From chemistry-request@ccl.net Wed Jun 23 22:17:54 2004 Received: from brass.metals.hope.edu (brass.metals.hope.edu [198.110.98.36]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i5O3Hrkq032367 for ; Wed, 23 Jun 2004 22:17:53 -0500 Received: from hope.edu ([198.110.98.17]) by brass.metals.hope.edu (SAVSMTP 3.1.1.32) with SMTP id M2004062323203901045 ; Wed, 23 Jun 2004 23:20:39 -0400 Received: from [198.110.101.2] (polik:at:hope.edu) by hope.edu; Wed, 23 Jun 2004 23:20:55 -0400 X-WM-Posted-At: hope.edu; Wed, 23 Jun 04 23:20:55 -0400 Message-Id: <5.2.0.9.2.20040623231711.02739920:at:webmail.hope.edu> X-Sender: polik:at:webmail.hope.edu (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.2.0.9 Date: Wed, 23 Jun 2004 23:20:59 -0400 To: CHEMISTRY:at:ccl.net From: "William F. Polik" Subject: CCL:Mopac7 under IRIX Cc: Yong Liang Yang In-Reply-To: Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_643931484==.ALT" X-Spam-Status: No, hits=3.0 required=7.5 tests=HTML_MESSAGE,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --=====================_643931484==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Yong, Try using the mopac 7 distribution and instructions available from the WebMO website "MOPAC 7 Installation Instructions for IRIX": http://www.webmo.net/support/mopac_sgi.html Will Polik At 11:02 AM 6/23/2004, you wrote: > I tried to compile mopac7 under IRIX6.5 using GCC compiler, >however I always get the error message as below: > >**Error code 1 (bug 21) >Too many arguments passed to intrinsic 'SECOND' at (^) >---------------------------------- > >The commnad line in Makefile is as below: > >g77 -w -O -static *.f -o $(EXE) > > >Does anybody know how to fix this bug? I downloaed the >binary from Webmo website. Any suggestion is highly >appreciated. Thanks in advance. ================================ Dr. William F. Polik Hofma Professor of Chemistry Department of Chemistry Hope College 35 East 12th Street Holland, MI 49422-9000 USA polik:at:hope.edu http://www.chem.hope.edu/~polik tel: (616) 395-7639 fax: (616) 395-7118 ================================ --=====================_643931484==.ALT Content-Type: text/html; charset="us-ascii" Yong,

Try using the mopac 7 distribution and instructions available from the WebMO website "MOPAC 7 Installation Instructions for IRIX":
http://www.webmo.net/support/mopac_sgi.html

Will Polik

At 11:02 AM 6/23/2004, you wrote:

I tried to compile mopac7 under IRIX6.5 using GCC compiler,
however I always get the error message as below:

**Error code 1 (bug 21)
Too many arguments passed to intrinsic 'SECOND' at (^)
----------------------------------

The commnad line in Makefile is as below:

g77 -w -O -static *.f -o $(EXE)

Does anybody know how to fix this bug? I downloaed the
binary from Webmo website. Any suggestion is highly
appreciated. Thanks in advance.

================================
Dr. William F. Polik
Hofma Professor of Chemistry

Department of Chemistry
Hope College
35 East 12th Street
Holland, MI 49422-9000
USA

polik:at:hope.edu
http://www.chem.hope.edu/~polik
tel: (616) 395-7639
fax: (616) 395-7118
================================
--=====================_643931484==.ALT-- From chemistry-request@ccl.net Thu Jun 24 01:09:58 2004 Received: from iqe1.ethz.ch (iqe1-hptf.ethz.ch [129.132.22.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5O69vkp004988 for >ccl.net>; Thu, 24 Jun 2004 01:09:57 -0500 Received: from 129.94.6.28 (iqe1 [129.132.22.196]) by iqe1.ethz.ch (8.9.3/8.9.3) with SMTP id IAA21961; Thu, 24 Jun 2004 08:14:47 +0200 (MET DST) Message-Id: <200406240614.IAA21961<>iqe1.ethz.ch> To: arashid<>phys.unsw.edu.au Cc: chemistry<>ccl.net From: arashid<>iqe.phys.ethz.ch Subject: Fwd: CCL:transition-state energies Date: Thu, 24 Jun 2004 06:14:47 +0000 X-Mailer: Endymion MailMan v2.0 X-Spam-Status: No, hits=1.3 required=7.5 tests=HTML_MESSAGE,MK_BAD_HTML_04, NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Forwarded Message: > To: Joe Harriman >unb.ca> > From: Per-Ola Norrby >kemi.dtu.dk> > Subject: CCL:transition-state energies > Date: Wed, 9 Jun 2004 08:30:16 +0200 > -----

>I have some transition-sate structures and their corresponding 
>energies.  In addition, I
>have the enantiomeric excess values for the products that arise from these
>transition-state structures.  Is there a method that can be used to 
>correlate in silico
>transition-state energies to the ee's reported in litterature.  I 
>have been searching
>in vain for a method, but have been unsuccesful to date.  Any help 
>would be greatly
>appreciated.

	This comes out of the Eyring or Arrhenius equations, which 
you find in any basic physical chemistry text book.  Arrhenius: k = A 
exp(-Ea/RT); I prefer Eyring, but they give the same results when 
you're looking at relative rates.  As a first approximation assume 
that the constant(s) are equal for both paths (usually including the 
entropy, a fairly strong approximation...).  I assume that you're 
looking at an irreversible step, then the ratio of products, r, can 
be obtained simply as the ratio of rate constants, r = exp(DEa/RT), 
where DEa is the difference in transition state energy (all the 
constants disappear in the division).  When you have the ratio, the 
ee is easily obtained from ee = (r-1)/(r+1), which is the excess 
divided by the total, the definition of ee.

	/Per-Ola
-- 
Per-Ola Norrby, Assoc. Professor, http://organisk.kemi.dtu.dk/PON/
Technical University of Denmark, Department of Chemistry
Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark
Email: pon<>kemi.dtu.dk  tel +45-45252123,  fax +45-45933968

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From chemistry-request@ccl.net Thu Jun 24 05:25:11 2004 Received: from mailfilter.diszk.unideb.hu ([193.6.138.70]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5OAPAbC013837 for ; Thu, 24 Jun 2004 05:25:10 -0500 Received: from mailfilter.diszk.unideb.hu (localhost [127.0.0.1]) by mailfilter.diszk.unideb.hu (Postfix) with SMTP id C41DAA2239; Thu, 24 Jun 2004 11:09:02 +0200 (CEST) Received: from Cthulhu (anti309.chem.klte.hu [193.6.133.108]) by delfin.unideb.hu (Postfix) with SMTP id 4BA52C85E; Thu, 24 Jun 2004 10:10:14 +0200 (DFT) Message-ID: <000801c459c2$adcb0ef0$6c8506c1@Cthulhu> From: "Tamas E. Gunda" To: "Steve Bowlus" , References: Subject: Re: CCL:Orient molecule Date: Thu, 24 Jun 2004 10:10:13 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1409 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Steve, Mol2mol has an advanced rotation toolbar, which has the options you are looking for. In addition, you can decide wheter to apply or not the screen rotations to the original coordinates and to save them. Look at: http://web.interware.hu/frenzy/mol2mol or the rotation stuff: http://web.interware.hu/frenzy/mol2mol/m2m/graphwin.htm#rot_summary Regards Tamas Gunda University of Debrecen, Hungary tgunda *at* puma.unideb.hu ----- Original Message ----- From: "Steve Bowlus" To: Sent: Thursday, June 24, 2004 5:42 AM Subject: CCL:Orient molecule > I am frantically searching for a simple piece of code that will allow me to: > > Read a standard file (mol, pdb, Sybyl ...) > select an atom to put at the Cartesian origin > select an atom to put on the X axis > select an atom to put in the XY plane > Do a rigid rotation > Do sequential rigid rotations about Cartesian axes > Freeze the molecule in the new orientation > Output the NEW, transformed coordinates. > > This is equivalent to the Sybyl "orient" command, plus rigid rotations, plus > "Freeze molecule". But I have not found a free (or even cheap) package that > will freeze a molecule in the new coordinates before output. > > Thanks in advance for any pointers, > Steve > > > -= 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^at^ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST^at^ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow^at^nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Thu Jun 24 17:57:57 2004 Received: from iqe1.ethz.ch (iqe1-hptf.ethz.ch [129.132.22.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5OMvt5d002388 for >ccl.net>; Thu, 24 Jun 2004 17:57:56 -0500 Received: from 129.94.6.28 (iqe1 [129.132.23.4]) by iqe1.ethz.ch (8.9.3/8.9.3) with SMTP id BAA26141; Fri, 25 Jun 2004 01:02:47 +0200 (MET DST) Message-Id: <200406242302.BAA26141<>iqe1.ethz.ch> To: arashid<>phys.unsw.edu.au Cc: chemistry<>ccl.net From: arashid<>iqe.phys.ethz.ch Subject: Fwd: CCL:Fwd: transition-state energies Date: Thu, 24 Jun 2004 23:02:47 +0000 X-Mailer: Endymion MailMan v2.0 X-Spam-Status: No, hits=1.7 required=7.5 tests=FCS_URI_NODOTS,HTML_MESSAGE, HTML_TAG_BALANCE_A,MK_BAD_HTML_04,NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Forwarded Message: > To: arashid<>phys.unsw.edu.au > From: arashid<>iqe.phys.ethz.ch > Subject: CCL:Fwd: transition-state energies > Date: Thu, 24 Jun 2004 06:14:47 +0000 > ----- > Forwarded Message: > > To: Joe Harriman >unb.ca> > > From: Per-Ola Norrby >kemi.dtu.dk> > > Subject: CCL:transition-state energies > > Date: Wed, 9 Jun 2004 08:30:16 +0200 > > ----- >

> >I have some transition-sate structures and their corresponding 
> >energies.  In addition, I
> >have the enantiomeric excess values for the products that arise from these
> >transition-state structures.  Is there a method that can be used to 
> >correlate in silico
> >transition-state energies to the ee's reported in litterature.  I 
> >have been searching
> >in vain for a method, but have been unsuccesful to date.  Any help 
> >would be greatly
> >appreciated.
> 
> 	This comes out of the Eyring or Arrhenius equations, which 
> you find in any basic physical chemistry text book.  Arrhenius: k = A 
> exp(-Ea/RT); I prefer Eyring, but they give the same results when 
> you're looking at relative rates.  As a first approximation assume 
> that the constant(s) are equal for both paths (usually including the 
> entropy, a fairly strong approximation...).  I assume that you're 
> looking at an irreversible step, then the ratio of products, r, can 
> be obtained simply as the ratio of rate constants, r = exp(DEa/RT), 
> where DEa is the difference in transition state energy (all the 
> constants disappear in the division).  When you have the ratio, the 
> ee is easily obtained from ee = (r-1)/(r+1), which is the excess 
> divided by the total, the definition of ee.
> 
> 	/Per-Ola
> -- 
> Per-Ola Norrby, Assoc. Professor,  href="http://organisk.kemi.dtu.dk/PON/">ht
tp://organisk.kemi.dtu.dk/PON/">http://organisk.kemi.dtu.dk/PON/
> Technical University of Denmark, Department of Chemistry
> Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark
> Email: pon<>kemi.dtu.dk  tel +45-45252123,  fax +45-45933968
> 
> 
> HOME Page: http://www.ccl.net">http://www.ccl.net">http://www
.ccl.net | Jobs Page:  href="http://www.ccl.net/jobs">http://www.ccl.net/j
obs">http://www.ccl.net/jobs
> 
> 
> 
> 
> 
> 
> 
>

> > > > -= 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 mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow<>nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Thu Jun 24 18:01:39 2004 Received: from iqe1.ethz.ch (iqe1-hptf.ethz.ch [129.132.22.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5ON1b5d002551 for ; Thu, 24 Jun 2004 18:01:38 -0500 Received: from 129.94.6.28 (iqe1 [129.132.23.4]) by iqe1.ethz.ch (8.9.3/8.9.3) with SMTP id BAA26869; Fri, 25 Jun 2004 01:06:17 +0200 (MET DST) Message-Id: <200406242306.BAA26869.-at-.iqe1.ethz.ch> To: arashid.-at-.phys.unsw.edu.au Cc: , From: arashid.-at-.iqe.phys.ethz.ch Subject: Fwd: CCL:Why program in Java? Date: Thu, 24 Jun 2004 23:06:17 +0000 X-Mailer: Endymion MailMan v2.0 X-Spam-Status: No, hits=1.3 required=7.5 tests=HTML_MESSAGE,MK_BAD_HTML_04, NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Forwarded Message: > To: "Mark Thompson" > From: Egon Willighagen > Subject: CCL:Why program in Java? > Date: Sat, 5 Jun 2004 16:27:13 +0200 > -----

On Friday 04 June 2004 18:00, Mark Thompson wrote:
> One major drawback to scientific programing in Java, at the present time,
> is good 3D graphics. 

I agree with the situation that OpenGL support for Java is not where it should 
be... Java3D had very many bugs, and I guess JOGL is its successor announced 
quite some time ago already, and have not heard much about it yet...

But, the good news is, that for top quality molecular graphics, you don't 
necessarily need hardware accelerated graphics... Unless you need a *very* 
general 3D library, but just focus on molecular stuff, I would suggest to 
have a look at the Jmol v10 prereleases of which demo's can be found on this 
website:

http://jmol.sourceforge.net/preview/

Note that thousands of atoms as in the Nanotech example are not really a 
problem. In the field of biomolecular sciences, there are nice examples of 3D 
rendering in cartoon, ribbon format and some others.

Not likely the best performance ever, but very close.

Egon

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From chemistry-request@ccl.net Thu Jun 24 02:09:52 2004 Received: from mailfilter.diszk.unideb.hu ([193.6.138.70]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5O79mkp006486 for >ccl.net>; Thu, 24 Jun 2004 02:09:48 -0500 Received: from mailfilter.diszk.unideb.hu (localhost [127.0.0.1]) by mailfilter.diszk.unideb.hu (Postfix) with SMTP id E5DD3A1C0C for >ccl.net>; Thu, 24 Jun 2004 09:13:41 +0200 (CEST) Received: from Cthulhu (anti309.chem.klte.hu [193.6.133.108]) by delfin.unideb.hu (Postfix) with SMTP id 09E0BC86D for >ccl.net>; Thu, 24 Jun 2004 09:13:31 +0200 (DFT) Message-ID: <003401c459ba$c10cfee0$6c8506c1@Cthulhu> From: "Tamas E. Gunda" >puma.unideb.hu> To: >ccl.net> Subject: Re: CCL: hyperchem in tandem with autodock Date: Thu, 24 Jun 2004 09:13:31 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1409 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Spam-Status: No, hits=4.2 required=7.5 tests=NO_EXPERIENCE,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Will, Try to use Mol2mol for converting hin files to pdbq files http://web.interware.hu/frenzy/mol2mol Tamas Gunda University of Debrecen, Hungary tgunda *AT* puma.unideb.hu ----- Original Message ----- From: will To: chemistry<>ccl.net Sent: Wednesday, June 23, 2004 10:24 PM Subject: CCL:hyperchem in tandem with autodock I'm a biochemistry grad student who has recently been given the task of learning basic molecular modeling independently. I have learned the basics of hyperchem and autodock, and, having no experience in computational chemistry, have blindly moved forward and my dockings. It was recently suggested to me that although hyperchem can be used to find docking/binding energies through geometry optimizations, I should just use it to assign charges to my substrates (which are rather small 10-15 C) and use these substrates for my autodock dockings. However, I was under the impression that charges were assigned through autodock without having to use hyperchem. Please correct me if I'm wrong. Also, .hin files are not compatible with autodock and must somehow be converted to .pdbq files if this method is indeed useful. I've found a python script hin2pdbq.py, but don't know how to use it since I have no real knowledge of how to use linux/python. I managed to get autodock up and running on cygwin with some help from the members of this board (thanks). Any input would be greatly appreciated. On a side note, I'm very interested in learning how to screen a database of possible substrate/inhibitors with autodock. I have no idea if an additional program is needed or what changes to make. Thanks a lot for the help in advance. Will University of south florida ewlowe<>helios.acomp.usf.edu From chemistry-request@ccl.net Thu Jun 24 14:40:10 2004 Received: from sccrmhc11.comcast.net (sccrmhc11.comcast.net [204.127.202.55]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5OJe95d030271 for ; Thu, 24 Jun 2004 14:40:09 -0500 Received: from planaria (c-24-18-55-169.client.comcast.net[24.18.55.169]) by comcast.net (sccrmhc11) with SMTP id <2004062419450301100nq86ve>; Thu, 24 Jun 2004 19:45:03 +0000 Reply-To: From: "Mark Thompson" To: "Steve Bowlus" , Subject: RE: Orient molecule Date: Thu, 24 Jun 2004 12:44:57 -0700 Message-ID: <000601c45a23$ba7ff640$0200a8c0@planaria> 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 9.0.6604 (9.0.2911.0) In-Reply-To: Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net ArgusLab 4.0 can do this. http://www.arguslab.com Mark *************************** Mark Thompson ArgusLab PO Box 55207 Seattle, WA 98155 FAX: 206.440.3305 mark=at=arguslab.com http://www.arguslab.com *************************** -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request=at=ccl.net]On Behalf Of Steve Bowlus Sent: Wednesday, June 23, 2004 8:42 PM To: chemistry=at=ccl.net Subject: CCL:Orient molecule I am frantically searching for a simple piece of code that will allow me to: Read a standard file (mol, pdb, Sybyl ...) select an atom to put at the Cartesian origin select an atom to put on the X axis select an atom to put in the XY plane Do a rigid rotation Do sequential rigid rotations about Cartesian axes Freeze the molecule in the new orientation Output the NEW, transformed coordinates. This is equivalent to the Sybyl "orient" command, plus rigid rotations, plus "Freeze molecule". But I have not found a free (or even cheap) package that will freeze a molecule in the new coordinates before output. Thanks in advance for any pointers, Steve -= 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=at=ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST(at)ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow(at)nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Thu Jun 24 01:52:30 2004 Received: from mxout2.netvision.net.il (mxout2.netvision.net.il [194.90.9.21]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5O6qPkp005483 for ; Thu, 24 Jun 2004 01:52:28 -0500 Received: from eli ([217.132.34.226]) by mxout2.netvision.net.il (iPlanet Messaging Server 5.2 HotFix 1.21 (built Sep 8 2003)) with ESMTP id <0HZS00M8EWN1TS(at)mxout2.netvision.net.il> for CHEMISTRY(at)ccl.net; Thu, 24 Jun 2004 09:57:09 +0300 (IDT) Date: Thu, 24 Jun 2004 08:56:58 +0200 From: Elie Cohen Subject: New Version of Molecular Conceptor In-reply-to: <5.2.0.9.2.20040623231711.02739920(at)webmail.hope.edu> To: CHEMISTRY(at)ccl.net Message-id: <000001c459b8$73612f60$9307000a@eli> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Mailer: Microsoft Outlook, Build 10.0.4510 Content-type: multipart/alternative; boundary="Boundary_(ID_Pe8432nGE8RSYRA1W3QOtw)" Importance: Normal X-Priority: 3 (Normal) X-MSMail-priority: Normal X-Spam-Status: No, hits=6.9 required=7.5 tests=HTML_70_80,HTML_MESSAGE, LINES_OF_YELLING,LINES_OF_YELLING_2,NO_RDNS2,RCVD_IN_DYNABLOCK, RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. --Boundary_(ID_Pe8432nGE8RSYRA1W3QOtw) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT Dear Colleagues, Please note that the new version of Molecular Conceptor - Medicinal Chemistry & Drug Design Courseware was released. This interactive course for teaching students and self-training of young scientists in pharmaceutical industry includes more than 20 chapters and 2000 pages: A - MOLECULAR MODELING Molecular Geometry Molecular Properties Stereochemistry Molecular Energies Conformational Analysis Selected Examples in 3D Analysis B - PROTEIN STRUCTURE AND MODELING Protein Structure C - RATIONAL DRUG DESIGN Principles of Rational Drug Design D - STRUCTURE-BASED DRUG DESIGN Structure-Based Drug Design: Analysis Structure-Based Drug Design: Design Structure-Based Drug Design: Examples Molecular Docking E - PHARMACOPHORE-BASED DRUG DESIGN Pharmacophore-Based Drug Design: Analysis Pharmacophore-Based Drug Design: Design Pharmacophore-Based Drug Design: Examples F - QSAR Introduction to QSAR H - PEPTIDOMIMETICS Peptidomimetics Peptidomimetics Examples I - ADME PROPERTIES AND PREDICTIONS ADME Properties K - GENERAL TOPICS Molecular Graphics General Introduction on drugs Drug Discovery Drug Development Designed by N. Claude Cohen and his team (Synergix Ltd.) More information: http://www.molecular-conceptor.com Download Demo: http://www.molecular-conceptor.com/demo_form.html Elie Cohen elie(at)drugdesign.com Synergix ltd. --Boundary_(ID_Pe8432nGE8RSYRA1W3QOtw) Content-type: text/html; charset=us-ascii Content-transfer-encoding: 7BIT

Dear Colleagues,

Please note that the new version of Molecular Conceptor – Medicinal Chemistry & Drug Design Courseware was released.

This interactive course for teaching students and self-training of young scientists in pharmaceutical industry includes more than 20 chapters and 2000 pages:

A – MOLECULAR MODELING

Molecular Geometry

Molecular Properties

Stereochemistry

Molecular Energies

Conformational Analysis

Selected Examples in 3D Analysis

B - PROTEIN STRUCTURE AND MODELING

Protein Structure

C - RATIONAL DRUG DESIGN

Principles of Rational Drug Design

D - STRUCTURE-BASED DRUG DESIGN

Structure-Based Drug Design: Analysis

Structure-Based Drug Design: Design

Structure-Based Drug Design: Examples

Molecular Docking

E - PHARMACOPHORE-BASED DRUG DESIGN

Pharmacophore-Based Drug Design: Analysis

Pharmacophore-Based Drug Design: Design

Pharmacophore-Based Drug Design: Examples

F - QSAR

Introduction to QSAR

H - PEPTIDOMIMETICS

Peptidomimetics

Peptidomimetics Examples

I - ADME PROPERTIES AND PREDICTIONS

ADME Properties

K - GENERAL TOPICS

Molecular Graphics

General Introduction on drugs

Drug Discovery

Drug Development

More information: http://www.molecular-conceptor.com

Download Demo: http://www.molecular-conceptor.com/demo_form.html

Elie Cohen

elie(at)drugdesign.com

Synergix ltd.

--Boundary_(ID_Pe8432nGE8RSYRA1W3QOtw)-- From chemistry-request@ccl.net Thu Jun 24 01:06:40 2004 Received: from iqe1.ethz.ch (iqe1-hptf.ethz.ch [129.132.22.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5O66ckp004859 for ; Thu, 24 Jun 2004 01:06:39 -0500 Received: from 129.94.6.28 (iqe1 [129.132.22.196]) by iqe1.ethz.ch (8.9.3/8.9.3) with SMTP id IAA21824; Thu, 24 Jun 2004 08:11:27 +0200 (MET DST) Message-Id: <200406240611.IAA21824(at)iqe1.ethz.ch> To: arashid(at)phys.unsw.edu.au Cc: chemistry(at)ccl.net From: arashid(at)iqe.phys.ethz.ch Subject: Fwd: CCL:Why program in Java? Date: Thu, 24 Jun 2004 06:11:27 +0000 X-Mailer: Endymion MailMan v2.0 X-Spam-Status: No, hits=0.8 required=7.5 tests=HTML_MESSAGE,MK_BAD_HTML_04, NO_REAL_NAME,SMILEY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Forwarded Message: > To: jle(at)theworld.com > From: Boris Gorelik > Subject: CCL:Why program in Java? > Date: Thu, 17 Jun 2004 17:31:52 +0300 > -----

There is an interesting benchmark that compares Java productivity (Sun Java 
1.4.2_01) vs C++ (gcc3.3.1).
The author claims that in most tasks Java performance was superior.
The full story is here:

http://www.sys-
con.com/story/?storyid=45250


On Friday 04 June 2004 14:46, jle(at)TheWorld.com wrote:
> Folks, I would appreciate pointers to any article/book discussing
> the pros and cons of programming in Java.  Either with regards to
> other interpreted languages such as Python/Perl, or with regards
> to compiled languages such as C/C++.  Truly comparative articles
> would be best, although evangelical texts would suffice (i.e. I've
> read some of the XP literature :-).
>
> Thanks in advance!
>
> Joe
>
>
> To send e-mail to subscribers of CCL put the string CCL: on your Subject:
>
> Send your subscription/unsubscription requests to:
> CHEMISTRY-REQUEST(at)ccl.net HOME Page: http://www.ccl.net  | Jobs Page:
> http://www.ccl.net/jobs
>

-- 
Boris Gorelik
-= ( 2*b || !(2*b)) That's the question =-
Thu, 17/Jun/2004, 28 Sivan 5764
-------------------------------------------------
! Molecular Modelling Group !
! Pharmacy School, Hadassa Faculty of medicine !
! The Hebrew University of Jerusalem !
! http: // www .md.huji.ac.il/models/group.html !
!
!------------------------------------------------


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From chemistry-request@ccl.net Thu Jun 24 10:00:58 2004 Received: from casbah.it.northwestern.edu (casbah.it.northwestern.edu [129.105.16.52]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5OF0wV0022157 for ; Thu, 24 Jun 2004 10:00:58 -0500 Received: (from mailnull@localhost) by casbah.it.northwestern.edu (8.12.10/8.12.10) id i5OF5pW9004179 for ; Thu, 24 Jun 2004 10:05:51 -0500 (CDT) Received: from chief (chief.chem-eng.northwestern.edu [129.105.205.171]) by casbah.it.northwestern.edu via smap (V2.0) id xma003821; Thu, 24 Jun 04 10:05:40 -0500 From: "Jim Pfaendtner" To: Subject: Gaussian 03 PES results Date: Thu, 24 Jun 2004 10:05:43 -0500 Message-ID: <000501c459fc$b8caddf0$abcd6981@chief> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0006_01C459D2.CFF4D5F0" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 This is a multi-part message in MIME format. ------=_NextPart_000_0006_01C459D2.CFF4D5F0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit Hi all, I have performed a potential energy scan over two coordinates with geometry optimization at each point. From what I could gather from the G03 manual and trying to get the simulations running, the way to do this is like this: # ... opt(addredundant,..) .. X Y S <#steps W Z S <#steps Where X,Y,W,Z are my coordinates of interest. The calculation ran and completed geometry optimization at each step. But I don't get a nice table like the Gaussian manual says I should by using the scan keyword. I don't want to just use the scan keyword, because I want geometry optimization at each step. Is there a way to get my results out of my log file? I know they are in there, but I have done post-processing w/Excel and it's not that fun and prone to errors. Thanks! ------=_NextPart_000_0006_01C459D2.CFF4D5F0 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable

Hi all,

I have performed a potential energy scan over two coordinates with geometry optimization at each point. From what I could gather from = the G03 manual and trying to get the simulations running, the way to do this is like = this:

# ….. opt(addredundant,….) ….

X Y <start> S <#steps <stepsize>

W Z <start> S <#steps <stepsize>

Where X,Y,W,Z are my = coordinates of interest.

The calculation ran and completed geometry = optimization at each step. But I = don’t get a nice table like the Gaussian manual says I should by using the scan keyword. = I don’t want to just use = the scan keyword, because I want geometry optimization at each = step.

Is there a way to get my results out of my log file? = I know they are in there, but I have done post-processing w/Excel and = it’s not that fun and prone to errors.

Thanks!

------=_NextPart_000_0006_01C459D2.CFF4D5F0-- From chemistry-request@ccl.net Thu Jun 24 00:55:01 2004 Received: from mail.yourhostingaccount.com (mail.yourhostingaccount.com [38.113.1.52]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5O5t0kp004373 for ; Thu, 24 Jun 2004 00:55:00 -0500 Message-Id: <200406240555.i5O5t0kp004373[at]server.ccl.net> Received: server.yourhostingaccount.com ([10.1.1.1] helo=server.yourhostingaccount.com) by mail.yourhostingaccount.com with esmtp (Exim 4.34) id 1BdNH7-0004Z9-Bw for chemistry[at]ccl.net; Thu, 24 Jun 2004 01:59:53 -0400 Received: from adsl-64-166-142-98.dsl.snfc21.pacbell.net ([64.166.142.98] helo=Hummer) by smtp.yourhostingaccount.com with asmtp (Exim 4.34) id 1BdNH2-00071W-Qe ; Thu, 24 Jun 2004 01:59:49 -0400 From: "Warren DeLano" To: "'Steve Bowlus'" , Cc: Subject: RE: Orient molecule Date: Wed, 23 Jun 2004 22:59:43 -0700 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Mailer: Microsoft Office Outlook, Build 11.0.5510 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 In-Reply-To: Thread-Index: AcRZnns15htCi7+yTtOSS3PSYCUhVgAERwxw X-UserInfo: dfab58b57aa3bb910bf055c23b06c5c7:c10f421fef69a2b5fe207cfa50def74f X-UserName: warren_1 Sender: "Warren DeLano" X-Spam-Status: No, hits=0.8 required=7.5 tests=MY_DSL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Steve, This is something PyMOL can do with a little help from Python... # PyMOL script: view2coord.pml # get the current camera matrix v=cmd.get_view() # translate atoms to the current origin of rotation alter_state 1, all, \ (x,y,z) = (x-v[12],y-v[13],z-v[14]) # apply the rotation (matrix multiplication) alter_state 1, all, \ (x,y,z) = (x*v[0]+y*v[3]+z*v[6], \ x*v[1]+y*v[4]+z*v[7], x*v[2]+y*v[5]+z*v[8]) # end script After loading a molecule and choosing a view (either with the mouse, or using commands like "orient", "turn", "move", "center", etc.), you then simply run the script and save the new coordinates: load original_mol.pdb orient center 10/ca @view2coord.pml save transformed_mol.pdb quit Oh, and yes, PyMOL is still free unless you choose to pay for it. Cheers, Warren -- mailto:warren[at]delsci.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -----Original Message----- > From: Computational Chemistry List > [mailto:chemistry-request[at]ccl.net] On Behalf Of Steve Bowlus > Sent: Wednesday, June 23, 2004 8:42 PM > To: chemistry[at]ccl.net > Subject: CCL:Orient molecule > > I am frantically searching for a simple piece of code that > will allow me to: > > Read a standard file (mol, pdb, Sybyl ...) select an atom to > put at the Cartesian origin select an atom to put on the X > axis select an atom to put in the XY plane Do a rigid > rotation Do sequential rigid rotations about Cartesian axes > Freeze the molecule in the new orientation Output the NEW, > transformed coordinates. > > This is equivalent to the Sybyl "orient" command, plus rigid > rotations, plus "Freeze molecule". But I have not found a > free (or even cheap) package that will freeze a molecule in > the new coordinates before output. > > Thanks in advance for any pointers, > Steve > > > -= 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[at]ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST[at]ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the > maintainer: > Jan Labanowski, jlabanow[at]nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Thu Jun 24 03:52:30 2004 Received: from mx5.informatik.uni-tuebingen.de (mx5.Informatik.Uni-Tuebingen.De [134.2.12.32]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5O8qSbC010083 for ; Thu, 24 Jun 2004 03:52:29 -0500 Received: from localhost (loopback [127.0.0.1]) by mx5.informatik.uni-tuebingen.de (Postfix) with ESMTP id 4989B12A; Thu, 24 Jun 2004 10:57:21 +0200 (MST) Received: from mx3.informatik.uni-tuebingen.de ([134.2.12.26]) by localhost (mx5 [134.2.12.32]) (amavisd-new, port 10024) with ESMTP id 24008-01; Thu, 24 Jun 2004 10:57:19 +0200 (DFT) Received: from informatik.uni-tuebingen.de (rapc90 [134.2.10.190]) by mx3.informatik.uni-tuebingen.de (Postfix) with ESMTP id 904F913B; Thu, 24 Jun 2004 10:57:18 +0200 (DFT) Message-ID: <40DA9822.50907~at~informatik.uni-tuebingen.de> Date: Thu, 24 Jun 2004 11:00:18 +0200 From: "Joerg K. Wegner" Organization: Department of Computer Architecture User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.6) Gecko/20040113 X-Accept-Language: en-us, en MIME-Version: 1.0 To: pharmacophore~at~accelrys.com Cc: chemistry~at~ccl.net Subject: Re: CCL:Pharmacophore Datamining Competition References: In-Reply-To: Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-new (McAfee AntiVirus) at informatik.uni-tuebingen.de X-Spam-Status: No, hits=6.9 required=7.5 tests=COMBINED_FROM,IMPRONONCABLE_1, MY_BAD_DOT,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL-users, Dear CCL users is anyone able to provide the whole community with an open available data set, which can be also used by the machine learning and data mining community as benchmark. E.g., like the NIPS feature selection challenge (only synthetic, no molecular structures). http://www.nipsfsc.ecs.soton.ac.uk/ In my opinion we need open QSAR and Pharmacophore benchmark data sets and not only small or synthetic benchmark data sets available by the machine learning community without any structural informations. And we need also a good standard-data set and framework to test against! Otherwise, we will compare 'apples-and-oranges'. And because there is a huge possibility to 'transform/convert' actual data sets, i mean really standard-data-sets, where the most users can agree with, in using it without any further needs to modify it. Otherwise this will become a new benchmark data set. With friendly regards, Joerg Kurt Wegner -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:wegnerj~at~informatik.uni-tuebingen.de WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) From chemistry-request@ccl.net Thu Jun 24 09:35:11 2004 Received: from hotmail.com (bay22-dav15.bay22.hotmail.com [64.4.16.195]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5OEZ0V0021414 for ; Thu, 24 Jun 2004 09:35:00 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 24 Jun 2004 07:39:54 -0700 Received: from 210.83.210.9 by bay22-dav15.bay22.hotmail.com with DAV; Thu, 24 Jun 2004 14:39:54 +0000 X-Originating-IP: [210.83.210.9] X-Originating-Email: [liuxin_dut~at~hotmail.com] X-Sender: liuxin_dut~at~hotmail.com From: "li" To: Subject: CCL: how to evaluate the contribution of atomic orbital to the molecular orbital Date: Thu, 24 Jun 2004 22:39:48 +0800 MIME-Version: 1.0 Content-Type: text/plain; charset="gb2312" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1409 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 Message-ID: X-OriginalArrivalTime: 24 Jun 2004 14:39:54.0709 (UTC) FILETIME=[1D558850:01C459F9] X-Spam-Status: No, hits=2.0 required=7.5 tests=MIME_BASE64_TEXT autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id i5OEZBV0021426 Hi! I have just calculated a large cluster of zinc sulfide with G98W. After intensive calculation, I got thousands of MOs(molecular orbital). At this time, I want to study the contribution of each AOs(atomic orbital) to every MO. For a small molecule of tens of MOs, it is an easy job. But for thousands of MOs, it is time killing and boring. So, I wonder if there are some software tools that can do the analysis. Please let me know if this kind of software is available. Sincerely yours Xin, Liu From chemistry-request@ccl.net Thu Jun 24 12:24:11 2004 Received: from out014.verizon.net (out014pub.verizon.net [206.46.170.46]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5OHO9Hm026671 for ; Thu, 24 Jun 2004 12:24:10 -0500 Received: from [165.106.240.196] by out014.verizon.net (InterMail vM.5.01.06.06 201-253-122-130-106-20030910) with ESMTP id <20040624172900.VLRG24784.out014.verizon.net@[165.106.240.196]>; Thu, 24 Jun 2004 12:29:00 -0500 Mime-Version: 1.0 (Apple Message framework v606) Content-Type: text/plain; charset=US-ASCII; format=flowed Message-Id: <093568B6-C604-11D8-BCFC-000D93508108~at~brynmawr.edu> Content-Transfer-Encoding: 7bit From: Michelle Francl-Donnay Subject: CCL: ACS COMP Division: Official announcements posted on CCL Date: Thu, 24 Jun 2004 13:29:24 -0400 To: CHEMISTRY~at~ccl.net X-Mailer: Apple Mail (2.606) X-Authentication-Info: Submitted using SMTP AUTH at out014.verizon.net from [165.106.240.196] at Thu, 24 Jun 2004 12:28:59 -0500 X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL, The American Chemical Society Division of Computers in Chemistry (COMP) is pleased to support the CCL. We will be posting occasional announcements about our activities on this list, hoping to reach our members, as well as other interested colleagues. All our announcements will be prefaced with "ACS COMP Division:" to facilitate filtering. More information about the COMP division and it's activities can be found at our website at http://membership.acs.org/C/COMP/. New members are always welcome! Michelle M. Francl COMP Chair, 2004 Professor of Chemistry Bryn Mawr College 101 N Merion Ave Bryn Mawr, PA 19010 "Qui cantat bis orat" From chemistry-request@ccl.net Thu Jun 24 07:06:09 2004 Received: from e500-gw1.utmb.edu (mx1.utmb.edu [129.109.195.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5OC5xbC016836 for ; Thu, 24 Jun 2004 07:06:03 -0500 Received: from mx1.utmb.edu(129.109.195.3) by e500-gw1.utmb.edu via csmap id 3aa2e10a_c5d8_11d8_8ac9_00304823f3bd_31685; Thu, 24 Jun 2004 07:15:53 -0500 (CDT) Received: from e500-gw1.utmb.edu (histidine.utmb.edu [129.109.65.24]) by utmb.edu (PMDF V6.1 #38124) with ESMTP id <0HZT00JKRB6E00|at|utmb.edu> for chemistry|at|ccl.net; Thu, 24 Jun 2004 07:11:02 -0500 (CDT) Received: from histidine.utmb.edu(129.109.65.24) by e500-gw1.utmb.edu via csmap id 3a4d4d12_c5d8_11d8_8ab9_00304823f3bd_31683; Thu, 24 Jun 2004 07:15:48 -0500 (CDT) Received: from localhost (localhost [[UNIX: localhost]]) by histidine.utmb.edu (8.12.11/8.12.11/Submit) id i5OCAr7K030706; Thu, 24 Jun 2004 07:10:53 -0500 (CDT envelope-from bdodson) Date: Thu, 24 Jun 2004 07:10:51 -0500 From: "M. L. Dodson" Subject: Re: CCL:Orient molecule In-reply-to: To: Steve Bowlus Cc: chemistry|at|ccl.net Reply-to: bdodson|at|scms.utmb.EDU Message-id: <200406240710.51998.bdodson|at|scms.utmb.edu> Organization: University of Texas Medical Branch MIME-version: 1.0 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7bit Content-disposition: inline User-Agent: KMail/1.6.2 References: On Wednesday 23 June 2004 10:42 pm, Steve Bowlus wrote: > I am frantically searching for a simple piece of code that will allow me > to: > > Read a standard file (mol, pdb, Sybyl ...) > select an atom to put at the Cartesian origin > select an atom to put on the X axis > select an atom to put in the XY plane > Do a rigid rotation > Do sequential rigid rotations about Cartesian axes > Freeze the molecule in the new orientation > Output the NEW, transformed coordinates. > > This is equivalent to the Sybyl "orient" command, plus rigid rotations, > plus "Freeze molecule". But I have not found a free (or even cheap) > package that will freeze a molecule in the new coordinates before output. > > Thanks in advance for any pointers, > Steve > > I do not know of a mouse and windows package that will do what you want, but it is easy with a 6-8 line nab program: http://www.scripps.edu/case/ As I have posted here in the past, nab is a "molecular manipulation" language with a syntax similar to C, but with atoms, molecules, etc as primitive data types. I use it extensively to create the starting structures of quite complex molecules for computational chemistry. E.g., creating a B-DNA molecule of arbitrary sequence is a 4-5 line program. Licensed under the GPL, very well documented, runs on any 32-bit Unix (e.g., Linux and BSD), and costs no money. But you will need to do some programming. Good luck. -- M. L. Dodson bdodson|at|scms.utmb.edu 409-772-2178 FAX: 409-772-1790 From chemistry-request@ccl.net Thu Jun 24 19:35:39 2004 Received: from smtp1.Stanford.EDU (smtp1.Stanford.EDU [171.67.16.123]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5P0Zc5d007666 for ; Thu, 24 Jun 2004 19:35:38 -0500 Received: from cardinal3.Stanford.EDU (cardinal3.Stanford.EDU [171.64.15.251]) by smtp1.Stanford.EDU (8.12.11/8.12.11) with ESMTP id i5P0eX9f001518; Thu, 24 Jun 2004 17:40:33 -0700 Date: Thu, 24 Jun 2004 17:40:33 -0700 (PDT) From: "S.I.Gorelsky" To: li cc: chemistry|at|ccl.net Subject: Re: CCL:how to evaluate the contribution of atomic orbital to the molecular orbital In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Here is the software to do it: http://www.sg-chem.net/aomix/ You can easily analyze molecular systems with up to 7000 molecular orbitals. With regards, S. Gorelsky On Thu, 24 Jun 2004, li wrote: > Hi! > > I have just calculated a large cluster of zinc sulfide with G98W. After intensive calculation, I got thousands of MOs(molecular orbital). At this time, I want to study the contribution of each AOs(atomic orbital) to every MO. For a small molecule of tens of MOs, it is an easy job. But for thousands of MOs, it is time killing and boring. > > So, I wonder if there are some software tools that can do the analysis. Please let me know if this kind of software is available. > > Sincerely yours > > Xin, Liu > > > > > -= 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|at|ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST|at|ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow|at|nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > ---------------------------------------------------------------- Dr S.I. Gorelsky, Department of Chemistry, Stanford University Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA Phone: (650) 723-0041. Fax: (650) 723-0553. ---------------------------------------------------------------- From chemistry-request@ccl.net Thu Jun 24 20:26:53 2004 Received: from einstein.physics.drexel.edu (einstein.physics.drexel.edu [129.25.7.60]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5P1Qr5d009698 for ; Thu, 24 Jun 2004 20:26:53 -0500 Received: from si (silicon.physics.drexel.edu [129.25.8.33]) by einstein.physics.drexel.edu (Postfix) with ESMTP id 8B6C6129162 for ; Thu, 24 Jun 2004 21:23:29 -0400 (EDT) Date: Thu, 24 Jun 2004 21:31:46 -0400 (EDT) From: Avijit Ghosh To: chemistry|at|ccl.net Subject: Re: CCL:Fwd: Why program in Java? In-Reply-To: <200406240611.IAA21824|at|iqe1.ethz.ch> Message-ID: References: <200406240611.IAA21824|at|iqe1.ethz.ch> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.3 required=7.5 tests=HTML_MESSAGE,MK_BAD_HTML_04 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On Thu, 24 Jun 2004 arashid|at|iqe.phys.ethz.ch wrote: > > http://www.sys- > con.com/story/?storyid=45250 > W/ regards to java/c++ benchmarks the following discussion may be relevant : http://developers.slashdot.org/article.pl?sid=04/06/15/217239&mode=nested&tid=108&tid=126&tid=156 Here are another set of benchmarks using both icc/gcc and slightly rewritten version of the same c++ benchmark set (addressing some of the original issues w/ the c++ benchmark) that was done : http://cpp.student.utwente.nl/benchmark/ -best, -avi