From owner-chemistry@ccl.net Fri May 23 06:14:01 2008 From: "Jennifer Clare Brookes ucapjcb:+:ucl.ac.uk" To: CCL Subject: CCL: Molecular Dynamics for Non-Adiabatic Processes Message-Id: <-37016-080523061127-5485-GepvH3PhACea5ij6Q6H3mQ{:}server.ccl.net> X-Original-From: "Jennifer Clare Brookes" Date: Fri, 23 May 2008 06:11:23 -0400 Sent to CCL by: "Jennifer Clare Brookes" [ucapjcb%a%ucl.ac.uk] Molecular Dynamics for Non-Adiabatic Processes ---------------------------------------------- Nanoscale phenomena, spanning multiple disciplines, share a unifying core problem: excitations away from equilibrium that evolve through non-adiabatic processes. Numerous techniques for modelling these have been designed and are undergoing rapid further development, usually within individual disciplines. A meeting is to be held to survey the spectrum of molecular dynamics based methods in order to highlight their strengths and weaknesses and to establish fundamental connections between them. It will be held on 21-22 July, 2008, at the Institute of Physics, 76 Portland Place, London The format will be of a discussion meeting with invited talks given by leaders in the field, followed by time for discussion. The speakers will include: John Tully Oleg Prezhdo Todd Martinez Arieh Warshel Sebastian Westenhoff Tchavdar Todorov E K U Gross Lev Kantorovitch Mads Brandbyge Jonathan Tennyson Dorothy Duffy There will also be a poster session which is open to anyone registered to attend the meeting. At registration please indicate if you will be presenting a poster. There will be a prize of 200 for the best student poster. Online registration for this meeting is at: http://www.iop.org/Conferences/Forthcoming_Institute_Conferences/2008/July/molecular_dynamics_for_non_adiabatic_processes/event_22243.html From owner-chemistry@ccl.net Fri May 23 09:06:01 2008 From: "David D phrm75{:}yahoo.com" To: CCL Subject: CCL: Unambigous comparison of 3D structures Message-Id: <-37017-080522173434-19466-ZizFqZ3Ok+6bTy2GfJrhzQ||server.ccl.net> X-Original-From: David D Content-Type: multipart/alternative; boundary="0-1825632821-1211488458=:32664" Date: Thu, 22 May 2008 13:34:18 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: David D [phrm75+*+yahoo.com] --0-1825632821-1211488458=:32664 Content-Type: text/plain; charset=us-ascii Hello, I need to perform analysis changes in 3D structures of small molecules in different PDB files. One way of doing this is to superimpose the molecules. The problem is that superposition algorithms need user input of paired atoms. Otherwise, unattended superposition results may depend on the initial orientation of the two molecules. Superposition is especially problematic in the case of molecules with multiple symmetry axes. Another possibility is to create connectivity matrix file (Z-matrix) that will contain molecules internal coordinates. Here, unattended processes rely heavily on the order of the atoms in the original PDB file. Thus, my questions are: - am I wrong in any of the above statements? - is there any way to bring to structures of small molecules to a "common denominator" that will enable reliable analysis of the 3D structure changes? - all the files originate from the PDB. Are there internal standards that enable unattended creation of Z-matrices? Assumptions: - only chemically identical structures are compared. - all the structures will be downloaded from the PDB Thank you --0-1825632821-1211488458=:32664 Content-Type: text/html; charset=us-ascii

Hello,
I need to perform analysis changes in 3D structures of small molecules in different PDB files. One way of doing this is to superimpose the molecules. The problem is that superposition algorithms need user input of paired atoms. Otherwise, unattended superposition results may depend on the initial orientation of the two molecules. Superposition is especially problematic in the case of molecules with multiple symmetry axes. Another possibility is to create connectivity matrix file (Z-matrix) that will contain molecules internal coordinates. Here, unattended processes rely heavily on the order of the atoms in the original PDB file.

Thus, my questions are:
- am I wrong in any of the above statements?
- is there any way to bring to structures of small molecules to a "common denominator" that will enable reliable analysis of the 3D structure changes?
- all the files originate from the PDB. Are there internal standards that enable unattended creation of Z-matrices?

Assumptions:
- only chemically identical structures are compared.
- all the structures will be downloaded from the PDB

Thank you

--0-1825632821-1211488458=:32664-- From owner-chemistry@ccl.net Fri May 23 09:41:00 2008 From: "=?GB2312?B?va+zvM3+?= cwjiang1983]|[gmail.com" To: CCL Subject: CCL:G: best function and basis set for Sn, Ti and V Message-Id: <-37018-080522105015-26870-APXAUPT2ISiNCRvfz8GO2A[a]server.ccl.net> X-Original-From: "=?GB2312?B?va+zvM3+?=" Content-Type: multipart/alternative; boundary="----=_Part_7778_14013722.1211456840406" Date: Thu, 22 May 2008 19:47:20 +0800 MIME-Version: 1.0 Sent to CCL by: "=?GB2312?B?va+zvM3+?=" [cwjiang1983^-^gmail.com] ------=_Part_7778_14013722.1211456840406 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear ahmad, You can try the LanL2DZ basis set. Because the Sn, Ti and V atoms are very heavy, the relativity basis set is needed. Best regards Chenwei 2008/5/22 Ahmad irfan irfaahmad[#]gmail.com : > > Sent to CCL by: "Ahmad irfan" [irfaahmad~~gmail.com] > Dear users > I am working on the molecules having Sn, Ti, V atoms along with C,N,O,Cl,H > I want to optimiz the molecules, by trying diffrerent functions as > PBE0,b3lyp with DZVP,3-21G and STO-3G basis sets, i couldnot get reliable > geometries. can sombody tell me which basis set and fuction will be suitable > by using gaussian. I also want accurarte energies. > > best wisher > > Dr. irfan ahmad > nenu, china> > > ------=_Part_7778_14013722.1211456840406 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear ahmad,

You can try the LanL2DZ basis set. Because the Sn, Ti and V atoms are very heavy, the relativity basis set is needed.

Best regards

Chenwei

2008/5/22 Ahmad irfan irfaahmad[#]gmail.com <owner-chemistry|ccl.net>:

Sent to CCL by: "Ahmad irfan" [irfaahmad~~gmail.com]
Dear users
I am working on the molecules having Sn, Ti, V atoms along with C,N,O,Cl,H
I want to optimiz the molecules, by trying diffrerent functions as PBE0,b3lyp with DZVP,3-21G and STO-3G basis sets, i couldnot get reliable geometries. can sombody tell me which basis set and fuction will be suitable by using gaussian. I also want accurarte energies.

best wisher

Dr. irfan ahmad
nenu, china

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------=_Part_7778_14013722.1211456840406-- From owner-chemistry@ccl.net Fri May 23 10:15:01 2008 From: "Alessandro Casoni alessandro.casoni*o*unimi.it" To: CCL Subject: CCL: Software for molrcular datanank creation Message-Id: <-37019-080523035808-22920-649KI8GEWCAYUvEXTXWWTQ/a\server.ccl.net> X-Original-From: Alessandro Casoni Content-transfer-encoding: 7bit Content-type: text/plain; charset=ISO-8859-15; format=flowed Date: Fri, 23 May 2008 09:00:22 +0200 MIME-version: 1.0 Sent to CCL by: Alessandro Casoni [alessandro.casoni###unimi.it] Michael Shokhen shokhen-x-mail.biu.ac.il ha scritto: > Sent to CCL by: "Michael Shokhen" [shokhen|,|mail.biu.ac.il] > Dear Colleagues, > > I want to collect information (molecular structure, biding affinity)about inhibitors from literature and molecular databanks. My purpose is to organize the collected data as input files for the following molecular modeling and drug design. In other words I am looking for MS Windows platform software tool for creation of my own molecular databank that can read/write SD,SDF, XLS files format and then represent these data as a table in MS Excel manner, where every field including molecular structures will be active for editing. > I would appreciate if somebody can recommend me a relevant software. > Please dont mention the Accelrys Accord for Excel ! > > Thank you, > Michael> > > > You can try ChemAxon software: http://www.chemaxon.com/ free for academic research and teaching.. Alessandro From owner-chemistry@ccl.net Fri May 23 10:50:01 2008 From: "Michael K. Gilson gilson{}umbi.umd.edu" To: CCL Subject: CCL: Unambigous comparison of 3D structures Message-Id: <-37020-080523095506-20956-T08lkNJdpyCC7L2T68jD7A{}server.ccl.net> X-Original-From: "Michael K. Gilson" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 23 May 2008 09:54:45 -0400 MIME-Version: 1.0 Sent to CCL by: "Michael K. Gilson" [gilson||umbi.umd.edu] Dear David, Yes, these symmetry issues are nontrivial. Vrms is an application that addresses this problem and is freely distributed to noncommercial users. Vrms computes the RMSDs among conformations of drug-like molecules, accounting for local and global symmetries. It has two modes. The first allows for overall translation and rotation. The second leaves out the overall translation/rotation superposition. It is designed for comparing different protein-bound conformations. See www.verachem.com/vrms.html For ready-made ligand files, you may want to look at the PDB's new Ligand Expo or HIC-Up (alpha2.bmc.uu.se/hicup/) Best regards, Mike David D phrm75{:}yahoo.com wrote: > Hello, > I need to perform analysis changes in 3D structures of small molecules > in different PDB files. One way of doing this is to superimpose the > molecules. The problem is that superposition algorithms need user > input of paired atoms. Otherwise, unattended superposition results may > depend on the initial orientation of the two molecules. Superposition > is especially problematic in the case of molecules with multiple > symmetry axes. Another possibility is to create connectivity matrix > file (Z-matrix) that will contain molecules internal coordinates. > Here, unattended processes rely heavily on the order of the atoms in > the original PDB file. > > Thus, my questions are: > - am I wrong in any of the above statements? > - is there any way to bring to structures of small molecules to a > "common denominator" that will enable reliable analysis of the 3D > structure changes? > - all the files originate from the PDB. Are there internal standards > that enable unattended creation of Z-matrices? > > Assumptions: > - only chemically identical structures are compared. > - all the structures will be downloaded from the PDB > > > Thank you > > From owner-chemistry@ccl.net Fri May 23 11:26:00 2008 From: "Mikko Vainio mivainio#%#abo.fi" To: CCL Subject: CCL: Unambigous comparison of 3D structures Message-Id: <-37021-080523102641-13084-fA+22vO2sbYOEdAewBZhOw()server.ccl.net> X-Original-From: Mikko Vainio Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 23 May 2008 17:26:25 +0300 MIME-Version: 1.0 Sent to CCL by: Mikko Vainio [mivainio(a)abo.fi] Hi David, Unambiguous comparison of 3D structures can be and has been automated, see for example http://www.verachem.com/vrms.html. The problematic part here is parsing the valence bond models of the ligands from PDB files. Because the hydrogens and formal charge information are missing (in the majority of cases) and the bond lengths and angles are often distorted, it becomes difficult to deduce the correct bond orders. One approach is given in http://dx.doi.org/10.1021/ci049915d. Regards, Mikko David D phrm75{:}yahoo.com wrote: > Hello, > I need to perform analysis changes in 3D structures of small molecules > in different PDB files. One way of doing this is to superimpose the > molecules. The problem is that superposition algorithms need user input > of paired atoms. Otherwise, unattended superposition results may depend > on the initial orientation of the two molecules. Superposition is > especially problematic in the case of molecules with multiple symmetry > axes. Another possibility is to create connectivity matrix file > (Z-matrix) that will contain molecules internal coordinates. Here, > unattended processes rely heavily on the order of the atoms in the > original PDB file. > > Thus, my questions are: > - am I wrong in any of the above statements? > - is there any way to bring to structures of small molecules to a > "common denominator" that will enable reliable analysis of the 3D > structure changes? > - all the files originate from the PDB. Are there internal standards > that enable unattended creation of Z-matrices? > > Assumptions: > - only chemically identical structures are compared. > - all the structures will be downloaded from the PDB > > > Thank you > > -- :: 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 Fri May 23 12:31:01 2008 From: "Michel PETITJEAN michel.petitjean*cea.fr" To: CCL Subject: CCL: RE : Unambigous comparison of 3D structures Message-Id: <-37022-080523112127-21974-Qx/8eilJSJNHhUaJwHX+eQ-x-server.ccl.net> X-Original-From: "Michel PETITJEAN" Content-class: urn:content-classes:message Content-Type: multipart/mixed; boundary="----_=_NextPart_001_01C8BCE3.A2487455" Date: Fri, 23 May 2008 16:41:45 +0200 MIME-Version: 1.0 Sent to CCL by: "Michel PETITJEAN" [michel.petitjean!A!cea.fr] This is a multi-part message in MIME format. ------_=_NextPart_001_01C8BCE3.A2487455 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable CSR superposes optimally without input pairwise correspondence: please download it from:=20 http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#CSR (once downloaded, call uudecode before the first execution) CSR works with different structures. Michel Petitjean DSV/iBiTec-S/SB2SM (CNRS URA 2096) CEA Saclay, bat. 528 91191 Gif-sur-Yvette Cedex, France. Phone: +331 6908 4006 / Fax: +331 6908 4007 E-mail: michel.petitjean[A]cea.fr http://petitjeanmichel.free.fr/itoweb.petitjean.html -------- Message d'origine-------- De: David D phrm75{:}yahoo.com [mailto:owner-chemistry[A]ccl.net] Date: jeu. 22/05/2008 22:34 =C0: Michel PETITJEAN Objet : CCL: Unambigous comparison of 3D structures =20 Hello, I need to perform analysis changes in 3D structures of small molecules = in different PDB files. One way of doing this is to superimpose the = molecules. The problem is that superposition algorithms need user input = of paired atoms. Otherwise, unattended superposition results may depend = on the initial orientation of the two molecules. Superposition is = especially problematic in the case of molecules with multiple symmetry = axes. Another possibility is to create connectivity matrix file = (Z-matrix) that will contain molecules internal coordinates. Here, = unattended processes rely heavily on the order of the atoms in the = original PDB file. Thus, my questions are: - am I wrong in any of the above statements? - is there any way to bring to structures of small molecules to a = "common denominator" that will enable reliable analysis of the 3D = structure changes? - all the files originate from the PDB. Are there internal standards = that enable unattended creation of Z-matrices? Assumptions: - only chemically identical structures are compared. - all the structures will be downloaded from the PDB Thank you ------_=_NextPart_001_01C8BCE3.A2487455-- From owner-chemistry@ccl.net Fri May 23 13:06:01 2008 From: "Mariusz Radon mariusz.radon . gmail.com" To: CCL Subject: CCL:G: best function and basis set for Sn, Ti and V Message-Id: <-37023-080523122851-2066-IdwwST7Z5mJR9wy+WDCrRQ:server.ccl.net> X-Original-From: "Mariusz Radon" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8 Date: Fri, 23 May 2008 17:34:18 +0200 MIME-Version: 1.0 Sent to CCL by: "Mariusz Radon" [mariusz.radon[A]gmail.com] Dear Ahmad! >> I am working on the molecules having Sn, Ti, V atoms along with C,N,O,Cl,H >> I want to optimiz the molecules, by trying diffrerent functions as >> PBE0,b3lyp with DZVP,3-21G and STO-3G basis sets, i couldnot get reliable >> geometries. can sombody tell me which basis set and fuction will be suitable >> by using gaussian. I also want accurarte energies. I suggest trying also non-hybrid density functionals, like PBE (not the same as "PBE0"!) or BP86. I don't claim they are better than others; only that they might give you results very different from the hybrid functionals (B3LYP, PBE0). [ A small remark: Please kindly note that various Density Functional Theory methods are *functionals*, not *functions* --- calling them "functions" might cause misunderstanding. ;) ] > You can try the LanL2DZ basis set. Because the Sn, Ti and V atoms are very > heavy, the relativity basis set is needed. > From my limited experience relativistic effects should not be crucial for geometries and energies of the first-row transition metals species (for some properties they might be of course very important...). The difference between various density functionals are likely to be more important than between considering or neglecting relativisitc effects. Remember also that relativistic ECPs, though very useful, are not silver bullets which provide complete treatment of the relativity! I also think that LanL2DZ basis is OK for you problem, especially for calculating structures. For accurate energy calculations it might be too small, though. :( In my opinion STO-3G basis is definitely too small to get quantitative results. However, larger Pople's basis (like e.g. 6-311G*, 6-311+G*) might be reasonable (although they don't have relativistic ECP on the metals). Best regards, Mariusz Radon -- Mariusz Radon, PhD student Department of Theoretical Chemistry Jagiellonian University mradon /at/ chemia.uj.edu.pl http://www.chemia.uj.edu.pl/~mradon From owner-chemistry@ccl.net Fri May 23 13:40:01 2008 From: "Lushington, Gerald Henry glushington##ku.edu" To: CCL Subject: CCL: small molecule amphiphilicity predictions Message-Id: <-37024-080523123043-2331-Q957g9hJnR68YGttXkW4Eg]*[server.ccl.net> X-Original-From: "Lushington, Gerald Henry" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 23 May 2008 10:48:17 -0500 MIME-Version: 1.0 Sent to CCL by: "Lushington, Gerald Henry" [glushington###ku.edu] Dear all, Do any of you know of (or have access to) programs that can generate = reasonable amphiphilicity calculations for small molecules? I wrote one = myself based on hydropathic moments, but it doesn't appear to reproduce = some key experimental trends that a colleague has observed. I know of a program named CAFCA that was produced by scientists at Roche = a number of years ago, but I'm not aware if it's being distributed. Thank you very much in advance for your thoughts! - Gerry ---------------------------------------------------- Gerald H. Lushington 1251 Wescoe Hall Rd. Associate Scientist & Lawrence, KS 66045 Director of Laboratories Office: 3021 Malott Courtesy Associate Professor 785-864-1140 Med. Chem. and Chemistry Lab: 785-864-1166 University of Kansas Fax: 786-864-5326 http://www.msg.ku.edu/~msg/mgm.html http://www.cmld.ku.edu http://www.bcf.ku.edu ---------------------------------------------------- From owner-chemistry@ccl.net Fri May 23 14:16:01 2008 From: "Andrew T Pudzianowski andrew.pudzianowski|-|bms.com" To: CCL Subject: CCL: Dalton installation on Ubuntu Linux? Message-Id: <-37025-080523124714-11081-+kLRHPYrfJDI8PzOibj/hg . server.ccl.net> X-Original-From: Andrew T Pudzianowski Content-return: prohibited Content-transfer-encoding: 7BIT Content-type: text/plain; format=flowed; charset=ISO-8859-1 Date: Fri, 23 May 2008 11:46:25 -0400 MIME-version: 1.0 Sent to CCL by: Andrew T Pudzianowski [andrew.pudzianowski^^bms.com] Hello, all. Has anybody been able to install the "Dalton" quantum chemistry program on an Ubuntu Linux system? I'm having problems at the "make" stage, but rather than going into details now I'm just curious as to whether anybody has done a successful installation. If so, that's when details would be helpful....Andrew Pudzianowski -- ---------------------------------------------------------------------------------------------- Andrew T. Pudzianowski, Ph.D. Computer-Aided Drug Design Bristol-Myers Squibb R & D Box 4000 Princeton NJ 08543-4000 office: (609) 252-4248 fax : (609) 252-6030 ))))))))))))))))))))))))))))))))))))))))))))) I used to shave with Ockham's razor but I kept getting Dedekind cuts. ((((((((((((((((((((((((((((((((((((((((((((( From owner-chemistry@ccl.net Fri May 23 14:52:00 2008 From: "maxim totrov max^molsoft.com" To: CCL Subject: CCL: Unambigous comparison of 3D structures Message-Id: <-37026-080523142241-27945-rrEaF90sNQl/QqND2fmxUg^_^server.ccl.net> X-Original-From: maxim totrov Content-Type: multipart/alternative; boundary=Apple-Mail-3--821149042 Date: Fri, 23 May 2008 09:56:08 -0700 Mime-Version: 1.0 (Apple Message framework v919.2) Sent to CCL by: maxim totrov [max,molsoft.com] --Apple-Mail-3--821149042 Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Content-Transfer-Encoding: 7bit Hello David, you may want to try free Molsoft icm-browser (www.molsoft.com). It can load PDBs, automatically assign chemical bond structure, and calculate RMSDs taking chemical symmetries into account. Max Totrov > Hello, > I need to perform analysis changes in 3D structures of small > molecules in different PDB files. One way of doing this is to > superimpose the molecules. The problem is that superposition > algorithms need user input of paired atoms. Otherwise, unattended > superposition results may depend on the initial orientation of the > two molecules. Superposition is especially problematic in the case > of molecules with multiple symmetry axes. Another possibility is to > create connectivity matrix file (Z-matrix) that will contain > molecules internal coordinates. Here, unattended processes rely > heavily on the order of the atoms in the original PDB file. > > Thus, my questions are: > - am I wrong in any of the above statements? > - is there any way to bring to structures of small molecules to a > "common denominator" that will enable reliable analysis of the 3D > structure changes? > - all the files originate from the PDB. Are there internal > standards that enable unattended creation of Z-matrices? > > Assumptions: > - only chemically identical structures are compared. > - all the structures will be downloaded from the PDB > > > Thank you > > > --Apple-Mail-3--821149042 Content-Type: text/html; charset=US-ASCII Content-Transfer-Encoding: quoted-printable Hello = David,

you may want to try free Molsoft icm-browser = (www.molsoft.com). It can load = PDBs, automatically assign chemical bond structure, and calculate RMSDs = taking chemical symmetries into account.

Max = Totrov

Hello,
I need to perform analysis changes in = 3D structures of small molecules in different PDB files. One way of = doing this is to superimpose the molecules. The problem is that = superposition algorithms need user input of paired atoms. Otherwise, = unattended superposition results may depend on the initial orientation = of the two molecules. Superposition is especially problematic in the = case of molecules with multiple symmetry axes. Another possibility is to = create connectivity matrix file (Z-matrix) that will contain molecules = internal coordinates. Here, unattended processes rely heavily on the = order of the atoms in the original PDB file.

Thus, my questions = are:
- am I wrong in any of the above statements?
- is = there any way to bring to structures of small molecules to a "common = denominator" that will enable reliable analysis of the 3D structure = changes?
- all the files originate from the PDB. Are there = internal standards that enable unattended creation of = Z-matrices?

Assumptions:
- only chemically identical = structures are compared.
- all the structures will be = downloaded from the PDB

Thank = you

= --Apple-Mail-3--821149042-- From owner-chemistry@ccl.net Fri May 23 16:08:01 2008 From: "Geoffrey Hutchison geoffh+],[pitt.edu" To: CCL Subject: CCL:G: Avogadro 0.8 Release Message-Id: <-37027-080523160154-27781-Bkz16V4fG3vDqlAr2M2ExQ{:}server.ccl.net> X-Original-From: Geoffrey Hutchison Content-transfer-encoding: 7bit Content-type: text/plain; delsp=yes; format=flowed; charset=US-ASCII Date: Fri, 23 May 2008 16:01:42 -0400 MIME-version: 1.0 (Apple Message framework v919.2) Sent to CCL by: Geoffrey Hutchison [geoffh+.:.pitt.edu] The Avogadro project is proud to announce the release of Avogadro 0.8. Avogadro is a free, open source, cross-platform molecular editor designed for flexible use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. Packages are available for Mac OSX, Windows and Linux, as well as source code provided under the GNU GPL. To download: http://avogadro.openmolecules.net/wiki/Get_Avogadro For more information: http://avogadro.openmolecules.net/wiki/ At the moment, Avogadro is best at small molecule building, including built-in molecular mechanics (MMFF94 and UFF), and input generation for Gaussian 03 and GAMESS-US. Some support for crystallographic unit cells is included, as well as a fragment database which includes a variety of small molecules, amino acids, nucleic acids, and saccharides. It also offers a variety of VdW surfaces and isosurfaces > from Gaussian cube or checkpoint files. Future plans include additional builder tools (crystals, biomolecules, nanotubes, etc.), embedded Python scripting, full documentation and tutorials, interfaces to additional computational packages, and more. It offers a framework for extending to new tools, rendering options, and plugins of all sorts. Our design for Avogadro makes it exceptionally easy to extend. Since the program is free, open source software, you can extend existing functions, or add your own plugins. Indeed, almost every feature is already a plugin. Need custom analysis tools? You can do it. How can you help? * We need your feedback, testing, and encouragement. Particular help would come from developers on Windows. * We need translators. Currently, we have English, French, and German, but other languages would be most welcome. * We need interest in coding (in C++ or Python) for new computational packages or other plugins. Why bother? While there are many very good visualization tools, there are very few good, intuitive molecular editing packages. We believe that open source can bring together a broad community of active developers. In ~18 months, we have gathered 12 developers and over 8,000 downloads. Not bad for a set of beta releases from a set of volunteers. We also think that Avogadro makes for a solid platform for using and developing a range of computational chemistry tools. We use customized plugins for our own research and want to make it easier for others. From owner-chemistry@ccl.net Fri May 23 22:12:00 2008 From: "Yi-Wen Dong typ2469-#-163.com" To: CCL Subject: CCL: Seeking for free software for calculations of association constant K Message-Id: <-37028-080523191844-4626-iISZevllvk+yX9Trnayj4w^^^server.ccl.net> X-Original-From: "Yi-Wen Dong" Date: Fri, 23 May 2008 19:18:39 -0400 Sent to CCL by: "Yi-Wen Dong" [typ2469[-]163.com] Dear all, Would you like please to tell me a software for the fitting calculations of association constants K of metal-ligand complexes for Uv-vis or fluorescence titrations? Any suggestions and comments are welcome and highly appreciated. Thank you in advance. Best wishes Dr. Yi-Wen Dong From owner-chemistry@ccl.net Fri May 23 23:11:01 2008 From: "Iain Wallace iain.m.wallace(-)gmail.com" To: CCL Subject: CCL: Weak acid/Weak base Message-Id: <-37029-080523193924-6605-N0hdDhGilJ/+MtzPCn8uFw-$-server.ccl.net> X-Original-From: "Iain Wallace" Content-Type: multipart/alternative; boundary="----=_Part_3139_11178208.1211579738837" Date: Fri, 23 May 2008 17:55:38 -0400 MIME-Version: 1.0 Sent to CCL by: "Iain Wallace" [iain.m.wallace/./gmail.com] ------=_Part_3139_11178208.1211579738837 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi all, I was wondering if someone could point me in the direction of some software that can calculate if a molecule is a weak acid or a weak base please? Thanks Iain ------=_Part_3139_11178208.1211579738837 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi all,

I was wondering if someone could point me in the direction of some software that can calculate if a molecule is a weak acid or a weak base please?

Thanks

Iain
------=_Part_3139_11178208.1211579738837--