1 I1 0.0128 -0.6508 0.1073 I 1 <1> 0.0000 2 C2 -0.0227 1.3988 0.0868 C.ar 1 <1> 0.0000 3 C3 -0.1419 4.2002 0.0594 C.ar 1 <1> 0.0000 4 C4 1.1607 2.1618 0.0335 C.ar 1 <1> 0.0000 5 C5 -1.2562 2.0567 0.1271 C.ar 1 <1> 0.0000 6 C6 -1.3155 3.4486 0.1137 C.ar 1 <1> 0.0000 7 C7 1.0949 3.5644 0.0195 C.ar 1 <1> 0.0000 8 O8 2.3620 1.4935 -0.0037 O.3 1 <1> 0.0000 9 H9 -2.1851 1.4663 0.1698 H 1 <1> 0.0000 10 H10 -2.2924 3.9525 0.1465 H 1 <1> 0.0000 11 H11 2.0218 4.1541 -0.0227 H 1 <1> 0.0000 12 H12 -0.1914 5.2994 0.0480 H 1 <1> 0.0000 13 H13 3.0687 2.1557 -0.0332 H 1 <1> 0.0000 @BOND 1 1 2 1 2 2 4 ar 3 2 5 ar 4 3 6 ar 5 3 7 ar 6 3 12 1 7 4 7 ar 8 4 8 1 9 5 6 ar 10 5 9 1 11 6 10 1 12 7 11 1 13 8 13 1 @SUBSTRUCTURE 1 **** 1 TEMP 0 **** **** 0 ROOT ------------------------------------------------------------------ From chemistry-request@server.ccl.net Fri Dec 1 05:30:30 2000 Received: from gensig.nibsc.ac.uk (gensig.nibsc.ac.uk [193.62.43.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA29211 for ; Fri, 1 Dec 2000 05:30:24 -0500 Received: from nibsc.ac.uk (dlinmf.nibsc.ac.uk [193.62.42.144]) by gensig.nibsc.ac.uk (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id KAA89561 for ; Fri, 1 Dec 2000 10:30:10 GMT Message-ID: <3A277DD8.31130020@nibsc.ac.uk> Date: Fri, 01 Dec 2000 10:30:48 +0000 From: Mark Forster Organization: NIBSC X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Discover trajectory files in mdxvu Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Computational Chemists The mdxvu program for analysing MD trajectories now offers support for archive files created by Discover and other codes (eg DGII) in the MSI suite of software. This is achieved by the use of filter (PERL) scripts that convert the MSI archive files into the default AMBER ascii files used by mdxvu. This would also allow conformations created by various tools in the MSI suite to be used as input to AMBER refinement methods (provided you also have an AMBER topology file). These utilities are available at the site http://www.nibsc.ac.uk/mdxvu/ If you have previously downloaded the mdxvu binaries you will only need to get the files manual.htm discover_utils.tar best wishes Mark -- Dr Mark J Forster Ph.D. Principal Scientist Informatics Laboratory National Institute for Biological Standards and Control Blanche Lane, South Mimms, Hertfordshire EN6 3QG, United Kingdom. Tel +44 (0)1707 654753 FAX +44 (0)1707 646730 E-mail mforster@nibsc.ac.uk From chemistry-request@server.ccl.net Fri Dec 1 06:29:46 2000 Received: from nic.upatras.gr (nic.upatras.gr [150.140.129.30]) by server.ccl.net (8.8.7/8.8.7) with SMTP id GAA29529 for ; Fri, 1 Dec 2000 06:25:01 -0500 Received: (qmail 6346 invoked from network); 1 Dec 2000 11:24:38 -0000 Received: from titanas.chemistry.upatras.gr (150.140.180.134) by nic.upatras.gr with SMTP; 1 Dec 2000 11:24:38 -0000 Received: (qmail 4074 invoked from network); 1 Dec 2000 11:29:49 -0000 Received: from orion.chemistry.upatras.gr (HELO Me) (150.140.180.144) by titanas.chemistry.upatras.gr with SMTP; 1 Dec 2000 11:29:49 -0000 Message-ID: <000c01c05b89$64de20a0$90b48c96@chemistry.upatras.gr> From: "Nikolaos Karatsis" To: Subject: G92 and Linux Date: Fri, 1 Dec 2000 13:25:22 +0200 I wonder if anyone has compile G92 under linux. If someone has, please send me a way to do it. Thank you. From chemistry-request@server.ccl.net Fri Dec 1 12:47:33 2000 Received: from post1.inre.asu.edu (post1.inre.asu.edu [129.219.110.72]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA01373 for ; Fri, 1 Dec 2000 12:47:33 -0500 Received: from conversion.post1.inre.asu.edu by asu.edu (PMDF V6.0-24 #47346) id <0G4W00G01DRJV9@asu.edu> for chemistry@ccl.net; Fri, 01 Dec 2000 09:28:31 -0700 (MST) Received: from smtp.asu.edu (smtp.asu.edu [129.219.13.92]) by asu.edu (PMDF V6.0-24 #47346) with ESMTP id <0G4W00FC8DRJEE@asu.edu> for chemistry@ccl.net; Fri, 01 Dec 2000 09:28:31 -0700 (MST) Received: from general2.asu.edu (general2.asu.edu [129.219.10.242]) by smtp.asu.edu (8.9.3/8.9.3) with ESMTP id JAA15413 for ; Fri, 01 Dec 2000 09:28:32 -0700 (MST) Date: Fri, 01 Dec 2000 09:28:30 -0700 (MST) From: Benjamin Moritz Subject: ENT files to ZMAT files X-Sender: bmoritz@general2.asu.edu To: chemistry@ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Hello everyone. I was wondering if someone could help me out in converting .ent files from hyperchem into z-matrix notation for G98. I've been using the following command to convert... newzmat -ipdb -ocom file.ent file.com Unfortunately I keep on getting a segmentation fault and some other error messages. My question is am I doing the conversion right or do I need to change my input command? Thanks in advance. Benjamin J. Moritz Dept. Chemistry Arizona State University Mailt0:bmoritz@asu.edu From chemistry-request@server.ccl.net Fri Dec 1 12:47:57 2000 Received: from ChE.UDel.Edu (che.udel.edu [128.175.117.64]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA01385 for ; Fri, 1 Dec 2000 12:47:57 -0500 Received: from che.udel.edu (cognac.che.udel.edu [128.175.117.54]) by ChE.UDel.Edu (8.9.3/8.9.3) with ESMTP id LAA21436 for ; Fri, 1 Dec 2000 11:42:54 -0500 (EST) Message-ID: <3A27D5A0.CA99FA1B@che.udel.edu> Date: Fri, 01 Dec 2000 11:45:20 -0500 From: Jeffery Klauda To: "'chemistry@ccl.net'" Subject: Raman Intensities in Gaussian 98 Hi, How does Gaussian 98 calculate the raman intensities in a frequency calculation? I understand that the raman intensity is proportional to scattering cross section or polarizability of the molecule but I am not sure how it calculates the intensity for each vibrational mode. If you could supply me with a reference or set of references on this issue it would be appreciated. Thanks in advance, Jeff Klauda -- *************************************** Jeffery Klauda Ph.D. Candidate in Chemical Eng. University of Delaware 119 Colburn Lab Newark, DE 19702 Phone: (302) 831-6857 Fax: (302) 831-1048 *************************************** From chemistry-request@server.ccl.net Fri Dec 1 13:05:00 2000 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA01842 for ; Fri, 1 Dec 2000 13:05:00 -0500 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id NAA32402; Fri, 1 Dec 2000 13:05:00 -0500 (EST) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Fri, 01 Dec 2000 13:04:20 -0500 (Eastern Standard Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0G4W003ISI2D5C@lvlmail.unitedcatalysts.com>; Fri, 01 Dec 2000 13:01:25 -0500 (EST) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Fri, 01 Dec 2000 13:04:31 -0500 Content-return: allowed Date: Fri, 01 Dec 2000 13:04:31 -0500 From: "Shobe, Dave" Subject: dumping fiocom To: "'help@gaussian.com'" , "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629DDAAB0E@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 I used to know this but I forgot. What causes Gaussian to dump fiocom and quit? And what am I supposed to do when this happens? --David Shobe From chemistry-request@server.ccl.net Fri Dec 1 16:32:31 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA02427; Fri, 1 Dec 2000 16:32:31 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id QAA15559; Fri, 1 Dec 2000 16:32:29 -0500 (EST) Date: Fri, 1 Dec 2000 16:32:29 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net cc: Jan Labanowski Subject: Time to cash on your holiday spirit {:-0}. CCL needs your help Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL subscribers... A moment ago I officially posted the supporting pages for CCL at: http://www.ccl.net/chemistry/aboutccl/supporting/ Be generous... I really need your donations and support. You do not have to give us much... Just whatever you think it is worth... If you cannot help us at this moment, consider doing this when you can... Ask yourself on how many occasions you got a tip or an idea, found about a good job, learned what people do, started a collaboration, hired a person, bought/got the right software... etc... etc... If you really did not, do not help us, but if you did, now is your turn to say: "keep it running...". I want to use this occasion to thank also all our previous sponsors http://www.ccl.net/cgi-bin/donors They donated money when I asked first time. Since that time I did not ask for support, but I remembered. Thank you a lot... As you can see, those are not the people from: "Who is Rich in the World" almanac. Those are people like you... Thank you again... Earlier this year, I shared with you an idea of sponsoring CCL through voluntary memberships. You would get in exchange services from CCL. You did not like it... So we changed the model substantially. We now count primarily on the goodness of your heart. We ask you for your individual donations whatever you think is appropriate. But please encourage also your organizations to sponsor the CCL Web Pages. This is a great way to show that they care about the community. It is also a nice way to get exposed to a focused readership. Moreover, maybe they still have some leftovers to spend before the end of tax year. Please help... Please do not understand me wrong... The CCL really enjoys the stable and cosy environment of Ohio Supercomputer Center. They are our major sponsor and thanks to this environment we enjoy the stability of 10 years of service to the community (yes, it is already 10 years -- do not worry, we will all live 100 years...). They give as room, network, students, computers, phones, and primarily encouragement. If not the OSC and its management, I am not sure I would have enough stamina to keep going all these years. However, without your help and contributions, I have only limited opportunity to get additional resources and further develop this resource. Last but not least, by helping CCL with donations, you educate young and enthusiastic students in the important arcanes of Web, Internet, system administration, hardware, networking, computer security, team work, etc., etc. I still get thanks from my past student assistants for the opportunity to learn the practice of running the Internet service. But these people need to eat, and while many of them work as volunteers, this resource should rely on more stable basis than my sleepless nights during finals or school breaks. Also, if you are a part of some organization, who can help us, we would consider housing the web site, news service, archives, etc., for you. Consider it. We are 10 years in the "business", so we are not likely to disappear tomorrow. And by entrusting us with your web site and discussion forum, you can not only assume that it is in experienced hands, but you also connect with the existing broad base of the CCL subscribers and visitors. If you have other ideas on how you can help, please share them with us. Please understand that your contributions are strictly voluntary. You do not get anything in exchange but the satisfaction that you help us together with others. I also wanted to thank you for your contributions to the archives, your discussions, and your patience. For all these years, I have so many friends on the net, and sometimes I did not have a chance to see your face... All the best for you in this holiday season... Jan jkl@ccl.net Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | http://www.ccl.net/