From owner-chemistry@ccl.net Wed Jan 31 01:21:01 2007 From: "Jim Harrison jim456harrison||yahoo.com" To: CCL Subject: CCL: Gaussian - Basis sets - negative frequency Message-Id: <-33478-070131001308-14526-JlOA4M4wJZnnt4F7XuOKdg~!~server.ccl.net> X-Original-From: Jim Harrison Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-909926776-1170216761=:76947" Date: Tue, 30 Jan 2007 20:12:41 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Jim Harrison [jim456harrison%x%yahoo.com] --0-909926776-1170216761=:76947 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear all My question is on negative frequency. Is it dependent on a particular basis set. If one basis set does not give a negative frequency for a specific geometry, is there a possibility that another basis set will give a negative frequency for the same geometry. Thanking you all Jim --------------------------------- Expecting? Get great news right away with email Auto-Check. Try the Yahoo! Mail Beta. --0-909926776-1170216761=:76947 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear all

My question is on negative frequency. Is it dependent on a particular basis set. If one basis set does not give a negative frequency for a specific geometry, is there a possibility that another basis set will give a negative frequency for the same geometry.

Thanking you all
Jim

Expecting? Get great news right away with email Auto-Check.
Try the Yahoo! Mail Beta. --0-909926776-1170216761=:76947-- From owner-chemistry@ccl.net Wed Jan 31 02:52:00 2007 From: "Silviu Polosan Spol68[#]yahoo.com" To: CCL Subject: CCL:G: stability Message-Id: <-33479-070131024908-11985-CQ7UEtZG1OI/CpHrwIuVfw:-:server.ccl.net> X-Original-From: "Silviu Polosan" Date: Wed, 31 Jan 2007 02:49:05 -0500 Sent to CCL by: "Silviu Polosan" [Spol68{}yahoo.com] Dear friends, I performed a Gaussian calculation for a large molecule (around 55 atoms) and after calculation, some bonds dissapears. Does this means the whole molecule is unstable (or not)? Any suggestion will be appreciate. Thank you. From owner-chemistry@ccl.net Wed Jan 31 03:27:01 2007 From: "Xunlei Ding dingxunlei*gmail.com" To: CCL Subject: CCL: Gaussian - Basis sets - negative frequency Message-Id: <-33480-070131024442-11653-B3Uk0F94odfmehEVJdXY9g_-_server.ccl.net> X-Original-From: Xunlei Ding Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 31 Jan 2007 08:27:01 +0100 MIME-Version: 1.0 Sent to CCL by: Xunlei Ding [dingxunlei : gmail.com] There is a possiblity, if one basis set is too small, or not suitable. Jim Harrison jim456harrison||yahoo.com wrote: > Dear all > > My question is on negative frequency. Is it dependent on a particular > basis set. If one basis set does not give a negative frequency for a > specific geometry, is there a possibility that another basis set will > give a negative frequency for the same geometry. > > Thanking you all > Jim > > ------------------------------------------------------------------------ > Expecting? Get great news right away with email Auto-Check. > > Try the Yahoo! Mail Beta. > From owner-chemistry@ccl.net Wed Jan 31 04:02:01 2007 From: "Luis Simon luissimonrubio+*+hotmail.com" To: CCL Subject: CCL:G: G03: SCF convergence with two metal atoms Message-Id: <-33481-070131032338-27320-zKZ2nq2dlxFPPPP6KIA1rQ .. server.ccl.net> X-Original-From: "Luis Simon" Date: Wed, 31 Jan 2007 03:23:35 -0500 Sent to CCL by: "Luis Simon" [luissimonrubio|,|hotmail.com] I have noticed that with both G03 and G98 SCF convergence with two metal atoms (for example, two separated TiH4 molecules) was unsuccessful (even using semiempirical methods), while such problems did not exists with just one molecule? Does anyone have any idea of the origin of this strange behaviour? Regards: Luis From owner-chemistry@ccl.net Wed Jan 31 04:37:00 2007 From: "=?ISO-8859-1?Q?=D6d=F6n?= Farkas farkas : chem.elte.hu" To: CCL Subject: CCL: Gaussian - Basis sets - negative frequency Message-Id: <-33482-070131033427-1670-SaYOmtiFoITEvETWnau7Gg- -server.ccl.net> X-Original-From: =?ISO-8859-1?Q?=D6d=F6n?= Farkas Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Wed, 31 Jan 2007 09:31:33 +0100 Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas{=}chem.elte.hu] Hi Jim, The short answer is yes. Since the potential energy surface depends on the used method, on flat potential regions, changes in basis set may result such behavior and give negative force constants and imaginary (not negative!) frequencies on places where an other method or basis set gives no imaginary frequency. Good example is the methyl rotation of toluene. Best wishes, Ödön On Tue, 2007-01-30 at 20:12 -0800, Jim Harrison jim456harrison|| yahoo.com wrote: > Dear all > > My question is on negative frequency. Is it dependent on a particular > basis set. If one basis set does not give a negative frequency for a > specific geometry, is there a possibility that another basis set will > give a negative frequency for the same geometry. > > Thanking you all > Jim > > > > ______________________________________________________________________ > Expecting? Get great news right away with email Auto-Check. > Try the Yahoo! Mail Beta. -- Ödön Farkas Associate professor Deparment of Organic Chemistry and Laboratory of Chemical Informatics, Institute of Chemistry, Eötvös Loránd University, Budapest Address: 1/A Pázmány Péter sétány, H-1117 Budapest, Hungary Phone: +36-1-372-2570 Cell phone: +36-30-255-3111 Fax: +36-1-372-2620 URL: http://organ.elte.hu/farkas From owner-chemistry@ccl.net Wed Jan 31 05:53:02 2007 From: "taye beyene beyene sene3095,,yahoo.com" To: CCL Subject: CCL: Problem with Freq calculation with large basis set and multi-step job Message-Id: <-33483-070131024030-11392-ToDF8qd/JJIzbJl17rGD5w%a%server.ccl.net> X-Original-From: taye beyene beyene Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1662754636-1170225620=:54597" Date: Tue, 30 Jan 2007 22:40:20 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: taye beyene beyene [sene3095-x-yahoo.com] --0-1662754636-1170225620=:54597 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit I think it is better to proceed starting from the lower basis set to the higher basis set. Start your calculation with the lower one and make it consistent, proceed with larger basis set. Most of the time frequency calculations need the exact structure, so, before all try to get the correct structure. Lower basis sets may not optimize exactly. Taye. "Tanguy Van Regemorter tanguy.vr#%#yucom.be" wrote: Sent to CCL by: "Tanguy Van Regemorter" [tanguy.vr()yucom.be] Hello everybody, I would like to perform a frequency analysis with a rather large basis set. In order to win time, I am using a multi-steps job where I am optimize first the geometry with a lower basis set then I perform a single point calculation with a large basis set. Unfortunatly, when I try to run the program, I obtain the following error message: "Illegal IType or MSType generated by parse." To run the second step, I am writing that: --link1-- %Chk=CH3 ubmk/6-311+g(3df,2p) Freq SP Guess=Read Geom=AllCheck SCF=Tight Does anybody know what I am doing wrong ? Thank you very much ! Best Regards Tanguy Van Regemorterhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- TV dinner still cooling? Check out "Tonight's Picks" on Yahoo! TV. --0-1662754636-1170225620=:54597 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
I think it is better to proceed starting from the lower basis set to the higher basis set. Start your calculation with the lower one and make it consistent, proceed with larger basis set. Most of the time frequency calculations need the exact structure, so, before all try to get the correct structure. Lower basis sets may not optimize exactly.
Taye.

"Tanguy Van Regemorter tanguy.vr#%#yucom.be" <owner-chemistry_+_ccl.net> wrote:

Sent to CCL by: "Tanguy Van Regemorter" [tanguy.vr()yucom.be]
Hello everybody,

I would like to perform a frequency analysis with a rather large basis set. In order to win time, I am using a multi-steps job where I am optimize first the geometry with a lower basis set then I perform a single point calculation with a large basis set.
Unfortunatly, when I try to run the program, I obtain the following error message:
"Illegal IType or MSType generated by parse."

To run the second step, I am writing that:

--link1--
%Chk=CH3
ubmk/6-311+g(3df,2p) Freq SP Guess=Read Geom=AllCheck SCF=Tight

Does anybody know what I am doing wrong ?

Thank you very much !

Best Regards
Tanguy Van Regemorter


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Check out "Tonight's Picks" on Yahoo! TV. --0-1662754636-1170225620=:54597-- From owner-chemistry@ccl.net Wed Jan 31 05:54:02 2007 From: "Georg Lefkidis lefkidis::physik.uni-kl.de" To: CCL Subject: CCL: AW: Gaussian - Basis sets - negative frequency Message-Id: <-33484-070131041154-28338-mMnVujfAs4yG9gkINI2NuQ:_:server.ccl.net> X-Original-From: "Georg Lefkidis" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 31 Jan 2007 09:39:43 +0100 MIME-Version: 1.0 Sent to CCL by: "Georg Lefkidis" [lefkidis\a/physik.uni-kl.de] Dear Jim, in theory this is not completely impossible, although highly unlikely. The geometry of a molecule and its stability are slightly basis set dependent. Negative frequencies means not stable molecule, so it could be that one has an extremely peculiar geometry, where the one basis set finds it OK, and the other not. However, I would consider it pure mathematical artifact. In other words, in such a case the geometry is questionable anyway, unless the small basis set is completely inadequate to describe the molecule/cluster/systerm. Best regards George Lefkidis >Dear all > >My question is on negative frequency. Is it dependent on a particular basis set. If one basis set does not give a negative frequency for a specific >geometry, is there a possibility that another basis set will give a negative frequency for the same geometry. > >Thanking you all >Jim -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.5.432 / Virus Database: 268.17.14/658 - Release Date: 29/01/07 14:49 From owner-chemistry@ccl.net Wed Jan 31 06:22:00 2007 From: "Marcel Swart marcel.swart:_:icrea.es" To: CCL Subject: CCL: Gaussian - Basis sets - negative frequency Message-Id: <-33485-070131042942-5035-d3BfejHNnC1KBJy5fhjHbg^_^server.ccl.net> X-Original-From: Marcel Swart Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=WINDOWS-1252; delsp=yes; format=flowed Date: Wed, 31 Jan 2007 10:29:19 +0100 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Marcel Swart [marcel.swart|,|icrea.es] Yes, of course, this is very well possible. The frequency calculation is only valid when the gradient is zero, and when you change the basis set, this will definitely change the gradient. More importantly is however, how much you change the basis set; for instance if you go from a TZ2P basis to a DZ basis, you'll probably end up in trouble; smaller changes are to be expected when you go > from TZ2P to TZP or QZ2P, although it is always best to perform the frequency calculation with the basis that you optimized the geometry with. On Jan 31, 2007, at 5:12 AM, Jim Harrison jim456harrison||yahoo.com wrote: > Dear all > > My question is on negative frequency. Is it dependent on a > particular basis set. If one basis set does not give a negative > frequency for a specific geometry, is there a possibility that > another basis set will give a negative frequency for the same > geometry. > > Thanking you all > Jim > –––––––––––––––––––––––––––––––––––––––––––– dr. Marcel Swart ICREA researcher at Institut de Química Computacional Universitat de Girona Campus Montilivi 17071 Girona Catalunya (Spain) fax +34-972-418356 e-mail marcel.swart(0)icrea.es marcel.swart(0)udg.es web http://www.icrea.es/pag.asp?id=Marcel.Swart http://iqc.udg.es/~marcel –––––––––––––––––––––––––––––––––––––––––––– From owner-chemistry@ccl.net Wed Jan 31 06:57:00 2007 From: "Karol Langner karol.langner,,kn.pl" To: CCL Subject: CCL:G: G03: SCF convergence with two metal atoms Message-Id: <-33486-070131043350-8145-yDgS9mZjHVKqnOFjb4M0/Q\a/server.ccl.net> X-Original-From: Karol Langner Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-2" Date: Wed, 31 Jan 2007 10:33:02 +0100 MIME-Version: 1.0 Sent to CCL by: Karol Langner [karol.langner::kn.pl] On Wednesday 31 of January 2007 09:23, Luis Simon luissimonrubio+*+hotmail.com wrote: > Sent to CCL by: "Luis Simon" [luissimonrubio|,|hotmail.com] > I have noticed that with both G03 and G98 SCF convergence with two metal > atoms (for example, two separated TiH4 molecules) was unsuccessful (even > using semiempirical methods), while such problems did not exists with just > one molecule? Does anyone have any idea of the origin of this strange > behaviour? > > > Regards: > > Luis What kind of separation between the two molecules are we talking about? Karol -- written by Karol Langner Wed Jan 31 10:32:33 CET 2007 From owner-chemistry@ccl.net Wed Jan 31 07:32:00 2007 From: "Ding Xunlei dingxunlei!=!gmail.com" To: CCL Subject: CCL: which software is more suitable for calculation on Luminescence Materials? Message-Id: <-33487-070131050208-29202-nKxIQREAREsdVyL+B1SLJw:+:server.ccl.net> X-Original-From: Ding Xunlei Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="gb2312" Date: Wed, 31 Jan 2007 09:58:31 +0800 Mime-Version: 1.0 Sent to CCL by: Ding Xunlei [dingxunlei-*-gmail.com] Dear All, I want to calculate properties of Luminescence Materials. Could you give me some suggestion on which software is more suitable? ¡¡¡¡ Thanks in advance! Yours sincerely, Ding Xunlei 2007-01-31 ______________________________________________ From owner-chemistry@ccl.net Wed Jan 31 09:52:00 2007 From: "Shobe, David David.Shobe[-]sud-chemie.com" To: CCL Subject: CCL:G: stability Message-Id: <-33488-070131094937-14752-jJeaYDk1EF2KHbBnoRYBSw::server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 31 Jan 2007 15:49:10 +0100 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe.:.sud-chemie.com] If you're using Gaussview, it's not unusual to have bonds disappear, i.e. not show up when viewing the Gaussian output file. I have always assumed that the "missing" bonds are stretched, rather than completely broken. You see, Gaussview needs some objective criteria as to whether a pair of atoms is boned or not, and I think they use a distant cutoff to make this decision, i.e., the atoms are bonded if and ony if the distance between them is less than some specified value. Thus, the "missing" bonds are stretched, and possibly weakened as a result, but they still exist. One more thing: In Gaussview you can always manually add the missing bonds, in case you need to use the structure in a presentation. Regards, --David Shobe Süd-Chemie, Inc. Attention to detial is essentail. -----Original Message----- > From: owner-chemistry+*+ccl.net [mailto:owner-chemistry+*+ccl.net] Sent: Wednesday, January 31, 2007 2:49 AM To: Shobe, David Subject: CCL:G: stability Sent to CCL by: "Silviu Polosan" [Spol68{}yahoo.com] Dear friends, I performed a Gaussian calculation for a large molecule (around 55 atoms) and after calculation, some bonds dissapears. Does this means the whole molecule is unstable (or not)? Any suggestion will be appreciate. Thank you.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Wed Jan 31 10:27:00 2007 From: "luis Simon Rubio luissimonrubio,,hotmail.com" To: CCL Subject: CCL:G: G03: SCF convergence with two metal atoms Message-Id: <-33489-070131083354-7969-R3zHl4Aet/WSrAt37V9ZcA]~[server.ccl.net> X-Original-From: "luis Simon Rubio" Content-Type: text/plain; charset=iso-8859-1; format=flowed Date: Wed, 31 Jan 2007 13:01:04 +0000 Mime-Version: 1.0 Sent to CCL by: "luis Simon Rubio" [luissimonrubio===hotmail.com] My first attempts were with two Ti atoms sharing atoms in the coordination sphere, but my final attempts were two TiH4 (the simplest system) separated arround 3-4 Angstroms, and without colose contatcs between the Hydrogens... Thanks: Luis >From: "Karol Langner karol.langner,,kn.pl" >Reply-To: "CCL Subscribers" >To: "Simón, Luis Manuel " >Subject: CCL:G: G03: SCF convergence with two metal atoms >Date: Wed, 31 Jan 2007 10:33:02 +0100 > > >Sent to CCL by: Karol Langner [karol.langner::kn.pl] >On Wednesday 31 of January 2007 09:23, Luis Simon >luissimonrubio+*+hotmail.com >wrote: > > Sent to CCL by: "Luis Simon" [luissimonrubio|,|hotmail.com] > > I have noticed that with both G03 and G98 SCF convergence with two metal > > atoms (for example, two separated TiH4 molecules) was unsuccessful (even > > using semiempirical methods), while such problems did not exists with >just > > one molecule? Does anyone have any idea of the origin of this strange > > behaviour? > > > > > > Regards: > > > > Luis > >What kind of separation between the two molecules are we talking about? > >Karol > >-- >written by Karol Langner >Wed Jan 31 10:32:33 CET 2007> > > _________________________________________________________________ Moda para esta temporada. Ponte al día de todas las tendencias. http://www.msn.es/Mujer/moda/default.asp From owner-chemistry@ccl.net Wed Jan 31 11:02:01 2007 From: "Shobe, David David.Shobe],[sud-chemie.com" To: CCL Subject: CCL:G: G03: SCF convergence with two metal atoms Message-Id: <-33490-070131093943-14028-SaYOmtiFoITEvETWnau7Gg++server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 31 Jan 2007 15:38:43 +0100 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe#,#sud-chemie.com] Luis, Putting the second Ti atom into the sytsem means introducing another set of 4s and 3d orbitals which are near in energy to those of the first Ti. Even systems with one transition metal are difficult to converge, due to the near-degeneracy of the valence s and d orbitals. With a second transition metal, you are doubling the number of near-degenerate orbitals, resulting in additional complexity. Regards, --David Shobe Süd-Chemie, Inc. Attention to detial is essentail. -----Original Message----- > From: owner-chemistry%ccl.net [mailto:owner-chemistry%ccl.net] Sent: Wednesday, January 31, 2007 3:24 AM To: Shobe, David Subject: CCL:G: G03: SCF convergence with two metal atoms Sent to CCL by: "Luis Simon" [luissimonrubio|,|hotmail.com] I have noticed that with both G03 and G98 SCF convergence with two metal atoms (for example, two separated TiH4 molecules) was unsuccessful (even using semiempirical methods), while such problems did not exists with just one molecule? Does anyone have any idea of the origin of this strange behaviour? Regards: Luishttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Wed Jan 31 11:47:00 2007 From: "ALBERT POATER TEIXIDOR albert.poater\a/udg.es" To: CCL Subject: CCL:G: [NBO problem] Message-Id: <-33491-070131114411-17666-O4RShB0BzUy61YVrC2/BZg^-^server.ccl.net> X-Original-From: "ALBERT POATER TEIXIDOR" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 31 Jan 2007 17:43:59 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: "ALBERT POATER TEIXIDOR" [albert.poater~!~udg.es] Dear NBO experts, I have a problem of ignorancy. I do not know how to interprete the meaning of the information given by a NBO analysis. I would like to know which is the contribution of each d orbital but I do not understant de meaning of the numbers. The list of numbers means: 1s, 2s, 2px, 2py, 2pz, 3s...? 85. (0.00015) RY*( 4) C 2 s( 87.28%)p 0.05( 4.51%)d 0.09( 8.22%) 0.0000 -0.0063 0.9342 -0.0179 0.1035 0.0000 0.0000 -0.0158 -0.1838 0.0000 0.0040 -0.0001 -0.2427 -0.1525 86. (0.00012) RY*( 5) C 2 s( 3.01%)p28.88( 86.82%)d 3.38( 10.17%) 0.0000 -0.0022 0.1734 -0.0032 -0.4856 0.0000 0.0001 -0.0031 0.7952 0.0000 0.0961 0.0000 -0.2494 0.1740 I have to observe the output file because when I put the keyword pop=(nbo,savenbo) the calculation fails (it has 41 atoms and it is an unrestricted calculation, I say the dimension because the same calculation for a simple molecule as H2 is possible): Sorting of NBOs: 157 139 148 200 179 207 88 191 193 120 Sorting of NBOs: 129 110 101 130 121 249 87 107 98 196 Sorting of NBOs: 198 199 147 195 190 189 194 192 NBStor is confused about NOcc. Error termination via Lnk1e in /estufa/soft/g03pedro/g03/l607.exe at Wed Jan 24 02:01:33 2007. Job cpu time: 0 days 0 hours 48 minutes 39.7 seconds. File lengths (MBytes): RWF= 104 Int= 0 D2E= 0 Chk= 11 Scr= 1 Thanks for your comments, and I would be pleased if there is any other option to visualize or way to explain the contributions of each orbital Best regards, Albert Dr. Albert Poater Teixidor University of Salerno From owner-chemistry@ccl.net Wed Jan 31 15:00:00 2007 From: "Rene Thomsen rt_+_molegro.com" To: CCL Subject: CCL: Molegro releases Molegro Virtual Docker 2007 v2.0 Message-Id: <-33492-070131145809-23569-jT+zEsHP98YYYvZUGGhmRw%x%server.ccl.net> X-Original-From: "Rene Thomsen" Date: Wed, 31 Jan 2007 14:58:05 -0500 Sent to CCL by: "Rene Thomsen" [rt^^^molegro.com] Aarhus, Denmark, January 31st, 2007 - Molegro is pleased to announce a new release of Molegro Virtual Docker, an integrated platform for predicting protein-ligand interactions available for Windows, Linux, and Mac OS X. Molegro Virtual Docker handles all aspects of the docking process from preparation of the molecules to determination of the potential binding sites of the target protein, and prediction of the binding modes of the ligands. Molegro Virtual Docker offers high-quality docking based on a novel optimization technique combined with a user interface experience focusing on usability and productivity. New features in version 2.0: * Docking with sidechain flexibility (taking induced fit interactions into account) * Sidechain Minimization Tool for optimizing receptor conformations before docking * Regression Tool for creating regression models (using neural networks) or customizing reranking/affinity scores * Native builds for Intel-based Mac OS X and 64-bit Linux distributions * A new clustering scheme (Tabu Clustering) * Support for Apple Mighty Mouse (use 360-degree scroll ball to rotate molecules) For more information, or to download a trial version, please visit our company website at: http://www.molegro.com or contact: Rene Thomsen, CEO Molegro Hoegh-Guldbergs Gade 10, Bldg. 1090 DK-8000 Aarhus Denmark E-mail: rt:-:molegro.com Phone: (+45) 89 42 31 65 About Molegro Molegro is a Danish company founded in 2005. Our company concentrates on developing high-performance drug discovery solutions leading to a faster drug-development process. Our goal is to provide scientifically superior products focusing on both state-of-the-art algorithms and an intuitive graphical user interface experience. From owner-chemistry@ccl.net Wed Jan 31 15:35:00 2007 From: "joerg.wegner joerg.wegner(-)web.de" To: CCL Subject: CCL: Teaching Wikipedia Chemistry - We need yout vote Message-Id: <-33493-070130173509-2298-2Eoq11JL2Tz8fvtKMoZ9kg-x-server.ccl.net> X-Original-From: "joerg.wegner" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 30 Jan 2007 22:38:42 +0100 MIME-Version: 1.0 Sent to CCL by: "joerg.wegner" [joerg.wegner]-[web.de] Dear all virtual chemistry fans, As you might know ... Wikipedia provides a lot of chemical information and special projects like Chemistry portal http://en.wikipedia.org/wiki/Portal:Chemistry Wikiproject Drugs http://en.wikipedia.org/wiki/Wikipedia:WikiProject_Drugs Since we are as chemists used to work with molecules and to search for substructure and similar molecules, some people would like to see SMILES support and substructure search services in public databases for Wikipedia articles. As usual this caused some discussions and we realized that those approaches must be tackled on a higher technical Mediawiki level. If you would like to see substructure searches and proper SMILES in Wikipedia it would push the priority, if you 'Vote for this bug' (actually feature request) at http://bugzilla.wikimedia.org/show_bug.cgi?id=7514 Unfortunately you have to create an account, so it's up to you if you really want to do that. History and details http://en.wikipedia.org/wiki/Template_talk:Drugbox#Substructure_search_in_eM olecules_and_PubChem_added Very kind regards, Joerg Kurt Wegner me**cheminformatics.eu From owner-chemistry@ccl.net Wed Jan 31 20:43:01 2007 From: "sam san seniorsamir^yahoo.com" To: CCL Subject: CCL:G: SCF source code Message-Id: <-33494-070131191544-23571-Gf932Oxxv/lQaTgr9uK80A . server.ccl.net> X-Original-From: "sam san" Date: Wed, 31 Jan 2007 19:15:40 -0500 Sent to CCL by: "sam san" [seniorsamir__yahoo.com] dear CCL Subscribers can any one send to me the SCF FORTRAN source code for many atoms if possible can any one send me a sorce code of the Gaussian 70