From owner-chemistry@ccl.net Mon Jul 21 02:26:01 2008 From: "Mikko Vainio mivainio^^^abo.fi" To: CCL Subject: CCL: free program for conformation searching Message-Id: <-37378-080720141429-31373-plGl9kmxyaPcRch4LsPMVg(~)server.ccl.net> X-Original-From: Mikko Vainio Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sun, 20 Jul 2008 20:23:34 +0300 MIME-Version: 1.0 Sent to CCL by: Mikko Vainio [mivainio=-=abo.fi] Balloon generates 3D coordinates and conformer ensembles using a genetic algorithm. It is free of charge. The program lives in http://www.abo.fi/~mivainio/balloon/ Regards, Mikko gnli gnli*_*dicp.ac.cn wrote: > *Dear CCLer,* > > *Can anyone recommend me some free charge program doing monte carlo > conformation searching, i.e. giving a initial structure, it can find > those energy lowest conformations under the absolute configuration.* > > *Easier to be learned is better.* > > *Any advice is appreciated.* > > * * > > best wishes > Guanna Li > gnli.##.dicp.ac.cn > > > > > -- :: Mikko Vainio tel + 358 2 215 4600 :: Structural Bioinformatics Laboratory :: Department of Biochemistry and Pharmacy :: Abo Akademi University, Tykistokatu 6A, FI-20520 Turku Finland From owner-chemistry@ccl.net Mon Jul 21 04:02:01 2008 From: "Tristan Youngs t.youngs+*+qub.ac.uk" To: CCL Subject: CCL: Aten version 0.99.2 released. Message-Id: <-37379-080721035818-8147-F8MrUIawu1/bKScXRlizng^server.ccl.net> X-Original-From: "Tristan Youngs" Date: Mon, 21 Jul 2008 03:58:15 -0400 Sent to CCL by: "Tristan Youngs" [t.youngs===qub.ac.uk] Esteemed Scientists, Release 0.99.2 of Aten is now available, containing a cornucopia of fixes and a healthy smattering of new features. There is still much work to be done (in between research work, of course) and some unscrupulous beta-testers would still be appreciated. Download from the newly-designed website (with a sort of neo-classical "garish" look) at http://www.projectaten.org. Who knows, next time you need to fiddle around with some coordinates or generate a movie, maybe Aten could help... Danke, Tris. From owner-chemistry@ccl.net Mon Jul 21 06:04:01 2008 From: "Alcides Simao alsimao##gmail.com" To: CCL Subject: CCL: Intramolecular Hydrogen bonding Message-Id: <-37380-080721055402-22165-upwbb9TZarHH3+Dy6nmO8w.@.server.ccl.net> X-Original-From: "Alcides Simao" Content-Type: multipart/alternative; boundary="----=_Part_116676_13845678.1216634031159" Date: Mon, 21 Jul 2008 10:53:51 +0100 MIME-Version: 1.0 Sent to CCL by: "Alcides Simao" [alsimao^gmail.com] ------=_Part_116676_13845678.1216634031159 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello, jolly good people! I'm having an headache to find out a suitable method for computing intramolecular hydrogen bonding in some of my compounds. I now that you can use BSSE to compute INTERmolecular hydrogen bonding. But how can you do it for INTRAmolecular hydrogen bonding (that is, h-bond with no dimer envolved!) Have a nice day! Yours, Alcides! ------=_Part_116676_13845678.1216634031159 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hello, jolly good people!

I'm having an headache to find out a suitable method for computing intramolecular hydrogen bonding in some of my compounds. I now that you can use BSSE to compute INTERmolecular hydrogen bonding. But how can you do it for INTRAmolecular hydrogen bonding (that is, h-bond with no dimer envolved!)

Have a nice day!

Yours,

Alcides!
------=_Part_116676_13845678.1216634031159-- From owner-chemistry@ccl.net Mon Jul 21 06:38:01 2008 From: "Alcides Simao alsimao**gmail.com" To: CCL Subject: CCL: Intramolecular Hydrogen bonding Message-Id: <-37381-080721063415-4571-ywyS3C5lFBFDbtqcN2PB8w[]server.ccl.net> X-Original-From: "Alcides Simao" Content-Type: multipart/alternative; boundary="----=_Part_117222_18981536.1216636444425" Date: Mon, 21 Jul 2008 11:34:04 +0100 MIME-Version: 1.0 Sent to CCL by: "Alcides Simao" [alsimao[-]gmail.com] ------=_Part_117222_18981536.1216636444425 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Nice! my system is an aromatic system. a dihydroxybenzene, to be more exact. So i have loads and loads of problems... Thank you Marcel, for you kind reply! I hoped that there were an easier way to do this... :\ Many thanks to all! ------=_Part_117222_18981536.1216636444425 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Nice! my system is an aromatic system. a dihydroxybenzene, to be more exact. So i have loads and loads of problems...

Thank you Marcel, for you kind reply! I hoped that there were an easier way to do this...

:\

Many thanks to all!
------=_Part_117222_18981536.1216636444425-- From owner-chemistry@ccl.net Mon Jul 21 07:13:01 2008 From: "Alcides Simao alsimao:gmail.com" To: CCL Subject: CCL: Intramolecular Hydrogen bonding Message-Id: <-37382-080721063855-8836-ba9XX8qOLg4KvgDYv6LqJw^^^server.ccl.net> X-Original-From: "Alcides Simao" Content-Type: multipart/alternative; boundary="----=_Part_117303_33399883.1216636713321" Date: Mon, 21 Jul 2008 11:38:33 +0100 MIME-Version: 1.0 Sent to CCL by: "Alcides Simao" [alsimao%gmail.com] ------=_Part_117303_33399883.1216636713321 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Thanks for your swift reply, Marcel. Somehow, my reply didn't get posted in CCL. I have an aromatic system, for my sins... I wished there were another way (besides not making the calculation). Thank you all! Alcides ------=_Part_117303_33399883.1216636713321 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Thanks for your swift reply, Marcel. Somehow, my reply didn't get posted in CCL.

I have an aromatic system, for my sins... I wished there were another way (besides not making the calculation).

Thank you all!

Alcides
------=_Part_117303_33399883.1216636713321-- From owner-chemistry@ccl.net Mon Jul 21 09:52:00 2008 From: "Andrea Ciccioli andrea.ciccioli]~[uniroma1.it" To: CCL Subject: CCL:G: Determination of the "Electronic State" in Gaussian03 Message-Id: <-37383-080721072416-10789-+2999OuyxCP9hTQkBQ42+w(~)server.ccl.net> X-Original-From: "Andrea Ciccioli" Date: Mon, 21 Jul 2008 07:24:12 -0400 Sent to CCL by: "Andrea Ciccioli" [andrea.ciccioli:_:uniroma1.it] Hi everybody. I am performing UHF calculations on the silicon trimer (Si3) at both DFT-B3LYP and CCSD(T) level, for the D3h (equilater triangle) geometry in the triplet state (S=1). The calculated Electronic State given in the output is 3A1', with an electron configuration e'2 (two unpaired electrons in degenerate e' orbitals). However, as far as I know, for D3h pointgroup, triplet states can only have the 3A2' state (as reported e.g. in the Herzberg book, third vol, polyatomic molecules, page332), due to the symmetric nature of the spin function, which makes mandatory to have a antisymmetric spatial part. A 3A1' should be, to my knowledge, inherently uncorrect. Note also that S(S+1) output value is 2.0267 (frankly, it is not clear to me if this spin contamination could be related to my problem). Can anyone help me with this ? More generally, can anyone give me some information on how gaussian derive the molecular electronic state for a given electron configuration and point group ? Thank you very much Andrea Ciccioli Sapienza University of Rome (ITALY) From owner-chemistry@ccl.net Mon Jul 21 14:44:01 2008 From: "Pedro Salvador pedro.salvador!^!udg.edu" To: CCL Subject: CCL: Intramolecular Hydrogen bonding Message-Id: <-37384-080721123440-27097-GHa3AL4khZxupve5hNN5Dw++server.ccl.net> X-Original-From: Pedro Salvador Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 21 Jul 2008 17:36:34 +0200 MIME-Version: 1.0 Sent to CCL by: Pedro Salvador [pedro.salvador : udg.edu] Hi Alcides, abour intramolecular BSSE see for instance J. Chem. Phys. 128 144108 (2008). You might get some ideas out of it. Yours, Pedro Alcides Simao alsimao##gmail.com wrote: > Hello, jolly good people! > > I'm having an headache to find out a suitable method for computing > intramolecular hydrogen bonding in some of my compounds. I now that > you can use BSSE to compute INTERmolecular hydrogen bonding. But how > can you do it for INTRAmolecular hydrogen bonding (that is, h-bond > with no dimer envolved!) > > Have a nice day! > > Yours, > > Alcides! From owner-chemistry@ccl.net Mon Jul 21 21:45:01 2008 From: "David A. Case case()scripps.edu" To: CCL Subject: CCL: Release of version 1.2 of AmberTools Message-Id: <-37385-080721140335-3174-iy2iebYC1nhQ5dP7TPRPiQ*|*server.ccl.net> X-Original-From: "David A. Case" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Mon, 21 Jul 2008 10:01:29 -0700 Mime-Version: 1.0 Sent to CCL by: "David A. Case" [case-.-scripps.edu] We have prepared a new version of the AmberTools package, version 1.2. This is mostly a bug-fix release to version 1.0, fixing compilation problems on some machines as well as incorporating bugfixes 1-7 from the Amber web page. There are other small fixes as well, and version 1.2 improves the SCF convergence in mopac calculations for some compilers. If you have not had obvious problems with AmberTools 1.0, you probably don't *need* to upgrade (although you are welcome to do so). The upgrade will be most useful to Linux users with older compilers, and users running BSD, MacOSX, and Solaris. To find out more about AmberTools, and to download version 1.2, please visit: http://ambermd.org/amber.html#ambertools [Note for the curious: version 1.1 of AmberTools was posted on the web site, but never "advertised", since we found the additional mopac problems immediately after that version was made.] ...dave case (For the Amber Development team: http://ambermd.org/contributors.html)