From chemistry-request@ccl.net Wed Oct 15 14:26:28 2003 Received: from smtp3.server.rpi.edu (smtp3.server.rpi.edu [128.113.2.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9FIPudH007903 for ; Wed, 15 Oct 2003 14:25:56 -0400 Received: from rpi.edu (rts17p11.xyp.rpi.edu [128.113.30.160]) by smtp3.server.rpi.edu (8.12.10/8.12.9) with ESMTP id h9FIPoF0017018; Wed, 15 Oct 2003 14:25:50 -0400 Message-ID: <3F8D9147.FD2A532A|at|rpi.edu> Date: Wed, 15 Oct 2003 14:26:15 -0400 From: "Curt M. Breneman" X-Mailer: Mozilla 4.77 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry|at|ccl.net, qsar_society|at|accelrys.com, Joan Luo , Wei Deng , Minghu Song , Sukumar , Dechuan Zhuang , Bill Katt , Hongmei Zhang , Rongrong Jiang , Lingling Shen , Mer Selecky , Sarah Cho Subject: CCG Excellence Award Application date Extended to October 24th!!! Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Scanned-By: CanIt (www . canit . ca) X-Spam-Status: No, hits=1.6 required=7.0 tests=PLING_PLING,USER_AGENT_MOZILLA_XM,X_ACCEPT_LANG version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear Computational Chemistry graduate students and advisors: Applications for CCG Excellence Awards are due October 17th, 2003 (EXTENDED to October 24th!) for the Anaheim ACS National Meeting! Application for these awards is a two-step process. First, an application for the Award must be submitted to the Treasurer of the COMP division for consideration. The application consists of an extended (2-page) abstract of the poster or presentation along with a letter of support from the research advisor, a two page CV, and a personal statement. Secondly, an abstract of a poster or oral presentation in the COMP program must be submitted through the ACS OASYS system for online submissions prior to the deadline for the meeting at which the awards will be presented (Anaheim, in this case). Awardees are chosen on the basis of the quality and significance of the research to be presented, as well as the strength of the supporting letter and other materials. All graduate students are encouraged to submit applications for the Awards. Students from the same research group are encouraged to apply. Students from research groups that have won awards at previous ACS meetings are also encouraged to submit applications. Awards will be given only to those individuals making presentations, and not co-authors. For questions, contact: Prof. Curt M. Breneman; Treasurer, ACS COMP Division; RPI Department of Chemistry; 110 8th St.; Troy, NY 12180 To see photos and details of previous winners, see: http://membership.acs.org/C/COMP/CCG/ccg.html#winners From chemistry-request@ccl.net Wed Oct 15 13:00:05 2003 Received: from mailhost.unt.edu (mailhost.unt.edu [129.120.209.40]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9FGxXdH004919 for ; Wed, 15 Oct 2003 12:59:33 -0400 Received: from iatro (localhost.localdomain [127.0.0.1]) by mail1 (Postfix) with SMTP id 4172A603D9 for ; Wed, 15 Oct 2003 11:59:32 -0500 (CDT) Received: from eaglemail.unt.edu (imp2.private.acs.unt.edu [192.168.221.72]) by mailhost.unt.edu (Postfix) with ESMTP id 281AA603CD for ; Wed, 15 Oct 2003 11:59:30 -0500 (CDT) Received: by eaglemail.unt.edu (Postfix, from userid 99) id 6D826474F8; Wed, 15 Oct 2003 11:59:30 -0500 (CDT) Received: from 129.120.42.54 ( [129.120.42.54]) as user gns0001 by eaglemail.unt.edu with HTTP; Wed, 15 Oct 2003 11:59:30 -0500 Message-ID: <1066237170.3f8d7cf22e66c{at}eaglemail.unt.edu> Date: Wed, 15 Oct 2003 11:59:30 -0500 From: gnsriniv{at}unt.edu To: chemistry{at}ccl.net Subject: Error linking DL_POLY MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.1 X-Spam-Status: No, hits=1.4 required=7.0 tests=MAILTO_TO_SPAM_ADDR,NO_REAL_NAME,RCVD_IN_UNCONFIRMED_DSBL, USER_AGENT_IMP version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear All, We are trying to compile dl_poly_2.14 version using f90 on an SGI Indigo-2 (R10000, IRIX64 release 6.5). The compilation seemed ok. However, during the linking of object files we received the following error (given below). If any of you have seen an error of this type and have any suggestions on how to rectify it, we would be most appreciative. Thanks in advance. Sincerely Srinivas Gantasala gns0001{at}unt.edu ERROR BELOW make LD="f90 -o" LDFLAGS="-lscs" \ FC=f90 FFLAGS="-c -O2 -OPT:Olimit=0 -lscs" TIMER="" \ CPFLAGS="-DSGICRAY -DSTRESS -DSERIAL - D'POINTER=integer'" \ EX=DLPOLY.X BINROOT=../execute 3pt f90 -o ../execute/DLPOLY.X angfrc.o bndfrc.o cfgscan.o corshl.o coul0.o coul4.o coul2.o coul3.o conscan.o dblstr.o dcell.o diffsn0.o diffsn1.o dlpoly.o duni.o error.o ewald1.o ewald3.o exclude.o exclude_atom.o fldscan.o exclude_link.o exitcomms.o extnfld.o fbpfrc.o fcap.o forces.o freeze.o gauss.o gdsum.o getrec.o gimax.o gisum.o gstate.o images.o initcomms.o intlist.o intstr.o invert.o invfrc.o jacobi.o lowcase.o lrcmetal.o lrcorrect.o machine.o merge.o merge1.o merge4.o multiple.o multiple_nsq.o npt_b1.o nst_b1.o parset.o npt_h1.o nst_h1.o nve_1.o nvt_b1.o nvt_e1.o nvt_h1.o parlst_nsq.o parlink.o parlst.o passcon.o passpmf.o pmf_1.o pmf_shake.o primlst.o quench.o rdf0.o rdf1.o rdshake_1.o result.o revive.o scdens.o shellsort.o shlfrc.o shlmerge.o shlqnch.o shmove.o simdef.o splice.o static.o strip.o strucopt.o sysdef.o sysgen.o systemp.o sysbook.o sysinit.o tethfrc.o thbfrc.o timchk.o traject.o vertest.o vscaleg.o warning.o xscale.o zden0.o zden1.o denloc.o dihfrc.o erfcgen.o ewald2.o ewald4.o forgen.o fortab.o metgen.o srfrce.o srfrceneu.o suttchen.o coul0neu.o coul2neu.o coul3neu.o excludeneu.o forcesneu.o multipleneu.o neutlst.o parneulst.o prneulst.o parlinkneu.o rdf0neu.o nptq_b1.o nptq_b2.o nstq_b1.o nstq_b2.o nptq_h1.o nptq_h2.o nstq_h1.o nstq_h2.o nveq_1.o nveq_2.o nvtq_b1.o nvtq_b2.o nvtq_h1.o nvtq_h2.o passquat.o qshake.o quatbook.o quatqnch.o crecv.o csend.o gsync.o mynode.o nodedim.o numnodes.o \ -lscs bspcoe.o bspgen.o cpy_rtc.o ele_prd.o ewald_spme.o scl_csum.o set_block.o spl_cexp.o spme_for.o dlpfft3.o hkgen.o hkewald1.o hkewald2.o hkewald3.o hkewald4.o cerfr.o ld32: FATAL 9 : I/O error (-lscs): No such file or directory *** Error code 2 (bu21) *** Error code 1 (bu21) From chemistry-request@ccl.net Wed Oct 15 14:09:17 2003 Received: from chem.udel.edu (chem.udel.edu [128.175.138.224]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9FI8kdH007348 for ; Wed, 15 Oct 2003 14:08:46 -0400 Received: from zxwang ([128.175.138.22]) by chem.udel.edu (8.9.3/8.9.3) with SMTP id OAA89160; Wed, 15 Oct 2003 14:10:31 -0400 (EDT) Reply-To: From: "Zhixiang Wang" To: Cc: Subject: GAUSSIAN need to clarify Date: Wed, 15 Oct 2003 14:07:34 -0400 Message-ID: <000701c39347$3653ab80$168aaf80@zxwang> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook CWS, Build 9.0.2416 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal In-Reply-To: X-Spam-Status: No, hits=-0.5 required=7.0 tests=IN_REP_TO version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi All I paln to study solvation free energies using gaussin. When I tried to understand the output file and compare the output results with the manual, I was totally confused, and found there are discrepancies between manual and the gaussin output file. I hope gaussian clarify this. Suggestions on how to calculate the solvation free energies will greately appreciated. For example, the solvatin free energy of methanol in water. Sincerely ZX *********************** Details In the current manual on web, SCF Done: E(RHF) = -98.569083211 A.U. after 5 cycles Convg = 0.4249D-05 -V/T = 2.0033 S**2 = 0.0000 -------------------------------------------------------------------- Variational PCM results ======================= (a.u.) = -98.568013 (a.u.) = -98.573228 Total free energy in solution: with all non electrostatic terms (a.u.) = -98.569083 -------------------------------------------------------------------- (Polarized solute)-Solvent (kcal/mol) = -3.27 -------------------------------------------------------------------- Cavitation energy (kcal/mol) = 5.34 Dispersion energy (kcal/mol) = -3.08 Repulsion energy (kcal/mol) = 0.34 Total non electrostatic (kcal/mol) = 2.60 -------------------------------------------------------------------- Note that the E(RHF) energy (-98.569083211) is equal to Total free energy in solution with all non electorstatic terms -98.569083. While in my output file give (G03, B.04) SCF Done: E(RB+HF-LYP) = -115.736036910 A.U. after 10 cycles Convg = 0.7861D-09 -V/T = 2.0067 S**2 = 0.0000 KE= 1.149665200488D+02 PE=-3.519462956324D+02 EE= 8.102355096224D+01 -------------------------------------------------------------------- Variational PCM results ======================= (a.u.) = -115.727169 (a.u.) = -115.736037 Total free energy in solution: with all non electrostatic terms (a.u.) = -115.728593 -------------------------------------------------------------------- (Polarized solute)-Solvent (kcal/mol) = -5.56 -------------------------------------------------------------------- Cavitation energy (kcal/mol) = 9.54 Dispersion energy (kcal/mol) = -5.23 Repulsion energy (kcal/mol) = 0.36 Total non electrostatic (kcal/mol) = 4.67 -------------------------------------------------------------------- here E(RB+HF-LYP) (-115.736036910)= (-115.736037) I also note that the manual printed out on Aug.11/03 tell me thia SCF Done: E(RHF) = -100.02918740 A.U. after 5 cycles Convg = 0.4249D-05 -V/T = 2.0033 S**2 = 0.0000 -------------------------------------------------------------------- Variational PCM results ======================= (a.u.) = -98.568013 (a.u.) = -98.573228 Total free energy in solution: with all non electrostatic terms (a.u.) = -98.569083 -------------------------------------------------------------------- (Polarized solute)-Solvent (kcal/mol) = -3.27 -------------------------------------------------------------------- Cavitation energy (kcal/mol) = 5.34 Dispersion energy (kcal/mol) = -3.08 Repulsion energy (kcal/mol) = 0.34 Total non electrostatic (kcal/mol) = 2.60 -------------------------------------------------------------------- The E(RHF) energy (-100.02918740) is neither equal to energy nor to Total free energy in solution: with all non electrostatic terms. From chemistry-request@ccl.net Wed Oct 15 12:50:54 2003 Received: from panda3.phys.unm.edu (panda3.phys.unm.edu [64.106.62.24]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9FGoNdH004457 for ; Wed, 15 Oct 2003 12:50:23 -0400 Received: from sapphire.phys.unm.edu (sapphire.phys.unm.edu [64.106.62.238]) by panda3.phys.unm.edu (Postfix) with ESMTP id 809FE4A89B; Wed, 15 Oct 2003 10:51:12 -0600 (MDT) Sender: susie{at}panda3.phys.unm.edu Message-ID: <3F8D7A23.7DAC51E3{at}sapphire.phys.unm.edu> Date: Wed, 15 Oct 2003 10:47:31 -0600 From: "Susan R. Atlas" Organization: Department of Physics and Astronomy, University of New Mexico X-Mailer: Mozilla 4.51C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: en MIME-Version: 1.0 To: chemistry{at}ccl.net Subject: Re: CCL:PhD and Deep Questions References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-0.6 required=7.0 tests=QUOTED_EMAIL_TEXT,RCVD_IN_UNCONFIRMED_DSBL,REFERENCES, X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) I would just add to Phil Hultin's very nice post that in earlier times, before the bifurcation of knowledge into so many specialized fragments, the study of science was referred to as 'natural philosophy' and indeed, this is how I like to think of it, myself. By the way, there is a recent (1999), beautifully-written book by Prof. E. O. Wilson, entitled Consilience, that addresses precisely this question of "the unity of knowledge." - Susan Atlas > Three cheers for Yao-Ying Chien's nephew! I have often said that if I > could teach a class of students who had the knowledge and skills of > 20-year olds combined with the intellectual drive of 3-year olds (I > have a 3-year old) together we could do miracles.There are a variety > of names for academic degrees depending on the country in question, > and even the individual school. Thus, Oxford gives a D. Phil. degree, > for example, which is similar to the PhD given elsewhere.The important > question is not what the degrees are called, but what they actually > MEAN. Yao-Ying's nephew had this bang on. Just what does it mean to > be a "Doctor of Philosophy"? Unfortunately, for many science students > this seems to be simply a certificate that they are really good at > mixing the right chemicals, or tweaking the right knob on a machine, > or writing code that actually runs. All of these things are good > skills to have, and very important for specific areas of science, but > they are of much less importance than what is implied by the word > "Philosophy".Being a "Doctor of Philosophy" should (IMHO) mean that > one is driven by a true love of knowledge and understanding of the > world (universe) around us to become ever more skilled in the quest > for more knowledge and understanding. It MAY also imply (and I think > probably should also imply) that one is skilled in applying one's > knowledge and understanding to improve the world around us, but since > this involves a value judgement it is difficult to include in a > definition.I think it is wonderful that most universities give the > same Ph.D. degree to graduates in what we like to call "the Arts", > "the Sciences", "Engineering", "the Social Sciences" etc etc. All of > these artificial distinctions are no more than convenient ways to > categorize the world around us in terms of specific classes of > questions that may be asked. The true Philosopher recognizes the > kinship of all branches of knowledge, and grants pre-eminence to no > particular branch a priori.Because all of us have only a little time > on this earth, we must by necessity specialize in order to achieve > anything, but we should nonetheless strive (whether we hold the degree > or not) to be true "Doctors of Philosophy" insofar as we are able.To > Yao-Ying Chien: keep that nephew of yours asking these questions. > Together, you and he are walking along the road to Philosophy. One of > the first steps on this road is to realize how little one actually > knows, and your posting shows that you and he are facing this > realization - and it showed me that I also could not answer his > questions except by indirection. Thank him for me, please. > > The gods did not reveal from the beginning > > All things to us; but in the course of time, > > Through seeking, men find that which is better. > > But as for certain truth, no man has known it. > > Nor will he know it. > > Xenophanes (6th Century B.C.) "urn:schemas-microsoft-com:office:office" /> > Dr. Philip G. Hultin > Associate Department Head and > Associate Professor of Chemistry > University of Manitoba > Winnipeg, MB, Canada R3T 2N2 > (vox) 204-474-9814 > (fax) 204-474-7608 > mailto:hultin{at}cc.umanitoba.ca > http://www.umanitoba.ca/chemistry/ -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ Susan R. Atlas _/ _/ Research Associate Professor, Physics and Astronomy _/ _/ _/ _/ Department of Physics & Astronomy _/ _/ MSC07 4220 phone: (505) 277-1509 _/ _/ 1 University of New Mexico email: susie{at}sapphire.phys.unm.edu _/ _/ Albuquerque, NM 87131-0001 http://www.phys.unm.edu/CompMaterials _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From chemistry-request@ccl.net Wed Oct 15 15:06:57 2003 Received: from alvin.unc.edu.ar (alvin.unc.edu.ar [170.210.248.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9FJ6NdH008807 for ; Wed, 15 Oct 2003 15:06:24 -0400 Received: from mail.fcq.unc.edu.ar (localhost.localdomain [127.0.0.1]) by alvin.unc.edu.ar (8.11.6/8.11.6) with ESMTP id h9FJ6Kr21624 for ; Wed, 15 Oct 2003 16:06:20 -0300 Received: from localhost (malisa@localhost) by mail.fcq.unc.edu.ar (8.11.2/8.11.2) with ESMTP id h9FIwkR08857 for ; Wed, 15 Oct 2003 15:58:46 -0300 Date: Wed, 15 Oct 2003 15:58:46 -0300 (ART) From: Malisa Chiappero To: Subject: Summary:Using GEN (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi A) QUestion Hi I should need help about GEN use in gaussian. I try to do some calculation using diferent basis set for different atoms Like this #P rhf/GEN geometry specification C F Cl O 0 6-311+G* **** I 0 SDD or LANL2DZ **** Br 0 6-31+g(d) but the calculations were aborted. It is possible that another keyword or specification we need take into account, or Are they incompatible? Thank you in advance. Malisa ______________________________________________________________________ B)This is the answer with examples _______________________________________ Dear Malisa, Your input still includes only the valence basis set information. Here is my example input again, but with added comments: #p hf/gen pseudo=read gfinput test Cr(CO)6 0 1 Cr 0.00 0.00 0.00 C 1.93 0.00 0.00 C -1.93 0.00 0.00 C 0.00 1.93 0.00 C 0.00 -1.93 0.00 C 0.00 0.00 1.93 C 0.00 0.00 -1.93 O 3.07 0.00 0.00 O -3.07 0.00 0.00 O 0.00 3.07 0.00 O 0.00 -3.07 0.00 O 0.00 0.00 3.07 O 0.00 0.00 -3.07 Cr 0 <<<<< valence basis set on all Cr atoms lanl2dz F 1 1.0 0.1 1.0 **** C O 0 <<<<< valence basis set on all C and O atoms 6-311G(d,p) **** <<<<<<< blank line terminates valence basis set input Cr 0 <<<<<<<< ECP on all Cr atoms lanl2 So, the keyword you need is pseudo=read, and you need an extra couple of lines of input after the valence basis set. For your case the extra lines of input would be: ----------------------------------------------------------------- 6-311+G* **** I 0 SDD (or LANL2DZ) **** I 0 SDD (or lanl2) Regards, Jim Hess ----------------------------------------------------------------- All the other comments are similar: -I think Gaussian quitted because the ECP for I is missing. So you can edit your input file as the following. #P rhf/GEN PSEUDO=Cards geometry specification C F Cl O 0 6-311+G* **** I 0 SDD or LANL2DZ **** Br 0 6-31+g(d) **** I 0 SDD or LANL2DZ Moreover, SDD is better for Br, too. And ECP can save your CPU time. Good luck, Malisa. Yubo ---------------------------------------------------------- Hi Malisa I'm not entirely sure about this but if you want to use an ECP (like LANL2DZ) along with a general basis set you should use the keyword 'GENECP'. Also - don't forget about the invisible blank line after the final line, so (for example) here is some input that did work for me - C N H 0 6-31G(d) **** Ru 0 LANL2DZ **** Ru 0 LANL2DZ After the final 'Z' above you need to press enter twice and then save before submitting the job to G03. Hope this helps Regards Roma --------------------------------------------------------- Hi Malisa Please add ECP to your I. so the input should be #P rhf/GEN psudo=read geometry specification C F Cl O 0 6-311+G* **** I 0 SDD or LANL2DZ **** Br 0 6-31+g(d) **** I 0 LANL2DZ That should fix your problem. Best wishes. Huajun ------------------------------------------------------------ two things may be related to your problem, 1) just below the basis set line of Br, **** is also required 2) you had better define PP for the atoms you will use SDD or Lanl2dz basis sets. hopefully it will work, Yixuan ------------------------------------------------------------ As long as you avoid pseudopotential basis sets (SDD and LANL2DZ), '#p rhf/gen' will work fine. However, since you want to use pseudopotentials, you need '#p rhf/gen pseudo=read' plus additional input to specify the pseudopotentials that go with the pseudopotential basis sets. --David Shobe S|d-Chemie, Inc. ----------------------------------------------------------- Hi, For one, I find that the keyword works better when each atom type is listed separately. So, C, F, and Cl would require their basis specifications listed one after the other. Also, you should specify the ECP separately at the end of the basis set specifications, terminated by a blank line. Hope this fixes your problems. Bala Balakrishnan Viswanathan Department of Chemistry Dalhousie University Halifax, Nova Scotia Canada B3H 4J3 (902) 494-7021 bviswan/at/chem1.chem.dal.ca ------------------------------------------------------------ \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ /////////////////////////////////////////////////////////// Another answer (My mistake to write the e-mail) ____________________________________________________________ You need to have a final **** at the end of your GEN block. You also need to make sure that you are reading in the effective core potential. Look at the keyword pseudo for more information. Joseph Han Department of Chemical Engineering Stanford University 650-723-0420 FAX: 650-725-7294 ____________________________________________________________ Hi, You should include four asterisks (****) after each basis set (you did not include them in the last one) and also a blank line after the last four asterisks at the end of the input file. I hope this would help. Juan F. Espinal ___________________________________________________________ Thank you very much to all Best regards MAlisa From jkl@ccl.net Thu Oct 16 09:08:13 2003 -0400 Return-Path: Message-ID: <006501c393c9$24f93fd0$c6b3ccc1:at:farmacia.uniba.it> From: "Angelo Favia" To: chemistry:at:ccl.net Subject: Running Amber 7.0 on a linux cluster Date: Thu, 16 Oct 2003 11:37:34 +0200 MIME-Version: 1.0 Dear CCl members, does anyone of you try to run Amber 7.0 on a linux cluster (openMosix patch)? I'd like to parallelize it... tanks in advance. angelo favia From chemistry-request@ccl.net Thu Oct 16 15:25:25 2003 Received: from cornell.edu (cornell.edu [132.236.56.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9GJOrdH004527 for ; Thu, 16 Oct 2003 15:24:53 -0400 Received: from dopey (dopey.ccmr.cornell.edu [128.84.241.121]) by cornell.edu (8.9.3p2/8.9.3) with SMTP id PAA22613 for ; Thu, 16 Oct 2003 15:24:54 -0400 (EDT) Message-ID: <000d01c3941b$2d1514d0$6400000a.-at-.ccmr.cornell.edu> From: "Connie Chang" To: Subject: CCL: Help with interpretation of Gaussian error message? Date: Thu, 16 Oct 2003 15:24:53 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000A_01C393F9.A5EDF100" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=1.9 required=7.0 tests=FROM_ENDS_IN_NUMS,HTML_40_50,HTML_MESSAGE version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------=_NextPart_000_000A_01C393F9.A5EDF100 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi -- What does this Gaussian03 error message mean? Fock matrices will be formed incrementally for 20 cycles. Integral accuracy reduced to 1.0D-05 until final iterations. Inconsistent input #3 in SPerMO. Error termination via Lnk1e in C:\g03w\l502.exe at Thu Oct 16 15:12:38 = 2003. Job cpu time: 0 days 0 hours 2 minutes 12.0 seconds. File lengths (MBytes): RWF=3D 496 Int=3D 0 D2E=3D 0 = Chk=3D 1 Scr=3D 1 I'm trying to do a force calculation on an already optimized geometry in = the presence of a field... thanks! connie ------=_NextPart_000_000A_01C393F9.A5EDF100 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi --
 
What does this Gaussian03 error message = mean?
 
Fock matrices will be formed = incrementally=20 for  20 cycles.
 Integral accuracy reduced to 1.0D-05 until = final=20 iterations.
 Inconsistent input #3 in SPerMO.
 Error = termination=20 via Lnk1e in C:\g03w\l502.exe at Thu Oct 16 15:12:38 2003.
 Job = cpu=20 time:  0 days  0 hours  2 minutes 12.0 = seconds.
 File=20 lengths (MBytes):  RWF=3D    496=20 Int=3D      0 = D2E=3D      0=20 Chk=3D      1 = Scr=3D     =20 1
 
 
I'm trying to do a force calculation on = an already=20 optimized geometry in the presence of a field...
 
thanks!
 
connie
------=_NextPart_000_000A_01C393F9.A5EDF100-- From chemistry-request@ccl.net Thu Oct 16 04:36:58 2003 Received: from violet.noc.ucla.edu (violet.noc.ucla.edu [169.232.47.18]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9G8aQdH022154 for ; Thu, 16 Oct 2003 04:36:26 -0400 Received: from orchid.noc.ucla.edu (orchid.noc.ucla.edu [169.232.48.12]) by violet.noc.ucla.edu (8.12.8p2/8.12.8) with ESMTP id h9G8aQ8c029995 for ; Thu, 16 Oct 2003 01:36:26 -0700 Received: from dsievers (23.226.nwc.net [207.151.226.23]) (authenticated bits=0) by orchid.noc.ucla.edu (8.12.9p1/8.12.9) with ESMTP id h9G8aOpD006666 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for ; Thu, 16 Oct 2003 01:36:25 -0700 Message-ID: <000701c393c0$3096d0e0$7700a8c0[at]ucla.triangle.org> From: "Doug Sievers" To: "CCL" Subject: gOpenMol Date: Thu, 16 Oct 2003 01:33:31 -0700 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 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Probable-Spam: no X-Spam-Hits: 0 X-Scanned-By: vscan.smtp.ucla.edu X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) In the most recent release of gOpenMol (for windows) By default, when one changes from global to local mode, the coordinates of the structure are reset. The user manual says that this default can be changed so that the coordinates do not change, which would be useful to set up several molecules for an MD run. Does anyone know how to change the default behavior? Thank you, Douglas Sievers Graduate Student Researcher Materials Science & Engineering 3049 Engineering 1 (310) 794-6491 dsievers[at]ucla.edu From chemistry-request@ccl.net Thu Oct 16 03:15:39 2003 Received: from ozone.cs.vu.nl (ozone.cs.vu.nl [130.37.24.158]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9G7F8dH020185 for ; Thu, 16 Oct 2003 03:15:08 -0400 Received: from chem.vu.nl (far27.chem.vu.nl [130.37.148.106]) by ozone.cs.vu.nl with esmtp (Smail #87) id m1AA2Lj-000NGxC; Thu, 16 Oct 2003 09:15 +0200 Message-ID: <3F8E462E.4060407~at~chem.vu.nl> Date: Thu, 16 Oct 2003 09:18:06 +0200 From: Anton Feenstra User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.4.1) Gecko/20031008 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry~at~ccl.net Subject: CCL:PhD and Deep Questions References: <3F8D7A23.7DAC51E3~at~sapphire.phys.unm.edu> In-Reply-To: <3F8D7A23.7DAC51E3~at~sapphire.phys.unm.edu> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-1.1 required=7.0 tests=IN_REP_TO,REFERENCES,USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, I'd just like to add that after reading these, shall I say philosophical, exchanges on Philosophy, I find the other postings on the list awfully mundane, like: "Error linking DL_POLY", or "Autodock output file format"... Let's not forget that these extremely specialized bits of knowledge only make sense in the larger context of our common quest for Knowledge! -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 | | | Feenstra~at~chem.vu.nl - www.chem.vu.nl/~feenstra/ | | | "If You See Me Getting High, Knock Me Down" | | | (Red Hot Chili Peppers) | |_____________|_______________________________________________________| From chemistry-request@ccl.net Thu Oct 16 00:55:48 2003 Received: from chem.udel.edu (chem.udel.edu [128.175.138.224]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9G4t7dH017693 for ; Thu, 16 Oct 2003 00:55:08 -0400 Received: from localhost (pradyu@localhost) by chem.udel.edu (8.9.3/8.9.3) with ESMTP id AAA114383; Thu, 16 Oct 2003 00:56:54 -0400 (EDT) Date: Thu, 16 Oct 2003 00:56:54 -0400 From: "Pradyumna S. Singh" To: "Susan R. Atlas" cc: chemistry~at~ccl.net Subject: Re: CCL:PhD and Deep Questions In-Reply-To: <3F8D7A23.7DAC51E3~at~sapphire.phys.unm.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-1.0 required=7.0 tests=IN_REP_TO,QUOTED_EMAIL_TEXT,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) > > By the way, there is a recent (1999), beautifully-written book by Prof. > E. O. Wilson, entitled Consilience, that addresses precisely this > question of "the unity of knowledge." Ohh and btw, there is a fabulous critique of that book by the American poet Wendell Berry in his book, "Life is a Miracle" ! Be sure to check it out as well. Pradyumna From chemistry-request@ccl.net Thu Oct 16 20:38:53 2003 Received: from mail.cybermesa.com (mail.cybermesa.com [198.59.109.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9H0cMdH010019 for ; Thu, 16 Oct 2003 20:38:22 -0400 Received: from dave (qwest96-dsl3.cybermesa.com [216.84.163.96]) by mail.cybermesa.com (8.11.6/8.11.6) with SMTP id h9H0ckA06859 for ; Thu, 16 Oct 2003 18:38:46 -0600 (MDT) From: "David Miller" To: Subject: CCL: ChemTK supports SMILES Date: Thu, 16 Oct 2003 18:40:29 -0500 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 X-Spam-Status: No, hits=-0.4 required=7.0 tests=MSGID_GOOD_EXCHANGE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) ChemTK version 2.7 is now available for download from: http://www.sageinformatics.com New features include: - Support for SMILES files (*.smi) in all ChemTK features, including visualization, scaffold-based class generation, descriptor and model generation, substructure/property search, R tables and MCS. - Display of individual SMILES strings entered into a custom dialog. - Support for SMILES files in Batch menu operations such as filter, virtual screen, similarity screen, random selection and error check. - Ability to enlarge molecule depictions in the Class/Molecule views. Visit http://www.sageinformatics.com to download the ChemTK product sheet, documentation, and release notes, and to learn more about the inexpensive licensing terms. Best regards, David W. Miller, Ph.D. Sage Informatics LLC dmiller~at~sageinformatics.com From chemistry-request@ccl.net Thu Oct 16 11:05:25 2003 Received: from soul.helsinki.fi (soul.helsinki.fi [128.214.3.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9GF4rdH031624 for ; Thu, 16 Oct 2003 11:04:54 -0400 Received: from localhost (mpjohans@localhost) by soul.helsinki.fi (8.9.2/8.9.3) with ESMTP id SAA78294 for ; Thu, 16 Oct 2003 18:04:52 +0300 (EEST) X-Authentication-Warning: soul.helsinki.fi: mpjohans owned process doing -bs Date: Thu, 16 Oct 2003 18:04:52 +0300 (EEST) From: Mikael Johansson X-X-Sender: mpjohans_at_soul.helsinki.fi To: chemistry_at_ccl.net Subject: Winter School in Theoretical Chemistry 2003 In-Reply-To: <006501c393c9$24f93fd0$c6b3ccc1_at_farmacia.uniba.it> Message-ID: References: <006501c393c9$24f93fd0$c6b3ccc1_at_farmacia.uniba.it> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-15 X-Spam-Status: No, hits=-1.4 required=7.0 tests=IN_REP_TO,REFERENCES,USER_AGENT_PINE,X_AUTH_WARNING version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id h9GF5PdH031645 Hello All! It's time for the annual Winter School in Theoretical Chemistry to take place again in Helsinki, Finland. This years topic is: "Quantum Chemistry Bordering Nanoscience and Nanotechnology" The School will be held on December 8-11, 2003, at the Department of Chemistry, University of Helsinki. This years speakers are: Reinhart Ahlrichs Roi Baer Hannu Hdkkinen Jouko Korppi-Tommola Yi Luo Bernadette Quinn Florian Weigend The School is free for university students and staff, but you are asked to register by November 15, by e-mailing Dr. Juha Vaara at jvaara_at_chem.helsinki.fi. For more details, please visit the home page of the School: http://www.chem.helsinki.fi/Info/WinterSchool/ws2003.html Have a nice day, Mikael Johansson University of Helsinki Department of Chemistry mikael.johansson_at_helsinki.fi http://www.helsinki.fi/~mpjohans/ Phone: +358-9-191 50185 FAX : +358-9-191 50169