From chemistry-request@server.ccl.net Thu Jan 27 01:31:21 2000 Received: from iitkgp.iitkgp.ernet.in ([202.141.127.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA27990 for ; Thu, 27 Jan 2000 01:31:18 -0500 Received: from cts.iitkgp.ernet.in (cts.iitkgp.ernet.in [144.16.192.220]) by iitkgp.iitkgp.ernet.in (8.9.3/8.9.3) with ESMTP id KAA11920 for ; Thu, 27 Jan 2000 10:56:01 -0500 (GMT) Received: from localhost (rajarshi@localhost) by cts.iitkgp.ernet.in (8.9.3/8.9.3) with ESMTP id KAA02036 for ; Thu, 27 Jan 2000 10:49:25 +0530 X-Authentication-Warning: cts.iitkgp.ernet.in: rajarshi owned process doing -bs Date: Thu, 27 Jan 2000 10:49:25 +0530 (IST) From: Rajarshi Guha Sender: rajarshi@cts.iitkgp.ernet.in To: CCL Subject: C source for dihedral angles Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, can anybody refer me to some C source code for calculating dihedral angles. TIA ------------------------------------------------------------------- Rajarshi Guha | ...but there was no Dept Of Chemistry, | one in it....! IIT Kharagpur. | | RG email: rajarshi@presidency.com | web : www.psynet.net/jijog | ------------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Jan 27 09:35:32 2000 Received: from rchsg38.chemie.uni-regensburg.de (rchsg38.chemie.uni-regensburg.de [132.199.48.138]) by server.ccl.net (8.8.7/8.8.7) with SMTP id JAA30812 for ; Thu, 27 Jan 2000 09:35:31 -0500 Received: from rchsg38 (localhost [127.0.0.1]) by rchsg38.chemie.uni-regensburg.de (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id OAA02494; Thu, 27 Jan 2000 14:28:59 +0100 Sender: hod01123@chemie.uni-regensburg.de Message-ID: <3890481A.167E@chemie.uni-regensburg.de> Date: Thu, 27 Jan 2000 14:28:58 +0100 From: Dominik Horinek Organization: Universitaet Regensburg X-Mailer: Mozilla 3.0 (X11; I; IRIX 6.2 IP22) MIME-Version: 1.0 To: chemistry@ccl.net Subject: bsse and second derivatives in G98 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, I'm trying to calculate the hessian of a cluster containing an organic molecule (formic acid) and an argon atom. To account for the bsse I have to do the calculation with ghost atoms for the organic molecule and electrons only at the argon atom. Unfortunately, with G98 this type of calculation fails: 'Molecule is non-linear but NTrRo=3'. Who knows how to fix this problem, or is there another convenient way to obtain the second derivatives without this problem. I used the following input: %Mem=12000000 %chk=cluster_1.chk # 6-311++G** MP2=Direct Freq Massage *cluster 1* 0 1 C 0.0000000 0.0000010 -0.0000110 O 0.0000000 -1.1524620 -0.3291650 H 0.0000000 0.3427030 1.0490010 O 0.0000000 1.0156520 -0.8967590 H 0.0000000 1.8484450 -0.4113800 Ar -5.3307700 -4.9821510 -5.6341740 1 Nuc 0.0 2 Nuc 0.0 3 Nuc 0.0 4 Nuc 0.0 5 Nuc 0.0 Thanks for any help, Dominik From chemistry-request@server.ccl.net Thu Jan 27 10:54:05 2000 Received: from mail-b.bcc.ac.uk (mail-b.bcc.ac.uk [144.82.100.22]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA31193 for ; Thu, 27 Jan 2000 10:54:04 -0500 Received: from socrates-a.ucl.ac.uk by mail-b.bcc.ac.uk with SMTP (XT-PP); Thu, 27 Jan 2000 14:47:12 +0000 From: uccatvm Message-Id: <9099.200001271447@socrates-a.ucl.ac.uk> Subject: Re: CCL:bsse and second derivatives in G98 To: chemistry@ccl.net Date: Thu, 27 Jan 2000 14:47:29 +0000 (GMT) Cc: T.vanMourik@UCL.ac.uk (Tanja van Mourik) In-Reply-To: <3890481A.167E@chemie.uni-regensburg.de> from "Dominik Horinek" at Jan 27, 2000 02:42:11 PM X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Dominik, > I'm trying to calculate the hessian of a cluster containing an organic > molecule (formic acid) and an argon atom. To account for the bsse I have > to do the calculation with ghost atoms for the organic molecule and > electrons only at the argon atom. Unfortunately, with G98 this type of > calculation fails: 'Molecule is non-linear but NTrRo=3'. Who knows how > to fix this problem, or is there another convenient way to obtain the > second derivatives without this problem. I used the following input: > > %Mem=12000000 > %chk=cluster_1.chk > # 6-311++G** MP2=Direct Freq Massage > > *cluster 1* > > 0 1 > C 0.0000000 0.0000010 -0.0000110 > O 0.0000000 -1.1524620 -0.3291650 > H 0.0000000 0.3427030 1.0490010 > O 0.0000000 1.0156520 -0.8967590 > H 0.0000000 1.8484450 -0.4113800 > Ar -5.3307700 -4.9821510 -5.6341740 > > 1 Nuc 0.0 > 2 Nuc 0.0 > 3 Nuc 0.0 > 4 Nuc 0.0 > 5 Nuc 0.0 What you are trying to do here is to calulate the frequency of the Ar atom (albeit with some basis functions on the formic acid ghost atoms). This is not possible. Similarly, you cannot calculate the frequencies of formic acid in the presence of ghost functions like this (i.e. by replacing the last 5 lines by "6 Nuc 0.0"). To calculate a hessian, your molecule has to be in the minimum (for the given method/basis), and this is not the case (I assume the geometry above comes from an optimization on the cluster). I am afraid that there is not an easy way to calculate counterpoise-corrected frequencies automatically. You would need a potential energy surface and calculate the frequencies on it numerically, but this is not practical on any higher level of theory. Best regards, Tanja -- ==================================================================== Tanja van Mourik phone University College London work: +44 (0)171-504-4665 Christopher Ingold Laboratories home: +44 (0)1895-259-312 20 Gordon Street e-mail London WC1H 0AJ work: T.vanMourik@ucl.ac.uk United Kingdom home: tanja@netcomuk.co.uk ==================================================================== -- ==================================================================== Tanja van Mourik phone University College London work: +44 (0)171-504-4665 Christopher Ingold Laboratories home: +44 (0)1895-259-312 20 Gordon Street e-mail London WC1H 0AJ work: T.vanMourik@ucl.ac.uk United Kingdom home: tanja@netcomuk.co.uk ==================================================================== From chemistry-request@server.ccl.net Thu Jan 27 10:55:04 2000 Received: from theo1.theochem.tu-muenchen.de (theo2.theochem.tu-muenchen.de [129.187.191.1]) by server.ccl.net (8.8.7/8.8.7) with SMTP id KAA31214 for ; Thu, 27 Jan 2000 10:55:04 -0500 Received: from theo3.theochem.tu-muenchen.de (theo3.theochem.tu-muenchen.de [129.187.157.6]) by theo1.theochem.tu-muenchen.de (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id PAA12920 for ; Thu, 27 Jan 2000 15:48:28 +0100 Received: from theochem.tu-muenchen.de by theo3.theochem.tu-muenchen.de (SMI-8.6/SMI-SVR4) id PAA19887; Thu, 27 Jan 2000 15:49:23 +0100 Sender: matveev@theochem.tu-muenchen.de Message-ID: <38905A73.44D1821C@theochem.tu-muenchen.de> Date: Thu, 27 Jan 2000 15:47:15 +0100 From: Alexei Matveev Organization: TUM X-Mailer: Mozilla 4.51 [en] (X11; I; Linux 2.2.10 i586) X-Accept-Language: en, de, ru MIME-Version: 1.0 To: CCL Subject: MPI on dual linux boxes Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Dear CCL'ers, Does anybody have experience in running (compiling) MPI programs on Linux cluster of _DUAL_ boxes. Is LAM/MPI distributed with SuSE 6.1 an appropriate choice? Particularly for running two processes on one box? Any other choices? We would appreciate any comments on that matter. Thanks in anticipation, Walter Alsheimer, Alexei Matveev From chemistry-request@server.ccl.net Thu Jan 27 11:32:21 2000 Received: from havana.ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA31454 for ; Thu, 27 Jan 2000 11:32:20 -0500 Received: from bilbao.ks.uiuc.edu (bilbao.ks.uiuc.edu [130.126.120.38]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with ESMTP id JAA08824; Thu, 27 Jan 2000 09:25:51 -0600 (CST) Received: (from justin@localhost) by bilbao.ks.uiuc.edu (980427.SGI.8.8.8/8.6.9)id JAA70494; Thu, 27 Jan 2000 09:25:33 -0600 (CST) From: Justin Gullingsrud Message-Id: <200001271525.JAA70494@bilbao.ks.uiuc.edu> Subject: Re: CCL:C source for dihedral angles To: dorina@ks.uiuc.edu (Dorina Kosztin) Date: Thu, 27 Jan 2000 09:25:33 -0600 (CST) Cc: rajarshi@presidency.com, chemistry@ccl.net In-Reply-To: <200001271510.JAA08737@havana.ks.uiuc.edu> from "Dorina Kosztin" at Jan 27, 2000 09:10:23 AM X-Mailer: ELM [version 2.5 PL2] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, VMD, a freely available program from the Theoretical Biophysics Group at the University of Illinois, has code for calculating dihedral that should be easy to adapt for your purposes. You can download both the program and the source from http://www.ks.uiuc.edu/Research/vmd/ . I should mention that the code and software is released under a license agreement; here's the relevant section; I hope it's not too restrictive for you. Justin Gullingsrud justin@ks.uiuc.edu 2. Licensee may, at its own expense, create and freely distribute complimentary works that interoperate with the Software, directing others to the TBG server to license and obtain the Software itself. Licensee may, at its own expense, modify the Software to make derivative works. Except as explicitly provided below, this License shall apply to any derivative work as it does to the original Software distributed by Illinois. Any derivative work should be clearly marked and renamed to notify users that it is a modified version and not the original Software distributed by Illinois. Licensee agrees to reproduce the copyright notice and other proprietary markings on any derivative work and to include in the documentation of such work the acknowledgement: "This software includes code developed by the Theoretical Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign." Licensee may redistribute without restriction works with up to 1/2 of their non-comment source code derived from at most 1/10 of the non-comment source code developed by Illinois and contained in the Software, provided that the above directions for notice and acknowledgement are observed. Any other distribution of the Software or any derivative work requires a separate license with Illinois. Licensee may contact Illinois (vmd@ks.uiuc.edu) to negotiate an appropriate license for such distribution. > > > ------------- Begin Forwarded Message ------------- > > X-Authentication-Warning: cts.iitkgp.ernet.in: rajarshi owned process doing -bs > Date: Thu, 27 Jan 2000 10:49:25 +0530 (IST) > From: Rajarshi Guha > X-Original-Sender: rajarshi@cts.iitkgp.ernet.in > To: CCL > Subject: CCL:C source for dihedral angles > MIME-Version: 1.0 > > Hi, > can anybody refer me to some C source code for calculating dihedral > angles. > > TIA > > ------------------------------------------------------------------- > Rajarshi Guha | ...but there was no > Dept Of Chemistry, | one in it....! > IIT Kharagpur. | > | RG > email: rajarshi@presidency.com | > web : www.psynet.net/jijog | > ------------------------------------------------------------------- > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > > ------------- End Forwarded Message ------------- > > > Dorina Kosztin > --------------------------------------------------------- > Theoretical Biophysics Group Email: dorina@ks.uiuc.edu > Beckman Institute, UIUC Phone: (217) 244-8946 > 405 North Mathews Ave. Fax: (217) 244-6078 > Urbana, IL 61801, USA http://www.ks.uiuc.edu/ > --------------------------------------------------------- > > -- Justin Gullingsrud 3111 Beckman Institute H: (217) 384-4220 W: (217) 244-8946 The time of purification is at hand... From chemistry-request@server.ccl.net Thu Jan 27 12:41:54 2000 Received: from chinon.cnrs-orleans.fr (chinon.cnrs-orleans.fr [163.9.6.107]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA31784 for ; Thu, 27 Jan 2000 12:41:51 -0500 Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.9.3/8.9.3) id RAA09951; Thu, 27 Jan 2000 17:35:55 +0100 Date: Thu, 27 Jan 2000 17:35:55 +0100 Message-Id: <200001271635.RAA09951@chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: hinsen@dirac.cnrs-orleans.fr To: kynn@panix.com CC: CHEMISTRY@ccl.net In-reply-to: <200001262239.RAA00586@panix3.panix.com> (kynn@panix.com) Subject: Re: CCL:Why WHAM? References: <200001262239.RAA00586@panix3.panix.com> > I've read Kumar's paper [1] on the WHAM method for combining multiple > histograms, but it's still not clear to me what's exactly the > advantage of this method over the original umbrella sampling method > proposed by Torrie and Valleau? In Chandler's textbook [2] (for The two main advantages are 1) WHAM can easily be extended to multiple dimension PMFs. 2) WHAM uses the available data more efficiently: in the overlap regions between the windows all the data is effectively combined in order to obtain the final PMF. For a more detailed explanation, see B. Roux, The Calculation of the Potential of Mean Force using Computer Simulations, Comp. Phys. Comm. 91, 275 (1995) > smooth curve (p. 172). This may be a bit crude compared to WHAM, but > at least it is completely transparent. It is true that this "naive The theory behind WHAM may be more involved, but it's no less transparent. > suffice. My concern is that, in such relatively simple cases, the > additional complexity of WHAM may not be justified by its advantages. Which complexity? Sure, the justification of WHAM is more complicated, but a practical implementation is very simple. I can offer a general WHAM implementation for any number of variables which consists of a mere 80 lines of Python code. Mail me if you are interested. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Jan 27 12:30:33 2000 Received: from chinon.cnrs-orleans.fr (chinon.cnrs-orleans.fr [163.9.6.107]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA31728 for ; Thu, 27 Jan 2000 12:30:30 -0500 Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.9.3/8.9.3) id RAA09941; Thu, 27 Jan 2000 17:24:15 +0100 Date: Thu, 27 Jan 2000 17:24:15 +0100 Message-Id: <200001271624.RAA09941@chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: hinsen@dirac.cnrs-orleans.fr To: rajarshi@presidency.com CC: chemistry@ccl.net In-reply-to: (message from Rajarshi Guha on Thu, 27 Jan 2000 10:49:25 +0530 (IST)) Subject: Re: CCL:C source for dihedral angles References: > can anybody refer me to some C source code for calculating dihedral > angles. Pick up the Molecular Modeling Toolkit source code at http://starship.python.net/crew/hinsen/MMTK/ or http://dirac.cnrs-orleans.fr/MMTK/ and look at the file Src/bonded.c. The routine cosine_dihedral_evaluator() (at the end of the file) calculated dihedral angles and Amber-style dihedral potential terms from atomic positions. It OpenSource code, so you can freely use it in your own projects. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Jan 27 10:39:44 2000 Received: from fsuj20.rz.uni-jena.de (fsuj20.rz.uni-jena.de [141.35.1.18]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA31110 for ; Thu, 27 Jan 2000 10:39:44 -0500 Received: from pc04.chemie.uni-jena.de (pc04.chemie.uni-jena.de [141.35.29.60]) by fsuj20.rz.uni-jena.de (8.9.1a/8.9.1) with ESMTP id PAA19982 for ; Thu, 27 Jan 2000 15:33:14 +0100 (MET) Received: from pc04.chemie.uni-jena.de by pc04.chemie.uni-jena.de (8.8.8/1.1.22.3/02Dec99-0338PM) id PAA0000003913; Thu, 27 Jan 2000 15:33:10 +0100 (MET) Sender: goeller@pc04.chemie.uni-jena.de Message-ID: <38905726.2482B9F3@pc04.chemie.uni-jena.de> Date: Thu, 27 Jan 2000 15:33:10 +0100 From: Andreas Goeller X-Mailer: Mozilla 4.5 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: German, de, en To: "CHEMISTRY@ccl.net" Subject: MCSCF/work15 Dear CCLers I'm trying to learn how to use MCSCF in Gamess. My test case is Ozone, since there should be interesting deviations from wrong HF solutions. I did a geom. opt. and used the MOs via $vec group in an SP calc. Ok, that works. I produce a dictnry-file and have now the following MCSCF input, where I have sorted the MOs to use only pi ones: $CONTRL SCFTYP=MCSCF irest=-1 geom=daf RUNTYP=ENERGY COORD=UNIQUE $END $basis gbasis=n31 ngauss=6 diffsp=.t. ndfunc=2 npfunc=1 $end $SYSTEM TIMLIM=1000000 mwords=10 $END $MCSCF cistep=guga MAXIT=50 $END $DRT fors=.t. GROUP=C2v NMCC=9 NDOC=3 NVAL=3 next=-1 $END $GUGDIA NSTATE=5 ITERMX=200 $END $GUESS GUESS=MOsaved NORB=75 NORDER=1 IORDER(7)= 9 7 10 11 8 12 13 $end $data Ozon Single Point cnv 2 o 8.0 0.0 0.0 0.6 o 8.0 0.9 0.0 -0.2 $end I get -------------- -DM2- ORDERING -------------- 30253 WORDS NEEDED ( 10000000 AVAILABLE) TO ORDER DM2 IN MEMORY CHOOSING IN MEMORY ORDERING... 1 RECORDS OF LENGTH 15000 READ FROM FILE 16 71 DM2 VALUES IN 1 RECORDS OF LENGTH 15000 WRITTEN TO FILE 15 ...... END OF -DM2- ORDERING ...... STEP CPU TIME = 0.00 TOTAL CPU TIME = 4.7 ( 0.1 MIN) TOTAL WALL CLOCK TIME= 4.7 SECONDS, CPU UTILIZATION IS 100.00% -------------------------------------- APPROXIMATE SECOND-ORDER MCSCF PROGRAM -------------------------------------- PROGRAM WRITTEN BY G.CHABAN, A.MARQUEZ, AND M.DUPUIS NUMBER OF WORDS NEEDED = 124407 NUMBER AVAILABLE = 10000000 PRD: NODE 0 ENCOUNTERED I/O ERROR READING UNIT 15 EXECUTION OF GAMESS TERMINATED ABNORMALLY AT Wed Jan 26 14:03:48 2000 STEP CPU TIME = 0.01 TOTAL CPU TIME = 4.7 ( 0.1 MIN) TOTAL WALL CLOCK TIME= 4.7 SECONDS, CPU UTILIZATION IS 100.00% 1416601 WORDS OF DYNAMIC MEMORY USED *** ERROR TERMINATION *** IN COMPUTE PROCESS 0 DATA SERVER STATS: TOTAL DISTRIBUTED MEMORY USED (MEMDDI)= 0 MWORDS. FIRST DATA SERVER'S MAXIMUM MEMORY= 0 WORDS, CPU= 0.0 SECONDS. IF YOU WANT A CORE FILE, SET COREFL=.TRUE. IN $SYSTEM. The $JOB.F15 file exists in the scratch dir. What is wrong? -- Andreas Goeller --------------------------------------------------------------- Dr. Andreas Goeller Institut fuer Physikalische Chemie Friedrich-Schiller-Universitaet Lessingstr. 10 phone: +49(0)-3641-948352 D-07743 Jena fax: +49(0)-3641-948302 (secretary) Germany email: goeller@pc04.chemie.uni-jena.de http://www.uni-jena.de/chemie/photo/goeller/goeller.html --------------------------------------------------------------- Dr. Andreas Goeller ehemals Computer Chemie Centrum email: goeller@organik.uni-erlangen.de http://www.organik.uni-erlangen.de/clark/goeller/goeller.html --------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Jan 27 10:53:01 2000 Received: from mjco-s2.ice.mpg.de (mjco-s2.ice.mpg.de [195.37.47.3]) by server.ccl.net (8.8.7/8.8.7) with SMTP id KAA31181 for ; Thu, 27 Jan 2000 10:53:01 -0500 Received: from ice.mpg.de (unverified [195.37.47.89]) by mjco-s2.ice.mpg.de (EMWAC SMTPRS 0.83) with SMTP id ; Thu, 27 Jan 2000 15:47:59 +0100 Message-ID: <389059D9.4F50434C@ice.mpg.de> Date: Thu, 27 Jan 2000 15:44:41 +0100 From: Christoph Steinbeck Reply-To: steinbeck@ice.mpg.de Organization: Max-Planck-Institute of Chemical Ecology X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en To: ccl , CHMINF-L@LISTSERV.INDIANA.EDU, "jchempaint-dev-list@vanilla.ice.mpg.de" , "jchempaint-list@vanilla.ice.mpg.de" Subject: ANNOUNCEMENT: JChemPaint V. 0.5 It is my pleasure to to announce the release of JChemPaint V. 0.5 JChemPaint is a Java 2 program for drawing 2D chemical structures like those found in most chemistry textbooks. Its GUI is based on the Swing tool kit. The program is developed as an Open Source Project and released under GNU General Public License. The code should be considered alpha quality, but there are enough features implemented to get an idea about where the program development is heading. JChemPaint development is coordinated by Christoph Steinbeck and his Chemical Information group (http://www.ice.mpg.de/departments/ChemInf) at the Max Planck Instiutute of Chemical Ecology (http://www.ice.mpg.de). Version 0.5 now features: 1.A subset of the regular drawing features of commercial programs, as there are drawing of single, double, triple and stereo bonds. stereo bonds deletion of bonds and atoms ring templates (3-8) one-click attachment of ring templates to an atom or a bond flipping and rotating selected parts of the molecule 2.Loading and saving of structures in Chemical Markup Language (CML) and as MDL Molfiles. 3.Automated Structure Layout, also known as Structure Diagram Generation. 4.Loading structures over the Internet from the "Dictionary of Organic Chemistry" (http://www.sci.kun.nl/woc/) using the CAS number. More information as well as a download option can be found on http://www.ice.mpg.de/~stein/projects/JChemPaint/ People a sought to join the development of JChemPaint. JChemPaint is associated with the OpenScience project (www.openscience.org) and the 3D molecular viewer JMol (http://www.openscience.org/jmol/), both initiated by Dan Gezelter at Columbia University (http://www.chem.columbia.edu/~gezelter/). I'd be happy to get some feedback from people who have downloaded the program and got it up and running. Cheers, Chris -- Dr. Christoph Steinbeck (http://www.ice.mpg.de/~stein) MPI of Chemical Ecology, Tatzendpromenade 1a, 07745 Jena, Germany Tel: +49(0)3641 643644 - Fax: +49(0)3641 643665 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. From chemistry-request@server.ccl.net Thu Jan 27 11:40:21 2000 Received: from rs5.thch.uni-bonn.de (rs5.thch.uni-bonn.de [131.220.44.15]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA31496 for ; Thu, 27 Jan 2000 11:40:20 -0500 Received: (from bernd@localhost) by rs5.thch.uni-bonn.de (8.8.8/8.8.5) id QAA12656 for chemistry@www.ccl.net; Thu, 27 Jan 2000 16:35:10 +0100 From: Bernd Engels Message-Id: <200001271535.QAA12656@rs5.thch.uni-bonn.de> Subject: Base Pairing To: chemistry@server.ccl.net (Computational Chemistry List) Date: Thu, 27 Jan 100 16:35:09 +0100 (MEZ) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit hy, I am interested in Base Pairing and expecially which method is able to handle such things. I know that MP2 using a smaller basis set gives reasonable results, but perhaps somebody can point to a review or other paper. Thanks, I will summarize Bernd Engels Organische Chemie Universität Würzburg From chemistry-request@server.ccl.net Thu Jan 27 15:51:24 2000 Received: from neon.chem.ucla.edu (neon.chem.ucla.edu [128.97.35.251]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA00330 for ; Thu, 27 Jan 2000 15:51:23 -0500 Received: from localhost (renxiao@localhost) by neon.chem.ucla.edu (8.8.0/8.8.0) with SMTP id LAA04146; Thu, 27 Jan 2000 11:53:43 -0800 (PST) X-Authentication-Warning: neon.chem.ucla.edu: renxiao owned process doing -bs Date: Thu, 27 Jan 2000 11:53:43 -0800 (PST) From: Renxiao Wang To: rajarshi@presidency.com cc: Computational Chemistry List Subject: Re: C codes for dihedral angle Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear rajarshi, I think you have already been overwhelmed by unrelevent answers. Here is exactly what you want: ---------------------------------------------------------------------------- float Torsion_Angle(float p1[3], float p2[3], float p3[3], float p4[3]) { int i; float angle; float v12[3],v23[3],v34[3],v1[3],v2[3],v3[3]; for(i=0;i<=2;i++) { v12[i]=p2[i]-p1[i]; v23[i]=p3[i]-p2[i]; v34[i]=p4[i]-p3[i]; } Cross_Multiply(v12,v23,v1); Cross_Multiply(v23,v34,v2); angle=Angle_Of_Two_Vectors(v1,v2); Cross_Multiply(v1,v2,v3); if((v23[0]/v3[0]>0)||(v23[1]/v3[1]>0)||(v23[2]/v3[2])>0) return angle; else return -angle; } void Cross_Multiply(float v1[3], float v2[3], float result[3]) { result[0]=v1[1]*v2[2]-v2[1]*v1[2]; result[1]=v1[2]*v2[0]-v2[2]*v1[0]; result[2]=v1[0]*v2[1]-v2[0]*v1[1]; return; } ---------------------------------------------------------------------------- This is cut from my program LigBuilder. Hope it helps. Best wishes, Arthur ------------------------------------------------------------------------ | Dr. Renxiao Wang | ------------------------------------------------------------------------ | Department of Chemistry and Biochemistry | 3281 Sawtelle Blvd. #104 | | University of California Los Angeles | Los Angeles, CA90066 | | Los Angeles, CA 90024 | U.S.A | | Phone: 310-8250269 (Lab) | Phone: 310-3904638 (Home) | ------------------------------------------------------------------------ | E-mail: renxiao@chem.ucla.edu | | WWW: http://zimbu.chem.ucla.edu/~arthur/ | ------------------------------------------------------------------------