From chemistry-request@server.ccl.net Mon Mar 4 01:24:43 2002 Received: from webmailmta.go.com ([204.202.140.198]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g246Og505560 for ; Mon, 4 Mar 2002 01:24:42 -0500 Received: from gomailjtp05 ([10.212.0.165]) by mta06.seamail.go.com (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) with ESMTP id <0GSF00L1OJVRV8@mta06.seamail.go.com> for chemistry@www.ccl.net; Sun, 3 Mar 2002 19:47:51 -0800 (PST) Date: Sun, 03 Mar 2002 19:47:40 -0800 (PST) From: parveen parveen <7parveen@go.com> Subject: Problem in transition state location. To: chemistry@server.ccl.net Message-id: <6688075.1015213660254.JavaMail.7parveen@gomailjtp05> MIME-version: 1.0 X-Mailer: GoMail 3.0.0 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT Dear readers, I am doing abinito studies on medium ring compounds. For finding the transition states of these compounds, i am trying to locate the transition state of the acrolein reduction with LiH. I am using Gamess. I found a geo. close to T.S with 321G. I did IRC and got reaction pathway. Taking the same T.S geometry (found at 321G). i did IRC calculations at 6-31G* and mp2 6-31G*. Now the results vary a lot and the reaction pathway found in the 321G is not reproduced at higer level of basis set. The input for IRC : $CONTRL SCFTYP=RHF RUNTYP=IRC MPLEVL=2 NZVAR=24 COORD=ZMT $END $SYSTEM TIMLIM=40000 MEMORY=9000000 $END $IRC PACE=GS2 SADDLE=.TRUE. TSENGY=.FALSE. FORWRD=.FALSE. NPOINT=100 $END $GUESS GUESS=HUCKEL $END $BASIS GBASIS=n31 NGAUSS=6 NDFUNC=1 $END $DATA Calculation of irc of the reduction of acrolein. C1 C C 1 1.3175934 C 2 1.4683773 1 121.4030998 O 3 1.2648895 2 122.3010428 1 163.4724430 0 LI 4 1.7609866 3 97.3461670 2 104.9555105 0 H 1 1.0717788 2 121.9830606 3 -178.3972017 0 H 1 1.0745947 2 121.6377641 3 2.2282555 0 H 2 1.0719380 3 116.3714314 4 -14.9501683 0 H 3 1.0769044 2 115.4048342 1 -1.2870086 0 H 5 1.7313003 4 93.5246257 3 0.5416822 0 $END $HESS ......... for saddle point. $CONTRL SCFTYP=RHF RUNTYP=SADPOINT NZVAR=24 COORD=ZMT $END $SYSTEM MEMORY=6000000 TIMLIM=6000 $END $STATPT METHOD=QA HESS=CALC IHREP=1 MOVIE=.TRUE. OPTTOL=1.0e-4 NSTEP=200 PURIFY=.TRUE. $END $BASIS GBASIS=n21 NGAUSS=3 $END $GUESS GUESS=HUCKEL $END $DATA ............................ The transition state geo coordinates are given in the IRC input. Can anyone tell me why the results vary and how can we refine the approximate transition state. regards Parveen ___________________________________________________ GO.com Mail Get Your Free, Private E-mail at http://mail.go.com From chemistry-request@server.ccl.net Mon Mar 4 04:24:27 2002 Received: from luc.ac.be ([193.190.2.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g249OQ507614 for ; Mon, 4 Mar 2002 04:24:26 -0500 Received: from sbg-ts (localhost [127.0.0.1]) by luc.ac.be (8.9.3/8.9.3) with SMTP id KAA12490 for ; Mon, 4 Mar 2002 10:23:56 +0100 (MET) Date: Mon, 4 Mar 2002 10:23:56 +0100 (MET) Message-Id: <200203040923.KAA12490@luc.ac.be> X-Sender: lucp1381@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: sergiusz kwasniewski Subject: MD in hyperchem Hi, does anyone know how to retrieve xyz coordinates from a MD snapshot file generated by hyperchem ? Thanks, Serge K ___________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 032 (0)11/268315 fax : 032 (0)11/268301 email : sergiusz.kwasniewski@luc.ac.be http://www.luc.ac.be/Research/TheoChem ___________________________________________________ From chemistry-request@server.ccl.net Mon Mar 4 06:15:36 2002 Received: from as1200.organik.uni-erlangen.de ([131.188.128.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g24BFZ509100 for ; Mon, 4 Mar 2002 06:15:36 -0500 Received: from chemie.uni-erlangen.de (excelsior.chemie.uni-erlangen.de [131.188.128.76]) by as1200.organik.uni-erlangen.de (8.8.7/8.1.11-FAU) with ESMTP id MAA27590 for ; Mon, 4 Mar 2002 12:15:06 +0100 (MET) Sender: Harald.Lanig@Organik.Uni-Erlangen.DE Message-ID: <3C835739.FB38E50@chemie.uni-erlangen.de> Date: Mon, 04 Mar 2002 12:15:06 +0100 From: Harald Lanig Organization: Computer-Chemie-Centrum X-Mailer: Mozilla 4.76C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: 16th Molecular Modelling Workshop - May 07-08, 2002 in Darmstadt, Germany Content-Type: multipart/alternative; boundary="------------E74E94D1E7FCEF485C8892C5" --------------E74E94D1E7FCEF485C8892C5 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear list members, let me please point your attention to 16th Molecular Modelling Workshop taking place in Darmstadt, Germany from May 07 to 08, 2002. Although the official conference language is German, this information may be useful to a lot of readers of this list. For further information please see the URL http://www.pc.chemie.tu-darmstadt.de/mmws/ Kind regards, Harald Lanig -- ------------------------------------------------------------------------ Dr. Harald Lanig Universitaet Erlangen/Nuernberg Computer-Chemie-Centrum Naegelsbachstr. 25, D-91052 Erlangen oder Lehrstuhl fuer Schuhstrasse 19 Pharmazeutische Chemie D-91052 Erlangen, Germany Phone +49(0)9131-85 26525 Mailto:lanig@chemie.uni-erlangen.de Fax +49(0)9131-85 26565 http://www.ccc.uni-erlangen.de/lanig ------------------------------------------------------------------------ --------------E74E94D1E7FCEF485C8892C5 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit  

Dear list members,

let me please point your attention to 16th Molecular Modelling Workshop taking place in Darmstadt, Germany from May 07 to 08, 2002.

Although the official conference language is German, this information may be useful to a lot of readers of this list. For further information please see the URL

http://www.pc.chemie.tu-darmstadt.de/mmws/
 

Kind regards,
Harald Lanig 

-- 
------------------------------------------------------------------------
 Dr. Harald Lanig            Universitaet Erlangen/Nuernberg
 Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen
 oder
 Lehrstuhl fuer              Schuhstrasse 19
 Pharmazeutische Chemie      D-91052 Erlangen, Germany
 
 Phone +49(0)9131-85 26525   Mailto:lanig@chemie.uni-erlangen.de
 Fax   +49(0)9131-85 26565   http://www.ccc.uni-erlangen.de/lanig
------------------------------------------------------------------------
 

 
 
 
  --------------E74E94D1E7FCEF485C8892C5-- From chemistry-request@server.ccl.net Mon Mar 4 03:11:12 2002 Received: from cns.FTA-Berlin.de ([141.16.244.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g248BC506601 for ; Mon, 4 Mar 2002 03:11:12 -0500 Received: from langmuir.aca-berlin.de (langmuir.ACA-Berlin.de [141.16.16.120]) by cns.FTA-Berlin.de (8.11.3/8.11.3/SuSE Linux 8.11.1-0.5) with ESMTP id g248AWE32051; Mon, 4 Mar 2002 09:10:32 +0100 Date: Mon, 4 Mar 2002 09:07:31 +0100 (CET) From: To: David Close cc: Subject: Re: CCL:G98 Dual Processor ?? In-Reply-To: <3.0.6.32.20020301145133.009dfcd0@access.etsu.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi David, some hints to your questions: > Now I have a question about the dual processors. What is the best > way to utilize this extra power? Run two jobs, each one on a separate > processor, or look into parallel G98 code? As I am rather inexperienced > in UNIX, I am not at all certain even how to run two jobs at the same time. > Any suggestions would be greatly appreciated. Two Jobs at the same time are great, because normally you will not get an ideal speedup of 2. You may consider starting even more jobs (perhaps 4) at one time: If you are doing heavy I/O your processor is mostly idle and waiting for the disk. If not, 2 are pretty good ... > One more thing. I often run big jobs strung together with the --link1-- > command. This is fine, but jobs tend to finish in the middle of the > night. Does anyone know how to start a new job automatically when a big > job is finished? I tried to add more --link1--'s to a .com file that > was currently executing, and the whole job crashed in just a few minutes. You should install a queueing systen like NQS or one of your Linux distribution. Check simply out your install routine ... Alex --- Dr. Alexander Hofmann Institute for Applied Chemistry Berlin-Adlershof P.O. Box 96 11 56 Richard-Willstaetter-Str. 12 D-12474 Berlin D-12489 Berlin hofmann@aca-berlin.de Tel.: +49-30-6392-4408 Fax.: +49-30-6392-4350 http://www.aca-berlin.de PGP-Private key: http://wwwkeys.de.pgp.net:11371 ID:0xF39A0BC8 From chemistry-request@server.ccl.net Mon Mar 4 04:19:58 2002 Received: from luc.ac.be ([193.190.2.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g249Jw507558 for ; Mon, 4 Mar 2002 04:19:58 -0500 Received: from sbg-ts (localhost [127.0.0.1]) by luc.ac.be (8.9.3/8.9.3) with SMTP id KAA13442 for ; Mon, 4 Mar 2002 10:19:28 +0100 (MET) Date: Mon, 4 Mar 2002 10:19:28 +0100 (MET) Message-Id: <200203040919.KAA13442@luc.ac.be> X-Sender: lucp1381@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: sergiusz kwasniewski Subject: line broadening in conjugated polymers Hi everyone, I've got an interesting question about the line broadening of the first electronic absorption band in conjugated polymers: - It seems that some people believe it's due to vibronic coupling, - others claim that it's due to a distribution of conformational 'subunits' (localized conjugated systems due to conformational disorder in the polymer), - still others say that the formation of aggregates in films are the main contributors, - ... Does anyone know if someone has tried to investigate all these effects in a e.g. review article ? What are the important references that try to tackle these problems ? I will summarize, Thanks in advance, Serge K. ___________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 032 (0)11/268315 fax : 032 (0)11/268301 email : sergiusz.kwasniewski@luc.ac.be http://www.luc.ac.be/Research/TheoChem ___________________________________________________ From chemistry-request@server.ccl.net Mon Mar 4 04:29:39 2002 Received: from linux16.theochem.uni-stuttgart.de ([129.69.55.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g249Td507701 for ; Mon, 4 Mar 2002 04:29:39 -0500 Received: from localhost (teomgs@localhost) by linux16.theochem.uni-stuttgart.de (8.11.3/8.11.2/SuSE Linux 8.11.1-0.5) with ESMTP id g249T7a25482; Mon, 4 Mar 2002 10:29:08 +0100 X-Authentication-Warning: linux16.theochem.uni-stuttgart.de: teomgs owned process doing -bs Date: Mon, 4 Mar 2002 10:29:07 +0100 (MET) From: "Dr. Martin Schuetz" To: Per-Ola Norrby cc: , Subject: Re: CCL:Linear scaling algorithms for QM calculations In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id g249Td507702 ---------------------------------------------------------------------------- PD Dr. Martin Schuetz Phone: 0049 (0)711-685-4397 University of Stuttgart Fax: 0049 (0)711-685-4442 Institute for Theoretical Chemistry Pfaffenwaldring 55 Room Nr: 8.161 D-70569 Stuttgart Email: schuetz@theochem.uni-stuttgart.de WWW : http://www.theochem.uni-stuttgart.de/~schuetz/ ---------------------------------------------------------------------------- On Sun, 3 Mar 2002, Per-Ola Norrby wrote: > To continue the linear scaling trend. > > The linear scaling CCSD is extremely interesting to me, > especially if CCSD(T) can also be made linear or near so. However, > I'm also interested in cases which are definitely multi-reference in > character (T1-diagnostic up to ca 0.1, invalidating any CC approach). > Is anyone aware of linear scaling multi-reference methods? How about > GVB, are there linear scaling implementations? From initial CASSCF > calculations, perfect pairing might be a good approximation in my > case. The local CCSD(T) is strictly linear scaling in the asymptotical limit. I am not aware of any genuine multireference methods with O(N) scaling. However, in certain cases (like breaking of covalent single bonds, biradicals) the triples contribution repairs the deficiencies of the single reference ansatz to large extends (one might have to go beyond the (T) approximation though). I just got a paper accepted by JCP, which presents an O(N) local CCSDT-1b method. CCSDT-1b appears to be substantially more stable than CCSD(T) for these cases. I will put a preprint of the paper on my web page within the next days.. > > A separate question: as far as I'm aware, these methods > become linear when the number of atoms is increased, by localizing > the calculations. I believe that the scaling is still bad if you're > interested in increasing the system size by going to larger basis > sets. Can anyone who knows this verify? I'm just assuming. It is exactly as you say. The linear scaling refers to the size, i.e., the number of electrons if you like, of the molecule. If you take a molecule of constant size and increase the number of functions per center you will observe the same N^4 scaling as in the canonical case. In order to improve the convergence of the correlation energy with basis set size we are presently exploring the possibility to combine local methods with explicitely correlated methods (Gaussian Geminals, R12). Furthermore, in order to reduce the prefactor we are introducing the RI approximation (Coulomb fitting). Best regards Martin > > Best, > > Per-Ola Norrby > > >For coupled cluster methods with linear scaling check references > >on my web site > > > > > >---------------------------------------------------------------------------- > >PD Dr. Martin Schuetz Phone: 0049 (0)711-685-4397 > >University of Stuttgart Fax: 0049 (0)711-685-4442 > >Institute for Theoretical Chemistry > >Pfaffenwaldring 55 Room Nr: 8.161 > >D-70569 Stuttgart > >Email: schuetz@theochem.uni-stuttgart.de > >WWW : http://www.theochem.uni-stuttgart.de/~schuetz/ > >---------------------------------------------------------------------------- > > > > > > > >On Fri, 1 Mar 2002, Julien MICHEL wrote: > > > >> Dear CCLers, > >> > >> I recently read a few words about algorithms for pure quantum mechanical > >> calculations that scales linearly with the number of electrons in the system > >> studied. > >> I was surprised to read this as I thought such rate was not feasible for any > >> kind > >> of quantum calculation. I would be curious to read more about these > >> algorithms and how they work. Furthermore, Iíd like to know if these > >> algorithms have been used to study fairly big molecular systems such as > >> proteins. I would be glad if someone could point some references or even > >> better internet resources focusing on that topic > >> > >> Julien MICHEL > >> > >> > >> > >> > >> > >> > >> > >> > >> > > > > > > > >-= 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 > > -- > > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > Per-Ola Norrby, Assoc. Professor, http://compchem.dfh.dk/PeO/ > Technical University of Denmark, Dept. of Chem., Org. Chem. > Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark > Email: pon@kemi.dtu.dk tel +45-45252123, fax +45-45933968 > From chemistry-request@server.ccl.net Mon Mar 4 08:27:35 2002 Received: from as1200.organik.uni-erlangen.de ([131.188.128.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g24DRZ510971 for ; Mon, 4 Mar 2002 08:27:35 -0500 Received: from as1200-1 (as1200-1 [131.188.128.6]) by as1200.organik.uni-erlangen.de (8.8.7/8.1.11-FAU) with ESMTP id OAA10001 for ; Mon, 4 Mar 2002 14:27:05 +0100 (MET) Date: Mon, 4 Mar 2002 14:27:05 +0100 (MET) From: Paul Winget X-Sender: winget@as1200-1 To: chemistry@ccl.net Subject: semi-empirical parameter table Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Colleagues, I would like to compile a table of various semiempirical methods and the parameters associated with them. While there are some differences in the formulation of these methods, I would still find such a comparison useful. Is anybody aware of such a compilation ? (An example is at the end of the message) The original publications list these parameters, however, I would find it quite tedious (and error prone) to manually reproduce the data. Parsing the parameter files of various software packages is also possible, although it is not a trivial process (at least for me). I appreciate your help/comments in this matter. Replies will be summarized. Paul Winget For example: ----------------------------------------------------------- Element Parameter MNDO AM1 PM3 ----------------------------------------------------------- H U_ss (eV) -11.906 -11.396 -16.073 H Zeta_s(au) 1.332 1.188 0.968 ... ==== Paul Winget Paul.Winget@chemie.uni-erlangen.de http://www.ccc.uni-erlangen.de/clark/winget/index.html Phone: +49 9131 85-26583 Fax: +49 9131 85-26565 From chemistry-request@server.ccl.net Mon Mar 4 09:57:44 2002 Received: from Salicet.ucd.ie ([137.43.1.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g24Evh512574 for ; Mon, 4 Mar 2002 09:57:44 -0500 X-Confirm-reading-to: Laurence.Cuffe@ucd.ie X-PMrqc: 1 Received: from CONVERSION-DAEMON.Salicet.ucd.ie by Salicet.ucd.ie (PMDF V6.1 #40617) id <0GSG00801EP7K8@Salicet.ucd.ie> for chemistry@ccl.net; Mon, 04 Mar 2002 14:53:34 +0000 (GMT) Received: from elvira.ucd.ie ([137.43.24.26]) by Salicet.ucd.ie (PMDF V6.1 #40617) with ESMTP id <0GSG0087GEP75X@Salicet.ucd.ie>; Mon, 04 Mar 2002 14:53:31 +0000 (GMT) Date: Mon, 04 Mar 2002 14:54:01 +0000 From: Laurence Cuffe Subject: Re: CCL:G98 Dual Processor ?? In-reply-to: <3.0.6.32.20020301145133.009dfcd0@access.etsu.edu> To: David Close , chemistry@ccl.net Message-id: <3C838A89.18459.1414D1C9@localhost> Organization: University College Dublin X-Mailer: Pegasus Mail for Win32 (v3.12c) Content-type: TEXT/PLAIN Priority: normal Date sent: Fri, 01 Mar 2002 14:51:33 -0500 From: David Close Subject: CCL:G98 Dual Processor ?? To: chemistry@ccl.net > To CCL: > Several weeks ago I asked for help installing G98 LINUX version on a >Dell 530 Dual Processor workstation. Several CCLers sent me helpful >suggestions on how to get G98 LINUX working on this machine. This >is working now. Many thanks for the help. > Now I have a question about the dual processors. What is the best >way to utilize this extra power? Run two jobs, each one on a separate >processor, This would be our preferred option, its not hard to do, for example if the jobs are job1 and job2 type g98 job1 & (return) g98 job2 & (return) then both jobs will run together. you can check this using the utility top just type top (return) and it will display how your procesors are doing. or look into parallel G98 code? We've run jobs using the parallel code, its not as efficient as running separate jobs. look up "Amdals law" for more details. As I am rather inexperienced >in UNIX, I am not at all certain even how to run two jobs at the same time. >Any suggestions would be greatly appreciated. see above! > One more thing. I often run big jobs strung together with the --link1-- >command. This is fine, but jobs tend to finish in the middle of the >night. Does anyone know how to start a new job automatically when a big >job is finished? This is very slightly harder to do. again jobs 1 and 2 first change into the cshell by typing csh (return) then type g98 job1.com;g98 job2.com;& (return) when job1 finishes job2 starts. I would typically use this to run ten or twelve jobs one after another over the weekend. remember, this is unix, there are many different ways of doing the same thing, but the above is what works for us. Hope this helps All the best Laurence Cufffe I tried to add more --link1--'s to a .com file that >was currently executing, and the whole job crashed in just a few minutes. > Regards, Dave Close. > > > >-= 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 > > > > > From chemistry-request@server.ccl.net Mon Mar 4 09:06:31 2002 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g24E6V511610 for ; Mon, 4 Mar 2002 09:06:31 -0500 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id JAA16063; Mon, 4 Mar 2002 09:05:56 -0500 (EST) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Mon, 04 Mar 2002 09:04:06 -0500 (Eastern Standard Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GSG007DLC8K5X@lvlmail.unitedcatalysts.com>; Mon, 04 Mar 2002 09:00:20 -0500 (EST) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Mon, 04 Mar 2002 09:04:10 -0500 Content-return: allowed Date: Mon, 04 Mar 2002 09:04:09 -0500 From: "Shobe, Dave" Subject: RE: gaussian: electron density To: "'Donald Keidel'" , chemistry@ccl.net Message-id: <157A51F55AAAD3119CD70008C7B1629D01C15A10@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g24E6V511611 The "elecron densities at the oxygen of the carboxylate" is ambiguous, as the electron density varies from point to point. The only unique point I can think of is the oxygen nucleus, but I suspect you'd more more interested in the "lone pair" area. Calculation of the electron density at a point is trivial; defining the point to use in a way that's consistent from molecule to molecule is the challenge. Yes, CHELPG is based on electrostatic potentials--although I would think those would be important in binding to Zn+2 also. It might be interesting to see which is more important. Come to think of it, I vaguely remember some kind of function, related to AIM analysis (atoms-in-molecues, based on the eletcron density distribution) that had a maximum in lone pair regions of a molecule. I don't remember any details and I'm not even sure what I recall is accurate, but it might be worth a trip to the library (or SciFinder) to investigate. --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: Donald Keidel [mailto:dkeidel397@att.net] Sent: Friday, March 01, 2002 1:45 PM To: chemistry@ccl.net Subject: CCL:gaussian: electron density Hello all, I want to use Gaussian to calculate or determine the electron density on the oxygen atoms of benzoic acids. I want to do this for various benzoic acids that are different from eachother only in their substitution at the ortho meta and para positions. I think that benzoic acids with different elecron densities at the oxygen of the carboxylate of the benzoate will coordinate to zinc differently with different affinities. I might be wrong. What method in Gaussian 98 is best suited for this. I was told to use CHELPG, but I believe that is used for electrostatic potentials and not electron densities. Thank you to all. Have a good day. Don --------------------------------------------------- Donald J. Keidel University of California, Riverside Department of Biochemistry and Molecular Biology Riverside, CA 92521 phone: (909) 787-5493 fax: (909) 787-4434 dkeidel397@att.net webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm From chemistry-request@server.ccl.net Mon Mar 4 12:04:49 2002 Received: from ks.uiuc.edu ([130.126.120.73]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g24H4n516099 for ; Mon, 4 Mar 2002 12:04:49 -0500 Received: from verdun.ks.uiuc.edu (verdun.ks.uiuc.edu [130.126.120.129]) by ks.uiuc.edu (8.11.2/8.11.2) with ESMTP id g24H4J724988 for ; Mon, 4 Mar 2002 11:04:19 -0600 (CST) Received: from localhost (jim@localhost) by verdun.ks.uiuc.edu (8.10.2+Sun/8.9.1) with ESMTP id g24H4JU23862 for ; Mon, 4 Mar 2002 11:04:19 -0600 (CST) X-Authentication-Warning: verdun.ks.uiuc.edu: jim owned process doing -bs Date: Mon, 4 Mar 2002 11:04:19 -0600 (CST) From: Jim Phillips To: chemistry@ccl.net Subject: Upcoming NAMD Workshop Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Biomedical Applications of Molecular Dynamics on the TeraGrid April 17-19, 2002 (space is limited, register by *** March 7 ***) http://www.ncsa.uiuc.edu/Divisions/eot/training/NAMD/ Hosted by NCSA and presented by the Theoretical Biophysics Group, this workshop will familiarize biomedical researchers with computational methods and provide practical training in applying supercomputing resources to molecular dynamics simulations. Lectures will cover computing resources available at NCSA, a general introduction to molecular modeling, its benefits to research through the use of case studies, and a review of available hardware and software tools. The use of the program NAMD will be discussed in detail, and an optional half-day hands-on session will allow participants to gain experience using NAMD and the visualization program VMD, or other applications of their choice that are available at NCSA. No prior supercomputing or molecular modeling experience is necessary. The workshop will be held in Champaign, IL and broadcast April 17-18 on the Access Grid to Boston University, North Dakota State University, and the Ohio Supercomputing Center. From chemistry-request@server.ccl.net Mon Mar 4 12:18:19 2002 Received: from electra.cc.umanitoba.ca (root@[130.179.16.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g24HII516364 for ; Mon, 4 Mar 2002 12:18:18 -0500 Received: from hultin (hultin.chem.umanitoba.ca [130.179.48.60]) by electra.cc.umanitoba.ca (8.12.0/8.12.0) with SMTP id g24HHmZl012362 for ; Mon, 4 Mar 2002 11:17:48 -0600 (CST) From: "Phil Hultin" To: "Computational Chemistry List" Subject: Gaussian, Electron Density and AIM Date: Mon, 4 Mar 2002 11:17:49 -0600 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 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Dave Shobe wrote: >Come to think of it, I vaguely remember some kind of function, related to >AIM analysis (atoms-in-molecues, based on the eletcron density distribution) >that had a maximum in lone pair regions of a molecule. Dave is referring to the Laplacian of the electron density, which can be interpreted in terms of electron pair densities. The short introduction to AIM by Paul Popelier (a paperback book, roughly 150 pages as I recall) discusses this idea in some detail. I am not a disciple or anything, but if one is trying to dissect the charge distribution in a molecule, it appears to me that AIM is probably the best way to do it. At least, it has the virtue of being based on mathematically rigorous analysis of the calculated or observed electron density. It does not impose any pre-conceptions on how charge is assigned to atoms. 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@cc.umanitoba.ca http://www.umanitoba.ca/chemistry/ From chemistry-request@server.ccl.net Mon Mar 4 15:14:50 2002 Received: from elin.scali.no (IDENT:root@[62.70.89.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g24KEn519249 for ; Mon, 4 Mar 2002 15:14:49 -0500 Received: from localhost (ole@localhost) by elin.scali.no (8.11.6/8.11.6) with ESMTP id g24KD3B13779; Mon, 4 Mar 2002 21:13:03 +0100 Date: Mon, 4 Mar 2002 21:13:03 +0100 (CET) From: "Ole W. Saastad" To: Laurence Cuffe cc: David Close , Subject: Re: CCL:G98 Dual Processor ?? In-Reply-To: <3C838A89.18459.1414D1C9@localhost> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII You could try to compile g98 with Intels compiler. This compiler has support for auto parallelization. It works for some problems, but not for all. It might work for g98, I do not have the source for g98 here so, I have not tried. (I would if I could fine the time to visit old frient at the Univ. of Oslo) The auto par. works fine for a couple of seismic problems I worked on. The Portland compiler also has this option, but it does not work well. The Intel compiler is outstanding in this respect. You could install threaded versions of the Blas libraries, but this does not really speed the g98 up very much. It improves some, but not enough time is spent in BLAS routines to justify this move. It would be a unseful exercise if someone could try to compile the g98 with Intel ifc (v. 6.0 for Linux) and report the outcome. It would also be a nice job if someone sat down and put OpenMP comments in the g98 source code, or even better rewrote the g98 to MPI ! Ole W. Saastad Scali A/S. From chemistry-request@server.ccl.net Mon Mar 4 15:39:30 2002 Received: from hermes.bmc.uu.se ([130.238.39.245]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g24KdU519601 for ; Mon, 4 Mar 2002 15:39:30 -0500 Received: from XRAY.bmc.uu.se ([130.238.37.10]) by hermes.bmc.uu.se (Post.Office MTA v3.5.3 release 223 ID# 0-62649U1500L1000S0V35) with ESMTP id se for ; Mon, 4 Mar 2002 21:38:46 +0100 Received: from zorn.bmc.uu.se (IDENT:spoel@zorn.bmc.uu.se [130.238.37.95]) by XRAY.bmc.uu.se (8.11.6/8.8.7) with ESMTP id g24KdXb25931 for ; Mon, 4 Mar 2002 21:39:33 +0100 Date: Mon, 4 Mar 2002 21:38:32 +0100 (CET) From: David van der Spoel X-Sender: spoel@zorn.bmc.uu.se cc: chemistry@ccl.net Subject: Re: CCL:G98 Dual Processor ?? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 4 Mar 2002, Ole W. Saastad wrote: > If you compiled gaussian with portland compiler you only have to set %nproc=2 it has a scaling of roughly 1.4, so 70% on 2 processors depending on your job. It works with threads. >-= 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 > > > > > Groeten, David. ________________________________________________________________________ Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry Husargatan 3, Box 576, 75123 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel@xray.bmc.uu.se spoel@gromacs.org http://zorn.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Mon Mar 4 20:00:26 2002 Received: from mail.laposte.net ([160.92.113.39]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2510Q522930 for ; Mon, 4 Mar 2002 20:00:26 -0500 Received: from nouveaupc (217.128.255.167) by mail.laposte.net (5.5.044) id 3C4BFED4002CEF5E for chemistry@ccl.net; Tue, 5 Mar 2002 01:59:47 +0100 Message-ID: <002601c1c3e1$064aae20$0b00000a@nouveaupc> From: "Alexandre Hocquet" To: "Computational Chemistry List" References: Subject: Re: CCL:Gaussian, Electron Density and AIM Date: Tue, 5 Mar 2002 01:59:34 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 It is also described in this paper : "On the Full Topology of the Laplacian of the Electron Density.", P.L.A. Popelier, Coord. Chem. Rev., 197, 169-189 (2000). with the example of the H2O molecule. ------------------------------------------------------------ Alexandre HOCQUET Laboratoire de Physicochimie Biomoléculaire et Cellulaire ESA CNRS 7033 hocquet@lpbc.jussieu.fr Fax: 33 1 44277560 LPBC, case courrier 138 4 Place Jussieu, 75252 PARIS Cedex 05 France ------------------------------------------------------------ From chemistry-request@server.ccl.net Mon Mar 4 11:28:05 2002 Received: from mhub2.bbsrc.ac.uk ([149.155.202.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g24GS4515215 for ; Mon, 4 Mar 2002 11:28:04 -0500 Received: from exrout.cc.bbsrc.ac.uk ([149.155.100.88]) by mhub2.bbsrc.ac.uk with esmtp (Exim 3.31 #1) id 16hvDu-0002wB-04 for chemistry@ccl.net; Mon, 04 Mar 2002 16:22:02 +0000 Received: from bits-exch1.bits.bbsrc.ac.uk ([149.155.108.13]) by exrout.cc.bbsrc.ac.uk with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id FZSH6Q9N; Mon, 4 Mar 2002 16:22:18 -0000 Received: by bits-exch1.bits.bbsrc.ac.uk with Internet Mail Service (5.5.2653.19) id ; Mon, 4 Mar 2002 16:22:17 -0000 Message-ID: <41773CEF2B8FD411920200508BDCDC12BE13A8@bits-exch1.bits.bbsrc.ac.uk> From: "michael hanlon (BITS)" To: "'chemistry@ccl.net'" Subject: molecular docking startup:summary Date: Mon, 4 Mar 2002 16:22:17 -0000 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" X-ECS-MailScanner-BBSRC: Found to be clean Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g24GS5515216 in response to guidance fo a newcomer to molecular docking: 1. please check out Glide from Schrödinger Inc. see www.schrodinger.com We also offer complete solutions for docking: i.e. Glide installed on a ready to use IBM-Linux cluster together with our partner IBM. Please contact schrodinger@anterio.com if you need further information. 2.Reviews in Computational Chemistry (KB Lipkowitz, DB Boyd, Eds.) Vol. 17, Wiley-VCH, New York 2001 contains comprehensive reviews on protein/ligand and protein/protein docking. 3. In my own experience of Docking packages I have found GOLD (Gareth Jones 1997) to be the most a) user friendly and b) reliable - so I would recommend that you start here. However, it has limitations - and if you are looking to dock largely hydrophobic ligands into hydrophobic structures it probably will frustrate you......saying that so will a lot of the other packages out there. Dr. Mike Hanlon Molecular Biology Computing Support BBSRC Bioscience IT Services West Common Harpenden Herts AL5 2JE Phone: 01582 714904 Email: molbio.support@bbsrc.ac.uk Web: http://www.molbiol.bbsrc.ac.uk From chemistry-request@server.ccl.net Mon Mar 4 12:49:05 2002 Received: from web14706.mail.yahoo.com ([216.136.224.123]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g24Hn5517032 for ; Mon, 4 Mar 2002 12:49:05 -0500 Message-ID: <20020304174823.31282.qmail@web14706.mail.yahoo.com> Received: from [129.13.64.203] by web14706.mail.yahoo.com via HTTP; Mon, 04 Mar 2002 18:48:23 CET Date: Mon, 4 Mar 2002 18:48:23 +0100 (CET) From: =?iso-8859-1?q?y=20tantirungrotechai?= Subject: dipole integral of slater orbital To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCLers, I am looking for some references on how to calculate the dipole integral of slater orbital I found some formulas in the MOPAC2000 manual but no references were given there. Best regards, Yuthana Tantirungrotechai __________________________________________________________________ Gesendet von Yahoo! Mail - http://mail.yahoo.de Ihre E-Mail noch individueller? - http://domains.yahoo.de