From chemistry-request@server.ccl.net Mon Oct 29 04:08:47 2001 Received: from luc.ac.be ([193.190.2.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9T98kB18682 for ; Mon, 29 Oct 2001 04:08:46 -0500 Received: from sbg-ts (localhost [127.0.0.1]) by luc.ac.be (8.9.3/8.9.3) with SMTP id KAA12008 for ; Mon, 29 Oct 2001 10:11:45 +0100 (MET) Date: Mon, 29 Oct 2001 10:11:45 +0100 (MET) Message-Id: <200110290911.KAA12008@luc.ac.be> X-Sender: lucp1381@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: sergiusz kwasniewski Subject: Pi-SCF in CHARMM Hi, does anyone know whether a Pi-SCF calculation is possible with the CHARMM force field ? Or is it not parametrized to be used for such calculations, as e.g. MM3 does ? Thanks in advance Serge ___________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 032 (0)11/268315 fax : 032 (0)11/268301 email : sergiusz.kwasniewski@luc.ac.be http://www.luc.ac.be/Research/TheoChem ___________________________________________________ From chemistry-request@server.ccl.net Mon Oct 29 08:48:53 2001 Received: from ciril.fr ([193.50.27.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9TDmqB23016 for ; Mon, 29 Oct 2001 08:48:52 -0500 Received: from host20.lctn.uhp-nancy.fr (host20.lctn.uhp-nancy.fr [193.50.239.24]) by ciril.fr (8.11.2/8.11.2/Guy-12-01-2001) with ESMTP id f9TDppM28453 for ; Mon, 29 Oct 2001 14:51:51 +0100 (MET) Received: from lctn.uhp-nancy.fr (host23.lctn.uhp-nancy.fr [193.50.239.30]) by host20.lctn.uhp-nancy.fr (AIX4.3/8.9.3/8.9.3) with ESMTP id OAA33236 for ; Mon, 29 Oct 2001 14:49:56 +0100 Sender: assfeld@host20.lctn.uhp-nancy.fr Message-ID: <3BDD5E91.CB1490D2@lctn.uhp-nancy.fr> Date: Mon, 29 Oct 2001 14:50:09 +0100 From: Xavier ASSFELD Organization: Chimie Theorique X-Mailer: Mozilla 4.51i [en] (X11; I; AIX 4.3) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: Group theory (summary) Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Many thanks to : Ioan Silaghi-Dumitrescu (Ioan Silaghi-Dumitrescu ) Gordon A. Gallup (ggallup@aloha.unl.edu) Christoph van Wullen (Christoph van Wullen ) for their helpful answers. In addition to their answers, I found the following ref : X.-F. Zhou and P. Pulay, J. Comp. Chem. 10(7), 1989, 935-938 Here follows their answers : #1 ...it must be a quartet and eight doublets. From the higher symmetric rotation group (3 p-Elektrons give a quartet-s, doublet-p, doublet-d, we know that the quartet is totally symmetric. the doublet-p should give doublet-t2 in Td symmetry, and doublet-d should factorize in doublet-e and doublet-t2. So, from my qualitative thoughts, a t2^3 configuration should give 1* singlet-a1 1* doublet-e 2* doublet-t2 However, with a decent group multiplication table this can probably derived more quickly and nicer.... +---------------------------------+-------------------------------------+ | Prof. Christoph van Wüllen | Tele-Phone (+49) (0)30 314 27870 | | Technische Universität Sekr. C3 | Tele-Fax (+49) (0)30 314 23727 | | Straße des 17. Juni 135 | eMail | | D-10623 Berlin, Germany | Christoph.vanWullen@TU-Berlin.De | +---------------------------------+-------------------------------------+ #2 Dear Prof Assfeld: I have two papers on this subject, J. Chem. Phys. _45_, 2304 (1966) and Intern. J. Quantum Chem. _8_, 267 (1974) looking at this problem from different viewpoints. The CRUNCH program suite, available for downloading at http://phy-ggallup.unl.edu/crunch has a module that makes calculations of this sort. Regards, Gordon A. Gallup Dept. of Physics and Astronomy University of Nebraska-Lincoln Lincoln, NE 68588-0111 Voice: (402)435-6967,(402)472-1230 FAX: (402)472-2879 http://physics.unl.edu/~ggallup/gallup.html http://www.unl.edu/Dissatt/ #3 Hi Xavier, You might find useful the following reference: J.Chem. Educ. 1972, 49, 336-340 (D.I.Ford, Molecular Term Symbols by Group Theory). Ioan -------------------------------- Prof.dr. Ioan Silaghi-Dumitrescu Department of Chemsitry Babes-Bolyai University RO-3400 Cluj-Napoca Romania -- ...Xav WARNING! NEW E-MAIL ADDRESS ! (u-nancy changed to uhp-nancy) Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.uhp-nancy.fr Laboratoire de Chimie theorique (T) 33 3 83 91 21 49 Universite Henri Poincare (F) 33 3 83 91 25 30 F-54506 Nancy BP 239 http://www.lctn.uhp-nancy.fr From chemistry-request@server.ccl.net Mon Oct 29 07:50:49 2001 Received: from mserv.rug.ac.be ([157.193.40.37]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9TConB22127 for ; Mon, 29 Oct 2001 07:50:49 -0500 Received: from hartree4.rug.ac.be (hartree4.rug.ac.be [157.193.91.12]) by mserv.rug.ac.be (8.9.3/8.9.3) with ESMTP id NAA16032; Mon, 29 Oct 2001 13:53:31 +0100 (MET) Received: (from tom@localhost) by hartree4.rug.ac.be (AIX4.2/UCB 8.7/8.7) id OAA07416; Mon, 29 Oct 2001 14:55:42 +0100 (NFT) Date: Mon, 29 Oct 2001 14:55:42 +0100 (NFT) From: Tom Kuppens To: CHEMISTRY@ccl.net Subject: SUM: RIMM vs SDRAM Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII My thanks goes out to all the people who responded to my Q. Original message and all replies are attached. Regards, Tom Kuppens -- http://allserv.rug.ac.be/~tkuppens ---- "Violence is the last refuge of the incompetent." -- Salvor Hardin Original Message: We have several linux machines that run Gaussian. Now we want to add some new power to our park i.e. a PIV - 1700MhZ with 512M RAM (SDRAM or RIMM). Is there someone who can provide me with some info on the Gaussian and/or overall performance with RIMM versus SDRAM modules. Listing of all Replies: === John McKelvey wrote Can't quote benchmarks, but all I've read on ZDNet points to a significant loss of performance using SDRAM over DDR memory and the more usual ram for P4's. === Jose Luis Garcia de Paz wrote It depends on your budget. You need to knowt what kind of memory support the main board of your computer. Low speed ram decrease performance of the computer for the same pentium IV chip. I have not idea on RIMM memory, but i know sdram, speed 133 mhz cheep and slow ddr or ddr-sdram , speed 266 mhz, similar price than sdram rdram, speed 800 mhz, the faster and expensive (and the best) In spanish pesetas (1euro = 166 pts) the change of the main board plus 256 Mb ram from sdram to ddr ram fro a pentium IV chip increase the price of the computer abour 50000 pts. Since september pentium iv can run with sdram, but whit low performaces of course. === Scott Anderson wrote Regarding your question about RIMM (RDRAM) v.s. SDRAM (or DDR SDRAM) for Gaussian: I have done a fair bit of comparing machines for Gaussian, as I am planning to buy a bunch in the near future. I have been using an MP2 Opt Freq job that takes a few hours as my benchmark. I have also run much longer Direct Dynamics trajectory jobs on several different configurations. The MP2 job was deliberately chose to avoid a lot of disk i/o because I really wanted to focus on the computational speed. I have compared 1 and 1.4 GHz Athlons, PIIIs, and P4s. The conclusion is that for Gaussian, the P4 is 20-30% faster than the Athlons for the same clock speed, and since you can get P4s with faster clocks, the P4 ends up being substantially faster. This speed difference is quite surprising because the P4 floating point unit is substantially inferior to that of the Athlon, and as far as I have been able to determine, the rate deterimining step for these fast chips is memory speed. Here the RDRAM really shines. I have also compared Athlons with PC133 SDRAM and PC2100 DDR ram, which is theoretically substantially faster. For Gaussian jobs, I see no difference. One interesting thing to look at in this regard is the review in the Tom's Hardware review of the new Athlon XP. http://www6.tomshardware.com/cpu/01q4/011009/index.html They compare several different Athlons with different memory configurations, and also 2GHz P4s with both RDRAM and DDR memory. The Athlon XP looks great on most of the benchmarks -- equalling or exceeding the P4, even though the P4 clock speed is much higher. The one area where the XP fails, however, is memory speed. Note that the P4 with RDRAM does 50% better than the P4 with DDR, and nearly a factor of two better than the Athlons with either PC133 or DDR memory. My conclusions: 1. Gaussian is probably memory-bandwidth limited, and you should spend the extra money RDRAM. 2. DDR memory doesn't really make a huge difference -- certainly nothing like the factor of two you might expect. 3. The ideal configuration is very application dependent. For Gaussian, I would go with the P4. If you are running a mix of programs, you really have a tough decision. === From chemistry-request@server.ccl.net Mon Oct 29 11:57:45 2001 Received: from mailhost1.rdg.ac.uk ([134.225.16.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9TGviB26138 for ; Mon, 29 Oct 2001 11:57:45 -0500 Received: from indyp.chemistry ([134.225.168.35] helo=reading.ac.uk) by mailhost1.rdg.ac.uk with esmtp (University of Reading Email Service) id {15yFmG-000467-00} for CHEMISTRY@www.ccl.net; Mon, 29 Oct 2001 17:00:44 +0000 Sender: dave@ccl.net Message-ID: <3BDDA72D.75443981@reading.ac.uk> Date: Mon, 29 Oct 2001 17:59:57 -0100 From: Dave Price Organization: none-what-so-ever X-Mailer: Mozilla 4.76C-SGI [en] (X11; I; IRIX 6.5 IP22) X-Accept-Language: en MIME-Version: 1.0 To: Comp Chem Mailing List Subject: Gaussian98 problem 'spurious integrated density' Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Fellow computational chemists, I get the following error with g98 A9 on an SGI Origin2000 under Irix 6.5.10. To save bandwidth I have not included the whole file, but the last few lines, which incorporate the error are as follows- Self energy of the charges = 6.9414866430 MM energy of the charges = 0.0000000000 Nuclear-Charge attraction = 161.7275946561 231 basis functions 509 primitive gaussians 55 alpha electrons 53 beta electrons nuclear repulsion energy 760.7391252112 Hartrees. Nuclear repulsion after solvent point charges= 929.4082065103 Hartrees. One-electron integrals computed using PRISM. 1 Symmetry operations used in ECPInt. ECPInt: NShTT= 2145 NPrTT= 13643 LenC2= 2102 LenP2D= 9399. LDataN: DoStor=F MaxTD1= 8 Len= 415 LDataN: DoStor=T MaxTD1= 8 Len= 415 NBasis= 231 RedAO= T NBF= 231 NBsUse= 230 1.00D-04 NBFU= 230 Projected Huckel Guess. of initial guess= 2.0000 Requested convergence on RMS density matrix=1.00D-04 within1000 cycles. Requested convergence on MAX density matrix=1.00D-02. Requested convergence on energy=5.00D-05. Virtual orbitals will be shifted by 0.200 hartree. No pruned grid is available for atomic number 92. Warning! Spurious integrated density: NE= 108 NElCor= 0 Integral= 107.18081 Tolerance=1.00D-03 Consistency failure #2 in CalDSu. Error termination via Lnk1e in /home/chem/scsprida/g98/l502.exe. Job cpu time: 0 days 0 hours 13 minutes 5.1 seconds. File lengths (MBytes): RWF= 59 Int= 0 D2E= 0 Chk= 2 Scr= 1 Any help? Gaussian have not even acknowledged my request for help. Cheers, Dave -- ------------------------------------------------------------------------ Dr. David W. Price MA CChem MRSC Tel: +44 (0)118 9875123 extn 7415 Department of Chemistry, Fax: +44 (0)118 9316331 University of Reading, mailto:d.w.price@reading.ac.uk Whiteknights, READING RG6 6AD U.K. ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Mon Oct 29 10:30:36 2001 Received: from sd.accelrys.com ([146.202.0.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9TFUaB24864 for ; Mon, 29 Oct 2001 10:30:36 -0500 Received: (from osman@localhost) by sd.accelrys.com (8.11.0/8.11.0) id f9TFaS929127 for chemistry@server.ccl.net; Mon, 29 Oct 2001 07:36:28 -0800 Received: from OGUNER-LAP.accelrys.com (dhcp388.sd.accelrys.com [172.30.201.134]) by sd.accelrys.com (8.11.0/8.11.0) with ESMTP id f9TFaRX29119; Mon, 29 Oct 2001 07:36:28 -0800 Message-Id: <5.1.0.14.2.20011029072617.04c8e300@sparky2.sd.accelrys.com> X-Sender: osman@sparky2.sd.accelrys.com X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Mon, 29 Oct 2001 07:33:12 -0800 To: chemistry@server.ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, qsar_society@accelrys.com From: "Osman F. Guner" Subject: Second Call for papers: ADME/Tox Informatics Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_2689587==_.ALT" --=====================_2689587==_.ALT Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: quoted-printable We have room for several more papers in this symposium. You can submit=20 your abstracts directly through http://oasys.acs.org/oasys.htm until=20 November 1st. If you miss the deadline, please let me know ASAP and I can= =20 submit your abstract on your behalf for another two weeks or so. ADME/TOX INFORMATICS At Spring ACS meeting in Orlando (April 7-11, 2002) Sponsored by the Chemical Information Division (CINF) Co-sponsored by Division of Medicinal Chemistry (MEDI), Division of Chemical Toxicology (TOXI), and Division of Computers in Chemistry (COMP) The symposium will be on the informatics challenges faced with the=20 increasing contribution of ADME/Tox studies in the early drug discovery. If= =20 you are working on predictive ADME/Tox in lead discovery, lead=20 optimization, or combinatorial library design and analysis, you may want to= =20 share your views and results with the scientific community by contributing= =20 to this symposium. How are you managing the information flow? How is=20 information captured and made available to scientists in a=20 multi-disciplinary set up? Are there examples of increased quality of=20 candidates through use of predictive ADME/Tox in early discovery? Please use the OASys to submit your abstract. You can access the CINF=20 symposia at OASys via http://oasys.acs.org/oasys.htm. The deadline for=20 submitting abstracts is November 1st. Thx...osman --- Osman F. G=FCner, Ph.D. Director, Lead Identification & Optimization Accelrys Inc. (858) 799-5341 osman@accelrys.com http://www.accelrys.com --=====================_2689587==_.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable We have room for several more papers in this symposium.  You can submit your abstracts directly through http://oasys.acs.org/oasys.htm until November 1st.  If you miss the deadline, please let me= know ASAP and I can submit your abstract on your behalf for another two= weeks or so.


ADME/TOX INFORMATICS

At Spring ACS meeting in Orlando (April 7-11, 2002)

Sponsored by the Chemical Information Division (CINF)
Co-sponsored by Division of Medicinal Chemistry (MEDI),
Division of Chemical Toxicology (TOXI),
and Division of Computers in Chemistry (COMP)

The symposium will be on the informatics challenges faced with the= increasing contribution of ADME/Tox studies in the early drug discovery. If= you are working on predictive ADME/Tox in lead discovery, lead= optimization, or combinatorial library design and analysis, you may want to= share your views and results with the scientific community by contributing= to this symposium. How are you managing the information flow? How is= information captured and made available to scientists in a= multi-disciplinary set up? Are there examples of increased quality of= candidates through use of predictive ADME/Tox in early discovery?

Please use the OASys to submit your abstract. You can access the CINF= symposia at OASys via http://oasys.acs.org/oasys.htm. The= deadline for submitting abstracts is November 1st.

Thx...osman


---
Osman F. G=FCner, Ph.D.
Director,  Lead Identification & Optimization
Accelrys Inc.   (858) 799-5341
osman@accelrys.com        http://www.accelrys.co= m --=====================_2689587==_.ALT-- From chemistry-request@server.ccl.net Mon Oct 29 11:42:12 2001 Received: from zimail2.unizh.ch ([130.60.128.12]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9TGgCB25817 for ; Mon, 29 Oct 2001 11:42:12 -0500 Received: from zisgi.unizh.ch (zisgi.unizh.ch [130.60.68.15]) by zimail2.unizh.ch (8.9.3/8.9.3/11) with ESMTP id RAA02468 for ; Mon, 29 Oct 2001 17:45:11 +0100 (MET) Date: Mon, 29 Oct 2001 17:45:11 +0100 From: "Dr. Peter Burger" To: CHEMISTRY@ccl.net Subject: harmonic oscillator for triatomic system Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, embarassing but I dare nevertheless to ask. I am looking for an expression of the angle bending term using the harmonic oscillator approximation for a triatomic system B-A-C in a form as for the bond stretch term in a diatomic system, i.e. nu = 1/2PI sqrt(k/mu). In particular, what form does the reduced mass term mu have in the triatomic system? Best regards, Peter From chemistry-request@server.ccl.net Mon Oct 29 11:11:12 2001 Received: from femail17.sdc1.sfba.home.com ([24.0.95.144]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9TGBBB25312 for ; Mon, 29 Oct 2001 11:11:12 -0500 Received: from C1353359A ([65.4.172.51]) by femail17.sdc1.sfba.home.com (InterMail vM.4.01.03.20 201-229-121-120-20010223) with SMTP id <20011029161406.MVKI14800.femail17.sdc1.sfba.home.com@C1353359A> for ; Mon, 29 Oct 2001 08:14:06 -0800 Message-ID: <004101c16094$5872cf30$33ac0441@sttln1.wa.home.com> Reply-To: "Mark A. Thompson" From: "Mark A. Thompson" To: References: <011028170534.10540@VAX.PHR.UTEXAS.EDU> Subject: Re: CCL:Ring perception algorithm Date: Mon, 29 Oct 2001 08:11:19 -0800 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 > >>Prof Pearlman wrote: > > Lastly, I can not resist pointing out that structures which chemists > justifyably regard as "cages" (such as cubane or buckyball) can and, in > some respects, should be regarded as planar fused ringsystems. Imagine > drawing the "front" face of a cube as a large dark square, drawing the > "back" face as a smaller lightly-drawn square centered inside the first > square, and drawing the other faces by making tapered connections from > the corners of the outer square to the corners of the inner square. Now, > replace all of the dark, light, and tapered "bonds" (edges) with lines of > uniform width and intensity and note that the resulting planar fused > ringsystem is topologically equivalent to the cube. Hence, neither our > ring perception algorithm nor Euler's Theorem see fullerenes or any other > "caged" ringsystems as particularly "tricky" problems because, in fact, > they are no different than non-tricky ringsystems. > > Thanks for the terrific response. Indeed, I was aware of this issue of topology vs. chemistry. I had used a 3-sided pyramid as my simple test case (has 3 linearly independant rings not 4). I had to modify my version of the B&P algorithm to also include rings I deemed chemically significant. I wonder how others have solved this issue. Given the usefullness of this approach to computational drug discover, I thought this may have gotten some thought from others on the CCL. Cheers, Mark Thompson www.planaria-software.com