From chemistry-request@server.ccl.net Wed Feb 26 07:52:39 2003 Received: from turmiel.ch.uj.edu.pl ([149.156.71.252]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1QCqda16499 for ; Wed, 26 Feb 2003 07:52:39 -0500 Received: from chemia.uj.edu.pl (localhost [127.0.0.1]) by turmiel.ch.uj.edu.pl (8.11.6/8.11.6) with SMTP id h1QCqXv04520 for ; Wed, 26 Feb 2003 13:52:33 +0100 Received: from ether311.ch.uj.edu.pl ([149.156.95.11]) (SquirrelMail authenticated user migda) by mail.ch.uj.edu.pl with HTTP; Wed, 26 Feb 2003 13:52:33 +0100 (CET) Message-ID: <1314.149.156.95.11.1046263953.squirrel@mail.ch.uj.edu.pl> Date: Wed, 26 Feb 2003 13:52:33 +0100 (CET) Subject: Force field for N,O-acetals From: "Wojciech Migda" To: X-Priority: 3 Importance: Normal Reply-To: migda@chemia.uj.edu.pl X-Mailer: SquirrelMail (version 1.2.8) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-2 Content-Transfer-Encoding: 8bit X-Virus-Scanned: by AMaViS-perl11-milter (http://amavis.org/) Hi, I am looking for forcefield parameters for moelcular mechanics calculation of geometries of N,O-acetals. Thank you in advance Wojciech Migda migda@chemia.uj.edu.pl Jagiellonian University, Krakow, POLAND From chemistry-request@server.ccl.net Wed Feb 26 08:45:32 2003 Received: from imaph.bas-net.by ([80.94.164.102]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1QDhha17720 for ; Wed, 26 Feb 2003 08:43:44 -0500 Received: from igor (igor [10.1.1.15]) by imaph.bas-net.by (8.12.5/8.12.5) with ESMTP id h1QEB9pl028936 for ; Wed, 26 Feb 2003 16:11:10 +0200 Date: Wed, 26 Feb 2003 15:43:43 +0200 From: Igor Avilov X-Mailer: The Bat! (v1.45) Educational Reply-To: Igor Avilov X-Priority: 3 (Normal) Message-ID: <6896844555.20030226154343@imaph.bas-net.by> To: chemistry@ccl.net Subject: error in Gaussian98 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCl users! Could you help me with the following problem, please? I'm trying to compute the vibrational spectrum of the large molecule in the triplet state at UB3LYP/6-31G(d) level. Basis include 638 basis functions. After several days computation ends up in the following way (without indication of the error type): Annihilation of the first spin contaminant: S**2 before annihilation 2.0607, after 2.0020 Range of M.O.s used for correlation: 1 638 NBasis= 638 NAE= 134 NBE= 132 NFC= 0 NFV= 0 NROrb= 638 NOA= 134 NOB= 132 NVA= 504 NVB= 506 **** Warning!!: The smallest alpha delta epsilon is 0.51253642D-01 **** Warning!!: The smallest beta delta epsilon is 0.57596594D-01 G2DrvN: will do 36 atoms at a time, making 2 passes doing MaxLOS=2. FoFDir used for L=0 through L=2. Differentiating once with respect to electric field. with respect to dipole field. Differentiating once with respect to nuclear coordinates. Integrals replicated using symmetry in FoFDir. MinBra= 0 MaxBra= 2 Meth= 1. IRaf= 0 NMat= 110 IRICut= 110 DoRegI=T DoRafI=T ISym2E= 2 JSym2E=2. Raff turned off since only 44.01% of shell-pairs survive. There are 219 degrees of freedom in the 1st order CPHF. writwa Best regards, Igor Avilov. From chemistry-request@server.ccl.net Tue Feb 25 23:49:47 2003 Received: from web12602.mail.yahoo.com ([216.136.173.225]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h1Q4nka26894 for ; Tue, 25 Feb 2003 23:49:47 -0500 Message-ID: <20030226044946.51375.qmail@web12602.mail.yahoo.com> Received: from [143.111.14.169] by web12602.mail.yahoo.com via HTTP; Tue, 25 Feb 2003 20:49:46 PST Date: Tue, 25 Feb 2003 20:49:46 -0800 (PST) From: Mao Xiang Subject: question about the protonated histidine To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello, everyone: I wonder if it is possible that there are protonated histidines in enzyme near active site. Thanks in advance. Best Regards, Teng __________________________________________________ Do you Yahoo!? Yahoo! Tax Center - forms, calculators, tips, more http://taxes.yahoo.com/ From chemistry-request@server.ccl.net Wed Feb 26 08:27:14 2003 Received: from sina.com ([202.106.187.156]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h1QDRBa17247 for ; Wed, 26 Feb 2003 08:27:12 -0500 Message-Id: <200302261327.h1QDRBa17247@server.ccl.net> Received: (qmail 92608 invoked from network); 26 Feb 2003 13:16:16 -0000 Received: from unknown (HELO njuitccwx) (202.119.32.30) by 202.106.187.156 with SMTP; 26 Feb 2003 13:16:16 -0000 Date: Wed, 26 Feb 2003 21:26:4 +0800 From: wxin To: "chemistry@ccl.net" Subject: Question about the initial guess in G98 X-mailer: FoxMail 3.11 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Dear ccl-listers, In program Gaussian98 one can use the converged wavefunction of one basis set as the initial guess wavefunction for another basis set. Who can tell me in detail that how the Gaussian program handle these wavefunctions expanded by different basis sets, that is how to use one wavefunction of one basis set as the initial guess for the wavefunction of another basis set. Thanks! Xin Wang Institute of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Nanjing University Nanjing, 210093 P. R. China From chemistry-request@server.ccl.net Wed Feb 26 09:57:02 2003 Received: from patronimo.umh.ac.be ([193.190.193.113]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1QEv1a19541 for ; Wed, 26 Feb 2003 09:57:02 -0500 Received: from patronimo (patronimo [193.190.193.113]) by patronimo.umh.ac.be (8.12.6/8.12.6) with ESMTP id h1QEugVn118446; Wed, 26 Feb 2003 15:56:42 +0100 Date: Wed, 26 Feb 2003 15:56:42 +0100 (NFT) From: Victor Geskin X-X-Sender: Victor@patronimo To: Igor Avilov cc: chemistry@ccl.net Subject: Re: CCL:error in Gaussian98 In-Reply-To: <6896844555.20030226154343@imaph.bas-net.by> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Scanned-By: MIMEDefang 2.1 (www dot roaringpenguin dot com slash mimedefang) I am forwarding the reply to a similar question, concerning the warning, I recently obtained from the Gaussian support. (Though my calculation terminated normally.) So, the problem might be in diffuse functions, see below. Victor GESKIN e-mail: Victor@averell.umh.ac.be TD-DFT Warning in Gaussian This message can be considered a warning. In other words, the results are not necessary erroneous. If the delta-epsilon were too small, the error message would be "Fatal Problem: The smallest beta delta epsilon...". The usual cause of this warning is too much linear dependence in the basis set. Basis set linear dependency is often associated with the presence of very diffuse functions in the basis set, so one must balance the desire to have diffuse functions to describe the excited states with the possible numerical problems associated with too many diffuse functions, or functions that are too diffuse. Regards, Jim Hess ++++++++++++++++++++++++++ James Hess, Ph.D. Customer Support Scientist Gaussian, Inc. e-mail: help@gaussian.com ++++++++++++++++++++++++++ On Wed, 26 Feb 2003, Igor Avilov wrote: > Dear CCl users! > > Could you help me with the following problem, please? > > I'm trying to compute the vibrational spectrum of the large molecule > in the triplet state at UB3LYP/6-31G(d) level. Basis include 638 > basis functions. After several days computation ends up in the > following way (without indication of the error type): > > Annihilation of the first spin contaminant: > S**2 before annihilation 2.0607, after 2.0020 > Range of M.O.s used for correlation: 1 638 > NBasis= 638 NAE= 134 NBE= 132 NFC= 0 NFV= 0 > NROrb= 638 NOA= 134 NOB= 132 NVA= 504 NVB= 506 > > **** Warning!!: The smallest alpha delta epsilon is 0.51253642D-01 > > > **** Warning!!: The smallest beta delta epsilon is 0.57596594D-01 > > G2DrvN: will do 36 atoms at a time, making 2 passes doing MaxLOS=2. > FoFDir used for L=0 through L=2. > Differentiating once with respect to electric field. > with respect to dipole field. > Differentiating once with respect to nuclear coordinates. > Integrals replicated using symmetry in FoFDir. > MinBra= 0 MaxBra= 2 Meth= 1. > IRaf= 0 NMat= 110 IRICut= 110 DoRegI=T DoRafI=T ISym2E= 2 JSym2E=2. > Raff turned off since only 44.01% of shell-pairs survive. > There are 219 degrees of freedom in the 1st order CPHF. > writwa > > Best regards, > Igor Avilov. > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > ___________________________________________________________________ Dr Victor GESKIN e-mail: Victor@averell.umh.ac.be Service de Chimie http://morris.umh.ac.be des Materiaux Nouveaux Universite de Mons-Hainaut phone: +32-(0)65.37.38.67 Place du Parc, 20 fax: +32-(0)65.37.38.61 B-7000 MONS, BELGIQUE GSM: +32-(0)486.779.799 ___________________________________________________________________ From chemistry-request@server.ccl.net Wed Feb 26 17:25:23 2003 Received: from facepe.dqf.ufpe.br ([150.161.5.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1QMPLa29456 for ; Wed, 26 Feb 2003 17:25:23 -0500 Received: from dqf.ufpe.br ([150.161.5.90]) by facepe.dqf.ufpe.br (8.12.6/8.12.6) with ESMTP id h1QK1N2G007153; Wed, 26 Feb 2003 17:01:25 -0300 (BRT) (envelope-from sidney@dqf.ufpe.br) Message-ID: <3E5D32C0.1040505@dqf.ufpe.br> Date: Wed, 26 Feb 2003 18:33:52 -0300 From: Sidney Ramos de Santana User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020830 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CPMD List , CCL List Subject: Problems in the Instalation of CPMD3.7 with IFC Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear CPMD and CCL Users, I tried to install the CPMD3.7 with Intel Fotran Compiler 7.0 in the RedHat Linux 8.0. But, I don't have sucessful. Please see below my Default Configuration in the Makefile: #--------------- Default Configuration for PC-IFC --------------- SRC = . DEST = . BIN = . #QMMM_FLAGS = -D__QMECHCOUPL #QMMM_LIBS = -L. -lmm FFLAGS = -c -r8 -w90 -w95 -O3 -pc64 -axM -ip -tpp7 #LFLAGS = -llapack-ifc -lf77blas-ifc -latlas-ifc -Vaxlib $(QMMM_LIBS) CFLAGS = -c -O3 -Wall CPP = /lib/cpp -P -C -traditional #CPPFLAGS = -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT -DLINUX_IFC CPPFLAGS = -D__Linux -DLAPACK -DFFT_DEFAULT -DLINUX_IFC NOOPT_FLAG = CC = gcc FC = ifc LD = ifc AR = ar In the end of the compilation, it stop and write: cpmd.o: In function `cpmd_': cpmd.o(.text+0x51): undefined reference to `signal_' cpmd.o(.text+0x68): undefined reference to `signal_' envir.o: In function `envir_': envir.o(.text+0x2f): undefined reference to `getenv_' envir.o(.text+0x3e): undefined reference to `getcwd_' envir.o(.text+0x46): undefined reference to `getpid_' envir.o(.text+0x50): undefined reference to `getuid_' control.o: In function `control_': control.o(.text+0x53): undefined reference to `iargc_' control.o(.text+0xf9): undefined reference to `sleep_' util.o: In function `my_flush_': util.o(.text+0x11): undefined reference to `flush_' util.o: In function `datum_': util.o(.text+0x143b): undefined reference to `fdate_' util.o: In function `invmat_': util.o(.text+0x14a1): undefined reference to `dgetrf_' util.o(.text+0x14d6): undefined reference to `dgetri_' util.o: In function `inversemat_': util.o(.text+0x1543): undefined reference to `dgetrf_' util.o(.text+0x157c): undefined reference to `dgetri_' util.o: In function `dspevy_': .... and it write a lot of this error in almost all .... rhoofr_kdp.o: In function `rhoofr_kdp_': rhoofr_kdp.o(.text+0x4a6): undefined reference to `dcopy_' mm_cpmd_esp_charges_f77.o: In function `mm_cpmd_esp_charges_f77_': mm_cpmd_esp_charges_f77.o(.text+0x2eb): undefined reference to `dcopy_' make: *** [cpmd.x] Error 1 Command exited with non-zero status 2 565.24user 28.62system 10:12.99elapsed 96%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (927583major+1588614minor)pagefaults 0swaps Please, could someone help me ? What can I do ? Respectfully, Sidney Ramos Graduate Program of Materials Science - CCEN - UFPE From chemistry-request@server.ccl.net Wed Feb 26 18:09:43 2003 Received: from mserv.itpa.lt ([193.219.53.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1QN9ga30328 for ; Wed, 26 Feb 2003 18:09:42 -0500 Received: from mserv.itpa.lt (localhost [127.0.0.1]) by mserv.itpa.lt (8.12.7/8.12.6) with ESMTP id h1QN9awk016134; Thu, 27 Feb 2003 01:09:41 +0200 (EET) (envelope-from tamulis@mserv.itpa.lt) Received: from localhost (tamulis@localhost) by mserv.itpa.lt (8.12.7/8.12.6/Submit) with ESMTP id h1QN9ZlG016131; Thu, 27 Feb 2003 01:09:35 +0200 (EET) Date: Thu, 27 Feb 2003 01:09:35 +0200 (EET) From: Arvydas Tamulis To: chemistry@ccl.net cc: rinkevic@TheoChem.kth.se Subject: UHF-TD ? Message-ID: <20030227005808.S13573-100000@mserv.itpa.lt> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, I have tried to calculate neutral radical molecule with one unpaired spin using G98: #P UHF EPR-II TD(NStates=9,Root=2) Density=all Pop=Full IOp(6/12=3) I have received two sets of results: 1) Population analysis using the CI one-particle density. Total atomic charges: ... Total atomic spin densities: ... etc. and 2) Population analysis using the CI density. Total atomic charges: ... Total atomic spin densities: ... etc. My question is which set of results corresponds to UHF-TD ? Maybe here are two UHF-TD results with different approximations. Or maybe here are just two variants of UHF-CIS and UHF-TD does not calculating at all? Regards, Arvydas Tamulis ******************************************************************* Temporal address until 30 April 2004: Los Alamos National Laboratory Center for Nonlinear Studies P.O. Box 1663, Mail Stop B258 Los Alamos, New Mexico 87545 Work Phone: 1 505 667-7278 Fax: 1 505 665-2659 e-mail: tamulis@cnls.lanl.gov *******************************************************************