From owner-chemistry@ccl.net Sun Nov 27 01:58:01 2005 From: "Ricky Shen hxhgxy2]-[163.com" To: CCL Subject: CCL:G: NBO error Message-Id: <-30076-051126215623-4558-LTWGvo9v0EpuGEdDzMOg9g(_)server.ccl.net> X-Original-From: "Ricky Shen" Sent to CCL by: "Ricky Shen" [hxhgxy2_+_163.com] Hi I'm a new subscriber of CCL. Im so sorry if the problem are repeated to previous. I searched the CCL but cant find the answer. A NBO calculation gives the error message: "NBO cannot handle linearly dependant basis sets" and does not give the result of NBO calcultions Gaussian version: G98 a11 Input file: p b3lyp 6-311++g** nmr iop(10/46=1) pop=nboread No title specified 0 1 16 0.000000 0.000000 -3.515383 7 0.000000 1.258723 -2.490845 ......... nbo nlmo bndidx ncs end How to resolve this problem? Thank You very much Richy Shen E-mail:hxhgxy2-.-163.com From owner-chemistry@ccl.net Sun Nov 27 04:02:00 2005 From: "Li Qiang chem_liqiang\a/sohu.com" To: CCL Subject: CCL: How to evaluate the difficulty of synthesize? Message-Id: <-30077-051127035843-589-NYAd8w2awG3ZSdlhihae2g,,server.ccl.net> X-Original-From: "Li Qiang" Sent to CCL by: "Li Qiang" [chem_liqiang#sohu.com] Dear all, I are finding a computational method to evaluate(or predict) the difficulty of synthesize. I have known that SYBYL(Tripos) has a very general method to evaluate it according to the complexity of molecular structure. But it is less physical meaning in real organic reaction. By the way, I hope to know the stability of compound from its structure, how to evaluate this property? Thank you for advance! Best regards, Li Qiang From owner-chemistry@ccl.net Sun Nov 27 05:05:00 2005 From: "Eugen Leitl eugen::leitl.org" To: CCL Subject: CCL: [geoff() geoffhutchison.net: [OpenBabel-Announce] ANNOUNCE: Open Babel 2.0 Released] Message-Id: <-30078-051127050120-29929-haKAV/2B9LYv4gwhJ92Rbw() server.ccl.net> X-Original-From: Eugen Leitl Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Sun, 27 Nov 2005 11:01:09 +0100 Mime-Version: 1.0 Sent to CCL by: Eugen Leitl [eugen++leitl.org] ----- Forwarded message from Geoffrey Hutchison ----- > From: Geoffrey Hutchison Date: Sat, 26 Nov 2005 20:12:53 -0500 To: OpenBabel discussion list Subject: [OpenBabel-Announce] ANNOUNCE: Open Babel 2.0 Released X-Mailer: Apple Mail (2.746.2) I'm extremely proud to announce the release of Open Babel 2.0.0, the latest stable version of the free chemistry file translation program and chemistry software library. This release marks the fourth "birthday" of the Open Babel project and a milestone for a stable, flexible interface for developers and users alike. OpenBabel is a project designed to pick up where Babel left off, as a cross-platform program and library designed to interconvert between many file formats used in molecular modeling, computational chemistry and related areas. Highlights of the 2.0 release include a new conversion framework making it easier to develop new translators, dramatically improved support for merging, splitting, and batch conversion, a framework for molecular fingerprints, similarity searching, a fast molecular database format, support for Perl and Python scripting "wrappers," automatic support for reading .gz (gzip) compressed files, support for the new IUPAC/NIST InChI identifiers and more. What's new? See the release notes at: http://openbabel.sourceforge.net/RELEASE.shtml To download, see: http://prdownloads.sourceforge.net/openbabel/openbabel-2.0.0.tar.gz For more information, see the project website at: http://openbabel.sourceforge.net/ Many thanks to all the contributors to Open Babel. Particular thanks go to (in no particular order) Jean Br?fort, Nick England, David Hoekman, Elmar Krieger, Christian Laggner, Chris Morley, and Chris Swain for helping to get this release out the door. Cheers, -Geoff ------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_idv37&alloc_id865&op=click _______________________________________________ OpenBabel-Announce mailing list OpenBabel-Announce**lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-announce ----- End forwarded message ----- -- Eugen* Leitl leitl ______________________________________________________________ ICBM: 48.07100, 11.36820 http://www.leitl.org 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE From owner-chemistry@ccl.net Sun Nov 27 07:34:00 2005 From: "Arvydas Tamulis tamulis-*-mserv.itpa.lt" To: CCL Subject: CCL: Quantum computing OR gate Message-Id: <-30079-051127072521-26843-22G/Rq5f0xbq5PJ/13cigw,,server.ccl.net> X-Original-From: Arvydas Tamulis Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Sun, 27 Nov 2005 13:37:35 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Arvydas Tamulis [tamulis**mserv.itpa.lt] Dear Colleagues, Would you please to give me description and truth table of quantum computing OR gate (function). Best regards, Arvydas Tamulis From owner-chemistry@ccl.net Sun Nov 27 10:29:00 2005 From: "Jim Kress ccl_nospam[a]kressworks.com" To: CCL Subject: CCL:G: NBO error Message-Id: <-30080-051127102717-27666-VIGG9D0YaIO6PlWNpvW6TA|*|server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Sun, 27 Nov 2005 10:27:01 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam*kressworks.com] Taken from: http://www.chem.wisc.edu/~nbo5/faq.htm My G98 job didn't produce any NBO output but instead gave the message, "NBO is unable to handle linearly dependant basis sets." What does this mean, and what can I do? G98 checks for numerical instabilities due to near-linear dependence of basis functions (chiefly due to inclusion of diffuse functions) and reduces the dimension of the basis set if necessary. When this occurs, G98 prints the above error message and bypasses entry to NBO. One possible solution is to run the same job with G94 or earlier G9X versions. (This usually works, because NBO has its own checks for numerical instabilities.) Another solution is to include IOP(3/32=2) to bypass the G98 linear dependence test. However, if linear dependence is truly severe, the only alternative may be to remove "+" or other basis functions until the G98 linear dependency fix is not triggered. Also, http://www.chem.wisc.edu/~nbo5/NewFeatures.htm Basis Linear Dependency Detection/Protection. NBO 5.0 reduces the dimensionality of the NAO basis as necessary to remove linearly dependent components of the input AO basis set. The dimensional reduction is often consistent with measures taken by the host program (e.g., Gaussian or GAMESS), but NBO 5.0 detects and removes linear dependency to enhance numerical stability even if the host ESS does not. Jim > -----Original Message----- > From: Ricky Shen hxhgxy2]-[163.com [mailto:owner-chemistry[]ccl.net] > Sent: Sunday, November 27, 2005 2:11 AM > To: Kress, Jim > Subject: CCL:G: NBO error > > Sent to CCL by: "Ricky Shen" [hxhgxy2_+_163.com] Hi > > I'm a new subscriber of CCL. Im so sorry if the problem are > repeated to previous. I searched the CCL but cant find the answer. > > A NBO calculation gives the error message: "NBO cannot > handle linearly dependant basis sets" and does not give the > result of NBO calcultions > > Gaussian version: G98 a11 > > Input file: > > p b3lyp 6-311++g** nmr iop(10/46=1) pop=nboread > > No title specified > > 0 1 > 16 0.000000 0.000000 -3.515383 > 7 0.000000 1.258723 -2.490845 > ......... > > nbo nlmo bndidx ncs end > > How to resolve this problem? Thank You very much > > Richy Shen > > E-mail:hxhgxy2:-:163.com > > > > -= This is automatically added to each message by the mailing > script =- To recover the email address of the author of the > message, please change the strange characters on the top line > to the [] sign. You can also look up the X-Original-From: line > in the mail header.> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > > From owner-chemistry@ccl.net Sun Nov 27 11:03:01 2005 From: "Arvydas Tamulis tamulis##mserv.itpa.lt" To: CCL Subject: CCL: Quantum computing OR gate Message-Id: <-30081-051127072523-26861-85r0OIhW4KZ7sC5L52weEQ],[server.ccl.net> X-Original-From: Arvydas Tamulis Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Sun, 27 Nov 2005 13:38:18 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Arvydas Tamulis [tamulis . mserv.itpa.lt] Dear Colleagues, Would you please to give me description and truth table of quantum computing OR gate (function). Best regards, Arvydas Tamulis From owner-chemistry@ccl.net Sun Nov 27 15:32:00 2005 From: "Geoffrey Hutchison grh25!A!cornell.edu" To: CCL Subject: CCL: ANNOUNCE: Open Babel 2.0 Released Message-Id: <-30082-051127152649-2065-6Ojb2Z9w3eCI9eHIdPauIQ,,server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Date: Sun, 27 Nov 2005 15:26:29 -0500 Mime-Version: 1.0 (Apple Message framework v746.2) Sent to CCL by: Geoffrey Hutchison [grh25/a\cornell.edu] I had a slightly different e-mail written for the CCL readers. I won't fill your e-mail, so I'll include a small addendum to the announcement that Dr. Leitl forwarded. Open Babel is largely volunteer project. It is free, open source chemistry software provided for the community at large. Besides converting between a range of computational chemistry (and other) file formats, the code library makes it easy to develop C++ chemistry programs. A range of examples is provided, including "obgrep" for SMARTS searching any file readable by Open Babel, "obfit" which can batch-align molecules by SMARTS patterns, and the new 2.0 release adds support for Python and Perl scripting. Again, check Open Babel website for release notes and more information: http://openbabel.sourceforge.net/ Open Babel is also a proud member of the Blue Obelisk movement, a collection of free and open source chemistry projects working together to produce better science and better software. http://www.blueobelisk.org/ Cheers, -Geoff -- -Dr. Geoffrey Hutchison Cornell University, Department of Chemistry and Chemical Biology Abruņa Group http://abruna.chem.cornell.edu/ On Nov 27, 2005, at 5:16 AM, Eugen Leitl eugen::leitl.org wrote: > Sent to CCL by: Eugen Leitl [eugen++leitl.org] > ----- Forwarded message from Geoffrey Hutchison geoffhutchison.net> ----- > Date: Sat, 26 Nov 2005 20:12:53 -0500 > To: OpenBabel discussion list lists.sourceforge.net> > Subject: [OpenBabel-Announce] ANNOUNCE: Open Babel 2.0 Released > > I'm extremely proud to announce the release of Open Babel 2.0.0, the > latest stable version of the free chemistry file translation program > and chemistry software library. This release marks the fourth > "birthday" of the Open Babel project and a milestone for a stable, > flexible interface for developers and users alike. > > OpenBabel is a project designed to pick up where Babel left off, as a > cross-platform program and library designed to interconvert between > many file formats used in molecular modeling, computational chemistry > and related areas. > > Highlights of the 2.0 release include a new conversion framework > making it easier to develop new translators, dramatically improved > support for merging, splitting, and batch conversion, a framework for > molecular fingerprints, similarity searching, a fast molecular > database format, support for Perl and Python scripting "wrappers," > automatic support for reading .gz (gzip) compressed files, support > for the new IUPAC/NIST InChI identifiers and more. > > What's new? See the release notes at: > http://openbabel.sourceforge.net/RELEASE.shtml > > To download, see: > http://prdownloads.sourceforge.net/openbabel/openbabel-2.0.0.tar.gz > > For more information, see the project website at: > http://openbabel.sourceforge.net/ > > Many thanks to all the contributors to Open Babel. Particular thanks > go to (in no particular order) Jean Br?fort, Nick England, David > Hoekman, Elmar Krieger, Christian Laggner, Chris Morley, and Chris > Swain for helping to get this release out the door. > > Cheers, > -Geoff > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through > log files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD > SPLUNK! > http://ads.osdn.com/?ad_idv37&alloc_id865&op=click > _______________________________________________ > OpenBabel-Announce mailing list > OpenBabel-Announce-.-lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-announce > > ----- End forwarded message ----- > -- > Eugen* Leitl leitl > ______________________________________________________________ > ICBM: 48.07100, 11.36820 http://www.leitl.org > 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > From owner-chemistry@ccl.net Sun Nov 27 23:27:00 2005 From: "kalpana krishnaswami kkalpana|-|vsnl.net" To: CCL Subject: CCL: Structures or connectivity tables toSMILES Message-Id: <-30083-051127225542-30115-2Zfa5gyNog1JtCXC6xptig,server.ccl.net> X-Original-From: "kalpana krishnaswami" Sent to CCL by: "kalpana krishnaswami" [kkalpana ~~ vsnl.net] I need a method to generate SMILES strings for a large number of structures. Does anyone know a way of doing this. Either a stand alone program that would read a text file(eg, SD file) or a class or component that we could access programatically that would work. I would appreciate any help. Regards Kalpana