From chemistry-request@ccl.net Thu Jul 7 04:00:09 2005 Received: from poster.sci.kun.nl (poster.sci.kun.nl [131.174.124.7]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j67806Po018543 for ; Thu, 7 Jul 2005 04:00:07 -0400 Received: from multi.science.ru.nl [131.174.16.159] (helo=multi.science.ru.nl) by poster.sci.kun.nl (8.12.10/5.0) with ESMTP id j67805v7001267 for ; Thu, 7 Jul 2005 10:00:05 +0200 (MEST) Received: from chemo14.sci.kun.nl [131.174.179.49] (helo=chemo14.sci.kun.nl) by multi.science.ru.nl (8.12.10/5.0) with ESMTP id j677xwEx004981; Thu, 7 Jul 2005 09:59:58 +0200 (MEST) From: Egon Willighagen Reply-To: e.willighagen/at/science.ru.nl Organization: Radboud Universiteit Nijmegen To: chemistry/at/ccl.net Subject: Re: CCL: Concord/Corina replacements for Linux X-Enigmail-Version: 0.90.2.0 X-Accept-Language: en Date: Thu, 7 Jul 2005 10:03:37 +0200 User-Agent: KMail/1.8.1 References: <94832e07b3c1.42cbfc0f/at/jhumail.jhu.edu> In-Reply-To: <94832e07b3c1.42cbfc0f/at/jhumail.jhu.edu> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Content-Disposition: inline Message-Id: <200507071003.37879.e.willighagen/at/science.ru.nl> X-Spam-Score: -1.665 () BAYES_00 X-Scanned-By: MIMEDefang 2.48 on 131.174.16.159 X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net On Wednesday 06 July 2005 09:43 pm, SANDEEP KUMAR wrote: > If you don't wish to use CORINA at all (not even the 1 month free trial > version), then you might like to try this. The 1 month trial does not allow you to use the results of 3D generation *after* that period. So for most research that is not useful. Egon From chemistry-request@ccl.net Thu Jul 7 03:39:08 2005 Received: from smtp-out.rrz.uni-koeln.de (smtp-out.rrz.uni-koeln.de [134.95.19.53]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j677d481017036 for ; Thu, 7 Jul 2005 03:39:04 -0400 Received: from smtp-auth.rrz.uni-koeln.de (smtp-auth.rrz.uni-koeln.de [134.95.19.93]) by smtp-out.rrz.uni-koeln.de (8.13.1/8.13.1) with ESMTP id j677d37m032320 for ; Thu, 7 Jul 2005 09:39:03 +0200 Received: from [134.95.200.21] (relax.cubic.uni-koeln.de [134.95.200.21]) (authenticated as user acc91 using CRAM-MD5 bits=0) by smtp-auth.uni-koeln.de (8.13.1/8.13.1) with ESMTP id j677d2Q4032317 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NO) for ; Thu, 7 Jul 2005 09:39:03 +0200 Message-ID: <42CCDC19.60407(at)uni-koeln.de> Date: Thu, 07 Jul 2005 09:39:05 +0200 From: Christoph Steinbeck User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry(at)ccl.net Subject: Re: CCL: 3D to chemical name References: <20050706203344.20245.qmail(at)web33803.mail.mud.yahoo.com> In-Reply-To: <20050706203344.20245.qmail(at)web33803.mail.mud.yahoo.com> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-new X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net michelle claro wrote: > Hello, > > I have about 50 pdb structures (no protein in the pdb just the ligand) > but I need the chemical names in order to purchase them. What is the > easiest way to get a chemical name from a pdb? Thanks in advance. > > M. Claro You could convert them to SMILES with one of the common tools (OpenBabel, for example) and use the SMILES to search the ZINC database (http://blaster.docking.org/zinc/). The result will even contain the vendor to buy from. Cheers, Chris -- Priv. Doz. Dr. Christoph Steinbeck (c.steinbeck(at)uni-koeln.de) Head of the Research Group for Molecular Informatics Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.de) Z|lpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. From chemistry-request@ccl.net Thu Jul 7 05:28:30 2005 Received: from mx1.ustc.edu.cn ([202.38.64.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j679SO55031225 for ; Thu, 7 Jul 2005 05:28:25 -0400 Received: from dxl ([210.45.66.65]) by mx1.ustc.edu.cn (8.11.6/8.11.6) with SMTP id j679Npf24153; Thu, 7 Jul 2005 17:23:51 +0800 Message-Id: <200507070923.j679Npf24153-.at.-mx1.ustc.edu.cn> Date: Thu, 7 Jul 2005 17:29:33 +0800 From: "Ding Xunlei" Reply-To: dxl-.at.-ustc.edu.cn To: "chemistry" , "molpro-user" Subject: why casscf not converge in an opt calculation in molpro Organization: University of Science and Technology of China X-mailer: Foxmail 5.0 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="gb2312" X-Spam-Status: No, score=1.8 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_WHOIS,MIME_BASE64_BLANKS,MIME_BASE64_TEXT autolearn=no version=3.0.4 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id j679SU55031272 Dear chemistry#: In molpro calculations with casscf, I found a puzzle. If omit the "optg" from the input file below, the casscf calculation will converge. If use the "optg", the casscf calculation will not converge. If use "frequencies" instead of "optg", the casscf calculation will also not converge. Why? **** CO2 scan r1=1.2 Ang geometry C O1 ,C, r1 O2 ,C, r1, O1,180 end gprint,basis,orbitals basis spd,c,vdz;c spd,o,vdz;c end hf casscf optg Thank you for your help! Yours sincerely, Ding Xunlei 2005-07-07 ______________________________________________ From chemistry-request@ccl.net Thu Jul 7 04:00:51 2005 Received: from hawk.dcu.ie (mail.dcu.ie [136.206.1.5]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j6780ncU018610 for ; Thu, 7 Jul 2005 04:00:49 -0400 Received: from [131.111.121.130] by hawk.dcu.ie with HTTP; Thu, 7 Jul 2005 09:00:46 +0100 Date: Thu, 7 Jul 2005 09:00:46 +0100 Message-ID: <4282FBD500041F54(at)hawk.dcu.ie> In-Reply-To: <20050706203344.20245.qmail(at)web33803.mail.mud.yahoo.com> From: "Noel O'Boyle" Subject: RE: CCL: 3D to chemical name To: chemistry(at)ccl.net Cc: mclaro2727(at)yahoo.com MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j6780pcU018614 Dear Claro, Many chemical don't have simple names, and many suppliers use different names for the same chemical. What you need is the supplier code for the chemical. It is sometimes possible (for example, on the sigma-aldrich webpage) to search the supplier's catalogue using the chemical formula, or by drawing the molecule on the web page. A note of warning: often the ligand structures taken from pdb files contain just the carbon skeleton, and are missing protons and bond orders. Just to make your life easier :-) Regards, Noel O'Boyle. >-- Original Message -- >Date: Wed, 6 Jul 2005 13:33:44 -0700 (PDT) >From: michelle claro >Subject: CCL: 3D to chemical name >To: chemistry(at)ccl.net >Reply-To: chemistry(at)ccl.net > > >Hello, > >I have about 50 pdb structures (no protein in the pdb just the ligand) but >I need the chemical names in order to purchase them. What is the easiest >way to get a chemical name from a pdb? Thanks in advance. > >M. Claro > > >__________________________________________________ >Do You Yahoo!? >Tired of spam? Yahoo! Mail has the best spam protection around >http://mail.yahoo.com From chemistry-request@ccl.net Thu Jul 7 17:07:26 2005 Received: from mailgate1.uni-kl.de (mailgate1.uni-kl.de [131.246.120.5]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j67L7OOA011293 for ; Thu, 7 Jul 2005 17:07:25 -0400 Received: from service.chemie.uni-kl.de (service.chemie.uni-kl.de [131.246.58.77]) by mailgate1.uni-kl.de (8.13.1/8.13.1) with ESMTP id j67KTZSx009920 for ; Thu, 7 Jul 2005 22:29:35 +0200 Received: from pc1.chemie.uni-kl.de (pc1.chemie.uni-kl.de [131.246.58.1]) by service.chemie.uni-kl.de (Postfix) with ESMTP id 515CD36CF2 for ; Thu, 7 Jul 2005 22:29:29 +0200 (CEST) Received: by pc1.chemie.uni-kl.de (Postfix, from userid 2017) id 3B53A8132C; Thu, 7 Jul 2005 22:29:35 +0200 (CEST) Date: Thu, 7 Jul 2005 22:29:35 +0200 From: Elmar Gerwalin To: CHEMISTRY !v! ccl.net Subject: CCL: dissociation problem in PCM model ? Message-ID: <20050707202935.GA10202 !v! pc1.chemie.uni-kl.de> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.5.6i X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Hi, I'm trying to describe dissociation processes in some small organic molecules. Therefore, I'm using B3LYP+SCRF(C-PCM, solvent=methanol) single point jobs to get the solvation energy at each step. Finally, a potential energy curve E(R) is my goal. R is the bond distance I'm interested in; e.g. a C-O, C-Cl bond or , for testing purposes Na-Cl. But, unfortunately, wrong asymptotic behaviour (like a "size inconsistency problem") is observed in all cases: the "supermolecule's" solvation energy at large distances (10 or 20 A) is differing about more than 20 kcal/mole from the sum of the solvation energies of the two ions. My question is: is the problem known (references ?)? How can be it be accounted for ? Do I have to use specific energy terms given in gaussian's output and/or male a correction to them ? Any help is appreciated. Bye, Yours, Elmar -- ======================================================== Elmar Gerwalin , University of Kaiserslautern,Germany Dept. of Theoretical Chemistry elg !v! chemie.uni-kl.de ======================================================== From chemistry-request@ccl.net Thu Jul 7 17:02:25 2005 Received: from www.eyesopen.com (eyesopen.com [208.41.78.163]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j67L2MZA010759 for ; Thu, 7 Jul 2005 17:02:22 -0400 Received: from [192.168.0.102] (216-161-132-6.dlth.qwest.net [216.161.132.6]) (authenticated) by www.eyesopen.com (8.11.6/8.11.6) with ESMTP id j67L2KJ26046 for ; Thu, 7 Jul 2005 15:02:21 -0600 Message-ID: <42CDA65A.5000608-.at.-eyesopen.com> Date: Thu, 07 Jul 2005 16:02:02 -0600 From: George Vacek Reply-To: vacek-.at.-eyesopen.com Organization: OpenEye Scientific Software User-Agent: Mozilla Thunderbird 1.0.2 (Windows/20050317) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry-.at.-ccl.net Subject: LexiChem 1.0 and Ogham 1.0 released - compound name/structure interconversion and 2D structure rendering Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net OpenEye is pleased to announce the official release of Ogham and LexiChem, state-of-the-art programs that handle the 2D rendering, naming of compounds and the generation of structures from names. Ogham is designed to artfully render 2D Kekule drawings from 3D structures or connectivity information. Ogham is easy to work with, offering a variety of display controls such as color, size, optional use of superatoms, or style of representation for aromatic and dative bonds. More importantly Ogham provides a consistent and specifiable orientation of core substructures, making it easy to spot common and alternate moieties in a series of compounds. LexiChem provides efficient conversion from chemical names into chemical structures and vice versa. Compounds can be named in a number of styles including fully systematic, preferred IUPAC 2005, acceptable common-usage IUPAC, CAS naming conventions, and non-IUPAC traditional common names. Both LexiChem and Ogham are available either as standalone applications or as C++ toolkits for software development purposes. Both programs, like all OpenEye software, are available at no charge for non-commercial purposes. For further information, please visit www.eyesopen.com or contact business-.at.-eyesopen.com. Regards, George Vacek VP, Business Development OpenEye Scientific Software From chemistry-request@ccl.net Thu Jul 7 11:09:21 2005 Received: from mr3.cc.ic.ac.uk (mr3.cc.ic.ac.uk [155.198.5.113]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j67F9Ieh023719 for < ccl.net>; Thu, 7 Jul 2005 11:09:19 -0400 Received: from icexp2.cc.ic.ac.uk ([155.198.3.42] helo=icex.imperial.ac.uk) by mr3.cc.ic.ac.uk with smtp (Exim 4.51) id 1DqY05-0003ta-NK for chemistry >< ccl.net; Thu, 07 Jul 2005 16:09:17 +0100 Received: from [155.198.215.23] ([155.198.215.23]) by icex.imperial.ac.uk with Microsoft SMTPSVC(6.0.3790.1830); Thu, 7 Jul 2005 16:08:29 +0100 Message-ID: <42CD4571.4030003 >< imperial.ac.uk> Date: Thu, 07 Jul 2005 16:08:33 +0100 From: James Kirkpatrick < imperial.ac.uk> User-Agent: Mozilla Thunderbird 0.9 (Windows/20041103) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry >< ccl.net Subject: problem installing GAMESS (US) on SPARC workstation Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-OriginalArrivalTime: 07 Jul 2005 15:08:29.0175 (UTC) FILETIME=[BB61C870:01C58305] X-Spam-Status: No, score=0.3 required=5.0 tests=FORGED_RCVD_HELO, UPPERCASE_25_50 autolearn=no version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Good day CCLers! I am currently trying to install GAMESS on one of my group's workstations. The previous computer administrator compiled the source code, I am left with the job of acutally making it function. If this list is not appropriate to the discussion of this type of problem, can anyone point me to someone who could help? I have modified the rungms script, to ensure that all environement variables are correctly set etc. I had a problem with lack of semaphores, upon reading the ddi documentation I learnt that the problem was that SPARCs are set with too low number of sempahore, I corrected this by adding the recomended lines to /etc/system. I will first give some information on the system which I hope is relevant, then give a print out of the input and of the output. I hope there is someone out there who has installed the program on similar systems, has had similar problems and will be able to tell me what's wrong! running these commands: /usr/sbin/sysdef -i | grep SHMMAX /usr/sbin/sysdef -i | grep SEM I receive the following answers now: 128 semaphore identifiers (SEMMNI) 128 semaphores in system (SEMMNS) 30 undo structures in system (SEMMNU) 25 max semaphores per id (SEMMSL) 10 max operations per semop call (SEMOPM) 10 max undo entries per process (SEMUME) 32767 semaphore maximum value (SEMVMX) 16384 adjust on exit max value (SEMAEM) and: * * IPC Shared Memory * 536870912 max shared memory segment size (SHMMAX) 1 min shared memory segment size (SHMMIN) 100 shared memory identifiers (SHMMNI) 6 max attached shm segments per process (SHMSEG) If I look at the active semaphores, by running ipcs -i and see the following information: IPC status from as of Thu Jul 7 14:57:43 bst 2005 T ID KEY MODE OWNER GROUP Semaphores: s 1 0 --ra------- root other s 2 0 --ra------- root other s 3 0 --ra------- root other s 4 0 --ra------- root other s 5 0 --ra------- root other s 6 0 --ra------- root other s 7 0 --ra------- root other s 8 0 --ra------- root other The system type is: SunOS exss-blade1.sc.ic.ac.uk 5.8 Generic_117350-25 sun4u sparc SUNW,Sun-Blade-1000 The input I am trying to run is exam01.inp from the tests suite. I paste the input/output at the end of this mail Once again I receive the same error message ... DONE SETTING UP THE RUN ..... DDI Process 0: semget return an error. semget errno=ENOSPC -- check system limit for sysv semaphores. A fatal error occurr on DDI Process 0. ddikick.x: application process 0 quit unexpectedly. ddikick.x: Fatal error detected. Does anyone know what this is about? Thanks very much for your help James Kirkpatrick -- James Kirkpatrick ------------------------------------------- Centre for Electronic Materials and devices Imperial College ------------------------------------------- 020 759 47519 ------------------------------------------------------------------------ ! EXAM01. ! 1-A-1 CH2 RHF geometry optimization using GAMESS. ! ! Although internal coordinates are used (COORD=ZMAT), ! the optimization is done in Cartesian space (NZVAR=0). ! This run uses a criterion (OPTTOL) on the gradient ! which is tighter than is normally used. ! ! This job tests the sp integral module, the RHF module, ! and the geometry optimization module. ! ! Using the default search METHOD=STANDARD, ! FINAL E= -37.2322678015, 8 iters, RMS grad= .0264308 ! FINAL E= -37.2308175306, 7 iters, RMS grad= .0320881 ! FINAL E= -37.2375723427, 7 iters, RMS grad= .0056557 ! FINAL E= -37.2379944433, 6 iters, RMS grad= .0017901 ! FINAL E= -37.2380387836, 8 iters, RMS grad= .0003391 ! FINAL E= -37.2380397697, 6 iters, RMS grad= .0000030 ! $CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE COORD=ZMT NZVAR=0 $END $SYSTEM TIMLIM=2 MEMORY=10000 $END $STATPT OPTTOL=1.0E-5 $END $BASIS GBASIS=STO NGAUSS=2 $END $GUESS GUESS=HUCKEL $END $DATA Methylene...1-A-1 state...RHF/STO-2G Cnv 2 C H 1 rCH H 1 rCH 2 aHCH rCH=1.09 aHCH=110.0 $END ------------------------------------------------------------------------ ----- GAMESS execution script ----- This job is running on host exss-blade1.sc.ic.ac.uk under operating system SunOS at Thu Jul 7 14:54:38 bst 2005 Available scratch disk space (Kbyte units) at beginning of the job is Filesystem 1024-blocks Used Available Capacity Mounted on /dev/dsk/c1t1d0s0 14687719 11328232 3212610 78% / cp tests/exam01.inp /home/sc00/bugs/scr/tests/exam01.F05 unset echo setenv ERICFMT ~bugs/gamess/ericfmt.dat setenv EXTBAS /dev/null setenv IRCDATA /home/sc00/bugs/scr/tests/exam01.irc setenv INPUT /home/sc00/bugs/scr/tests/exam01.F05 setenv PUNCH /home/sc00/bugs/scr/tests/exam01.dat setenv AOINTS /home/sc00/bugs/scr/tests/exam01.F08 setenv MOINTS /home/sc00/bugs/scr/tests/exam01.F09 setenv DICTNRY /home/sc00/bugs/scr/tests/exam01.F10 setenv DRTFILE /home/sc00/bugs/scr/tests/exam01.F11 setenv CIVECTR /home/sc00/bugs/scr/tests/exam01.F12 setenv CASINTS /home/sc00/bugs/scr/tests/exam01.F13 setenv CIINTS /home/sc00/bugs/scr/tests/exam01.F14 setenv WORK15 /home/sc00/bugs/scr/tests/exam01.F15 setenv WORK16 /home/sc00/bugs/scr/tests/exam01.F16 setenv CSFSAVE /home/sc00/bugs/scr/tests/exam01.F17 setenv FOCKDER /home/sc00/bugs/scr/tests/exam01.F18 setenv WORK19 /home/sc00/bugs/scr/tests/exam01.F19 setenv DASORT /home/sc00/bugs/scr/tests/exam01.F20 setenv DFTINTS /home/sc00/bugs/scr/tests/exam01.F21 setenv DFTGRID /home/sc00/bugs/scr/tests/exam01.F22 setenv JKFILE /home/sc00/bugs/scr/tests/exam01.F23 setenv ORDINT /home/sc00/bugs/scr/tests/exam01.F24 setenv EFPIND /home/sc00/bugs/scr/tests/exam01.F25 setenv PCMDATA /home/sc00/bugs/scr/tests/exam01.F26 setenv PCMINTS /home/sc00/bugs/scr/tests/exam01.F27 setenv MLTPL /home/sc00/bugs/scr/tests/exam01.F28 setenv MLTPLT /home/sc00/bugs/scr/tests/exam01.F29 setenv DAFL30 /home/sc00/bugs/scr/tests/exam01.F30 setenv SOINTX /home/sc00/bugs/scr/tests/exam01.F31 setenv SOINTY /home/sc00/bugs/scr/tests/exam01.F32 setenv SOINTZ /home/sc00/bugs/scr/tests/exam01.F33 setenv SORESC /home/sc00/bugs/scr/tests/exam01.F34 setenv SIMEN /home/sc00/bugs/scr/tests/exam01.simen setenv SIMCOR /home/sc00/bugs/scr/tests/exam01.simcor setenv GCILIST /home/sc00/bugs/scr/tests/exam01.F37 setenv HESSIAN /home/sc00/bugs/scr/tests/exam01.F38 setenv SOCCDAT /home/sc00/bugs/scr/tests/exam01.F40 setenv AABB41 /home/sc00/bugs/scr/tests/exam01.F41 setenv BBAA42 /home/sc00/bugs/scr/tests/exam01.F42 setenv BBBB43 /home/sc00/bugs/scr/tests/exam01.F43 setenv MCQD50 /home/sc00/bugs/scr/tests/exam01.F50 setenv MCQD51 /home/sc00/bugs/scr/tests/exam01.F51 setenv MCQD52 /home/sc00/bugs/scr/tests/exam01.F52 setenv MCQD53 /home/sc00/bugs/scr/tests/exam01.F53 setenv MCQD54 /home/sc00/bugs/scr/tests/exam01.F54 setenv MCQD55 /home/sc00/bugs/scr/tests/exam01.F55 setenv MCQD56 /home/sc00/bugs/scr/tests/exam01.F56 setenv MCQD57 /home/sc00/bugs/scr/tests/exam01.F57 setenv MCQD58 /home/sc00/bugs/scr/tests/exam01.F58 setenv MCQD59 /home/sc00/bugs/scr/tests/exam01.F59 setenv MCQD60 /home/sc00/bugs/scr/tests/exam01.F60 setenv MCQD61 /home/sc00/bugs/scr/tests/exam01.F61 setenv MCQD62 /home/sc00/bugs/scr/tests/exam01.F62 setenv MCQD63 /home/sc00/bugs/scr/tests/exam01.F63 setenv MCQD64 /home/sc00/bugs/scr/tests/exam01.F64 setenv NMRINT1 /home/sc00/bugs/scr/tests/exam01.F61 setenv NMRINT2 /home/sc00/bugs/scr/tests/exam01.F62 setenv NMRINT3 /home/sc00/bugs/scr/tests/exam01.F63 setenv NMRINT4 /home/sc00/bugs/scr/tests/exam01.F64 setenv NMRINT5 /home/sc00/bugs/scr/tests/exam01.F65 setenv NMRINT6 /home/sc00/bugs/scr/tests/exam01.F66 setenv DCPHFH2 /home/sc00/bugs/scr/tests/exam01.F67 setenv DCPHF21 /home/sc00/bugs/scr/tests/exam01.F68 setenv GVVPT /home/sc00/bugs/scr/tests/exam01.F69 unset echo Entering Serial Mode The generated host list is exss-blade1.sc.ic.ac.uk /home/sc00/bugs/gamess/ddikick.x /home/sc00/bugs/gamess/gamess.01.x tests/exam01 -ddi 1 1 exss-blade1.sc.ic.ac.uk -scr /home/sc00/bugs/scr Distributed Data Interface kickoff program. Initiating 1 compute processes on 1 nodes to run the following command: /home/sc00/bugs/gamess/gamess.01.x tests/exam01 ****************************************************** * GAMESS VERSION = 22 NOV 2004 (R1) * * FROM IOWA STATE UNIVERSITY * * M.W.SCHMIDT, K.K.BALDRIDGE, J.A.BOATZ, S.T.ELBERT, * * M.S.GORDON, J.H.JENSEN, S.KOSEKI, N.MATSUNAGA, * * K.A.NGUYEN, S.J.SU, T.L.WINDUS, * * TOGETHER WITH M.DUPUIS, J.A.MONTGOMERY * * J.COMPUT.CHEM. 14, 1347-1363(1993) * ************ SUN MICROSYSTEMS INC. VERSION *********** SINCE 1993, STUDENTS AND POSTDOCS WORKING AT IOWA STATE UNIVERSITY AND ALSO IN THEIR VARIOUS JOBS AFTER LEAVING ISU HAVE MADE IMPORTANT CONTRIBUTIONS TO THE CODE: IVANA ADAMOVIC, CHRISTINE AIKENS, ROB BELL, PRADIPTA BANDYOPADHYAY, BRETT BODE, GALINA CHABAN, WEI CHEN, CHEOL HO CHOI, PAUL DAY, TIM DUDLEY, DMITRI FEDOROV, GRAHAM FLETCHER, MARK FREITAG, KURT GLAESEMANN, GRANT MERRILL, HEATHER NETZLOFF, RYAN OLSON, MIKE PAK, JIM SHOEMAKER, TETSUYA TAKETSUGU, SIMON WEBB. ADDITIONAL CODE HAS BEEN PROVIDED BY COLLABORATORS IN OTHER GROUPS: IOWA STATE UNIVERSITY: JOE IVANIC, KLAUS RUEDENBERG UNIVERSITY OF TOKYO: KIMIHIKO HIRAO, HARUYUKI NAKANO, TAKAHITO NAKAJIMA, TAKAO TSUNEDA, MUNEAKI KAMIYA, SUSUMU YANAGISAWA, KIYOSHI YAGI ODENSE UNIVERSITY: FRANK JENSEN UNIVERSITY OF IOWA: VISVALDAS KAIRYS, HUI LI NATIONAL INST. OF STANDARDS AND TECHNOLOGY: WALT STEVENS, DAVID GARMER UNIVERSITY OF PISA: BENEDETTA MENNUCCI, JACOPO TOMASI UNIVERSITY OF MEMPHIS: HENRY KURTZ, PRAKASHAN KORAMBATH UNIVERSITY OF ALBERTA: MARIUSZ KLOBUKOWSKI UNIVERSITY OF NEW ENGLAND: MARK SPACKMAN MIE UNIVERSITY: HIROAKI UMEDA MICHIGAN STATE UNIVERSITY: KAROL KOWALSKI, PIOTR PIECUCH UNIVERSITY OF SILESIA: MONIKA MUSIAL, STANISLAW KUCHARSKI FACULTES UNIVERSITAIRES NOTRE-DAME DE LA PAIX: OLIVIER QUINET, BENOIT CHAMPAGNE UNIVERSITY OF CALIFORNIA - SANTA BARBARA: BERNARD KIRTMAN INSTITUTE FOR MOLECULAR SCIENCE: KAZUYA ISHIMURA AND SHIGERU NAGASE EXECUTION OF GAMESS BEGUN Thu Jul 7 14:54:38 2005 ECHO OF THE FIRST FEW INPUT CARDS - INPUT CARD>! EXAM01. INPUT CARD>! 1-A-1 CH2 RHF geometry optimization using GAMESS. INPUT CARD>! INPUT CARD>! Although internal coordinates are used (COORD=ZMAT), INPUT CARD>! the optimization is done in Cartesian space (NZVAR=0). INPUT CARD>! This run uses a criterion (OPTTOL) on the gradient INPUT CARD>! which is tighter than is normally used. INPUT CARD>! INPUT CARD>! This job tests the sp integral module, the RHF module, INPUT CARD>! and the geometry optimization module. INPUT CARD>! INPUT CARD>! Using the default search METHOD=STANDARD, INPUT CARD>! FINAL E= -37.2322678015, 8 iters, RMS grad= .0264308 INPUT CARD>! FINAL E= -37.2308175306, 7 iters, RMS grad= .0320881 INPUT CARD>! FINAL E= -37.2375723427, 7 iters, RMS grad= .0056557 INPUT CARD>! FINAL E= -37.2379944433, 6 iters, RMS grad= .0017901 INPUT CARD>! FINAL E= -37.2380387836, 8 iters, RMS grad= .0003391 INPUT CARD>! FINAL E= -37.2380397697, 6 iters, RMS grad= .0000030 INPUT CARD>! INPUT CARD> $CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE COORD=ZMT NZVAR=0 $END INPUT CARD> $SYSTEM TIMLIM=2 MEMORY=10000 $END INPUT CARD> $STATPT OPTTOL=1.0E-5 $END INPUT CARD> $BASIS GBASIS=STO NGAUSS=2 $END INPUT CARD> $GUESS GUESS=HUCKEL $END INPUT CARD> $DATA INPUT CARD>Methylene...1-A-1 state...RHF/STO-2G INPUT CARD>Cnv 2 INPUT CARD> INPUT CARD>C INPUT CARD>H 1 rCH INPUT CARD>H 1 rCH 2 aHCH INPUT CARD> INPUT CARD>rCH=1.09 INPUT CARD>aHCH=110.0 INPUT CARD> $END ..... DONE SETTING UP THE RUN ..... DDI Process 0: semget return an error. semget errno=ENOSPC -- check system limit for sysv semaphores. A fatal error occurr on DDI Process 0. ddikick.x: application process 0 quit unexpectedly. ddikick.x: Fatal error detected. The error is most likely to be in the application, so check for input errors, disk space, memory needs, application bugs, etc. ddikick.x will now clean up all processes, and exit... ddikick.x: Sending kill signal to DDI processes. ddikick.x: Execution terminated due to error(s). unset echo ----- accounting info ----- Thu Jul 7 14:54:39 bst 2005 Files used on the master node exss-blade1.sc.ic.ac.uk were: -rw-r--r-- 1 root other 1085 Jul 7 14:54 /home/sc00/bugs/scr/tests/exam01.F05 -rw-r--r-- 1 root other 0 Jul 7 14:54 /home/sc00/bugs/scr/tests/exam01.dat 0.0u 0.0s 0:01 0% 0+0k 0+0io 0pf -- James Kirkpatrick ------------------------------------------- Centre for Electronic Materials and devices Imperial College ------------------------------------------- 020 759 47519 From chemistry-request@ccl.net Thu Jul 7 10:49:32 2005 Received: from outgoing.cambridgesoft.com (outgoing.cambridgesoft.com [198.112.111.56]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j67EnN5a022266 for ; Thu, 7 Jul 2005 10:49:27 -0400 Received: from 172.16.1.207 [172.16.1.207] by outgoing.cambridgesoft.com with XWall v3.33 ; Thu, 7 Jul 2005 09:45:35 -0400 X-MimeOLE: Produced By Microsoft Exchange V6.5.7226.0 Content-class: urn:content-classes:message Subject: RE: 3D to chemical name MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 7 Jul 2005 09:48:36 -0400 Message-ID: <4F7EC9B21FB40043A33952CF23582FE903C89823 {} EXCHANGE.camsoft.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: 3D to chemical name Thread-Index: AcWC+NwxtgkYIpjhSgSS4iouSnBeEQAATf5A From: "Tony Yuan" To: Cc: X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j67EnW5a022296 Try ChemDraw. It can do 3D => 2D => Chemical Name. Also try ChemFinder.com and ChemACX.com, you can search suppliers by doing structure query. Chem3D can convert PDB files to MDL mol files and CDX files. Good luck! -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request {} ccl.net] On Behalf Of Noel O'Boyle Sent: Thursday, July 07, 2005 4:01 AM To: chemistry {} ccl.net Cc: mclaro2727 {} yahoo.com Subject: CCL: 3D to chemical name Importance: Low Dear Claro, Many chemical don't have simple names, and many suppliers use different names for the same chemical. What you need is the supplier code for the chemical. It is sometimes possible (for example, on the sigma-aldrich webpage) to search the supplier's catalogue using the chemical formula, or by drawing the molecule on the web page. A note of warning: often the ligand structures taken from pdb files contain just the carbon skeleton, and are missing protons and bond orders. Just to make your life easier :-) Regards, Noel O'Boyle. >-- Original Message -- >Date: Wed, 6 Jul 2005 13:33:44 -0700 (PDT) >From: michelle claro >Subject: CCL: 3D to chemical name >To: chemistry {} ccl.net >Reply-To: chemistry {} ccl.net > > >Hello, > >I have about 50 pdb structures (no protein in the pdb just the ligand) but >I need the chemical names in order to purchase them. What is the easiest >way to get a chemical name from a pdb? Thanks in advance. > >M. Claro > > >__________________________________________________ >Do You Yahoo!? >Tired of spam? Yahoo! Mail has the best spam protection around >http://mail.yahoo.com -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY {} ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST {} ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your is mail bouncing from ccl.net domain due to spam filters, please use the Web based form from CCL Home Page -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Thu Jul 7 16:07:38 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j67K7clX007175 for ; Thu, 7 Jul 2005 16:07:38 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j67K7coC007174 for chemistry _+_ ccl.net; Thu, 7 Jul 2005 16:07:38 -0400 Date: Thu, 7 Jul 2005 16:07:38 -0400 Message-Id: <200507072007.j67K7coC007174 _+_ server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request _+_ ccl.net using -f From: "Chemical, , Bond" To: chemistry _+_ ccl.net X-Web-Message-Number: 050707160553-7025 Subject: W:Solvation free energy for aromatic hydrocarbon X-Spam-Status: No, score=-0.1 required=5.0 tests=ALL_TRUSTED, FORGED_YAHOO_RCVD,FROM_ENDS_IN_NUMS autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Hi there, I am confused with a single concept: what should be the sign for the solvation free energy for a fragment like phenyl? There are many experimental data of solvation free energy for aromatic hydrocarbons, such as benzene, naphthalene, etc, but they are all negative surprisingly. I looked at several papers with models of solvation energy, and their predictions all all have negative solvation energies for those compounds, just like the experiments. Typically when a phenyl group is transfered from water into protein, we would like to say there is a negative(beneficial) desolvation energy, or the usual called hydrophobic effect. And this has been used in tons of models for protein simulation or protein-ligand binding. Note, in this context, the solvation energy (from gas into water) is positive! Is there something wrong over here? Or just some artifact from the fitting? Hope there would be some good comments. Thanks a lot, Bond From chemistry-request@ccl.net Thu Jul 7 14:52:03 2005 Received: from mailx.u-picardie.fr (oban.u-picardie.fr [193.49.184.8]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j67Iq0jk003289 for ; Thu, 7 Jul 2005 14:52:00 -0400 Received: from localhost (localhost [127.0.0.1]) by mailx.u-picardie.fr (Postfix) with ESMTP id 4570898050; Thu, 7 Jul 2005 19:58:59 +0200 (CEST) Received: from mailx.u-picardie.fr ([127.0.0.1]) by localhost (oban [127.0.0.1]) (amavisd-new, port 10024) with LMTP id 07411-01-8; Thu, 7 Jul 2005 19:58:55 +0200 (CEST) Received: from webmail.u-picardie.fr (oban.u-picardie.fr [193.49.184.8]) by mailx.u-picardie.fr (Postfix) with ESMTP id E097E980AF; Thu, 7 Jul 2005 19:58:54 +0200 (CEST) Received: from neumann.scripps.edu (neumann.scripps.edu [137.131.252.63]) by webmail.u-picardie.fr (IMP) with HTTP for ; Thu, 07 Jul 2005 19:58:54 +0200 Message-ID: <1120759134.42cd6d5eaeef1(at)webmail.u-picardie.fr> Date: Thu, 07 Jul 2005 19:58:54 +0200 From: FyD To: amber(at)scripps.edu, chemistry(at)ccl.net Cc: adrien.pigache1(at)etud.univ-ubs.fr, strumgash(at)caramail.com, nicogri(at)free.fr, rspeedake(at)yahoo.fr, alexandre.dubois(at)u-picardie.fr Subject: Release of R.E.D-II MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.6 X-Originating-IP: 137.131.252.63 X-Virus-Scanned: by amavisd-new-20030616-p10 (Debian) at UPJV X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Dear All, I am pleased to announce the release of the R.E.D. program, version 2.0., http://www.u-picardie.fr/labo/lbpd/RED/. We developed the R.E.D. I program (RESP ESP charge Derive, version 1.0) to automatically derive 'RESP' and 'ESP' charges starting from an un-optimized PDB structure. R.E.D. sequentially executes (i) either the "GAMESS" program or the "Gaussian" program to optimize the target structure and to compute the corresponding MEP, and (ii) the "RESP" program to fit the atom-centered charges to the grid previously determined. Format conversions needed during the procedure and "GAMESS", "Gaussian" and "RESP" inputs are automatically generated by R.E.D. By controlling the molecular orientation of the optimized geometry, a new RESP fitting procedure based on multi-orientation feature is proposed and allows getting highly reproducible 'RESP' and 'ESP' charges whatever the QM software and starting Cartesian coordinates are. With R.E.D. II (version 2.0), multi-conformation RESP and ESP fit has been implemented, and can also be automatically carried out using a well defined set of molecular conformations. Thus, 'multi-conformation' and 'multi-orientation' RESP fit can be performed together or independently according to the user choice. 'Standard' but also 'non-standard' RESP inputs can now be generated. The geometry optimization ouput generated by one of the two QM programs can be used as input for MEP computation using the second QM program. Finally, RESP and ESP charges can be derived for chemical elements having up to a total number of electrons, Z = 35. And much more... Thus, R.E.D. makes the derivation of the 'RESP' and 'ESP' charges a straightforward, simple and highly reliable procedure. R.E.D. has been written with the "Perl" programming language, and X R.E.D. with the "tcl/tk" programming language, making these two programs highly flexible and portable. R.E.D. and X R.E.D. have been tested on PC-LINUX and SGI-IRIX workstations, but should work on all other UNIX platforms. They are "free" (i. e. provided at no cost) for academic users after signing a license. On the contrary, a fee is demanded to commercial users for the use of R.E.D. & X R.E.D. - A new manual has been written taking into account most of the problems discussed in the AMBER mailing list. See http://www.u-picardie.fr/labo/lbpd/RED/RED-II.pdf - The FAQ about R.E.D. I has been updated, and contains now more than 50 FAQs. See http://www.u-picardie.fr/labo/lbpd/RED/FAQ-I.htm - The FAQ about R.E.D II will be updated and is be available at: http://www.u-picardie.fr/labo/lbpd/RED/FAQ-II.htm - The six bugs reported for R.E.D. I, http://www.u-picardie.fr/labo/lbpd/RED/bugs-I, have been corrected. - The future bugfixes for the R.E.D. II bugs will be available at http://www.u-picardie.fr/labo/lbpd/RED/bugs-II - The X R.E.D. graphical interface, http://www.u-picardie.fr/labo/lbpd/RED/XRED.htm, has been updated to execute R.E.D. II. - Finally, all the users which used a R.E.D.-II beta version, should re-download R.E.D.-II since new features have just been added in the final version. Best regards, Francois -- F.-Y. Dupradeau DMAG EA 3901 & Faculte de Pharmacie, Amiens, France The Scripps Research Institute, La Jolla, CA, USA -- http://www.u-picardie.fr/labo/lbpd/FyD.htm From chemistry-request@ccl.net Thu Jul 7 19:56:48 2005 Received: from web54507.mail.yahoo.com (web54507.mail.yahoo.com [68.142.225.177]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j67NujQn021203 for ; Thu, 7 Jul 2005 19:56:46 -0400 Received: (qmail 84735 invoked by uid 60001); 7 Jul 2005 22:56:27 -0000 DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=Message-ID:Received:Date:From:Subject:To:MIME-Version:Content-Type:Content-Transfer-Encoding; b=u5ZkeUEY3GRJ4k1Vv4y8n4jYc476KrLI5B3xS2Ui5WBrBnNoCYb45igyVQM4BOK2nBusCKhqHOF6fbngmZeFY6vrq+alIXvPim6zd15pry14tbLwal79AZSSynLfIOmt39K5PVn9JhEchWDQsPjkr5BmmClKKylS3siJpcn+Pi0= ; Message-ID: <20050707225627.84733.qmail {} web54507.mail.yahoo.com> Received: from [62.14.68.158] by web54507.mail.yahoo.com via HTTP; Thu, 07 Jul 2005 15:56:27 PDT Date: Thu, 7 Jul 2005 15:56:27 -0700 (PDT) From: Lolek BOLEK Subject: MP2 virial value To: chemistry {} ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1113526416-1120776987=:84652" Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=0.9 required=5.0 tests=DNS_FROM_RFC_ABUSE,HTML_20_30, HTML_MESSAGE autolearn=no version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net --0-1113526416-1120776987=:84652 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi everybody Can anybody tell me how to obtain the virial (-V/T) value for the MP2 calculations in Gaussian? There is no problem on the HF or DFT level, but this property is not listed for MP2. How can I print it Thank you in advance Pasikonik __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com --0-1113526416-1120776987=:84652 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hi everybody
Can anybody tell me how to obtain the virial (-V/T) value for the MP2 calculations in Gaussian?
There is no problem on the HF or DFT level, but this property is not listed for MP2. How can I print it
 
Thank you in advance
 
Pasikonik

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