From owner-chemistry@ccl.net Fri Jan 9 07:32:00 2009 From: "Tamas Gunda tgunda2-*-puma.unideb.hu" To: CCL Subject: CCL: Mol2Mol 5.6.1 available Message-Id: <-38404-090108145734-15486-LcGpFIc45uGYSkfShCiqtw~~server.ccl.net> X-Original-From: "Tamas Gunda" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-2"; reply-type=original Date: Thu, 8 Jan 2009 20:16:41 +0100 MIME-Version: 1.0 Sent to CCL by: "Tamas Gunda" [tgunda2+/-puma.unideb.hu] Dear CCL Members, A new 5.6.1 service version of the molecule file conversion, manipulation and utility program Mol2Mol is now available > from http://www.gunda.hu/mol2mol as trial or shareware version. The current version of Mol2Mol recognizes, and interconverts about 50 different file formats (including subtypes). By entering a format string practically every Cartesian or MOPAC type Z matrix formats can be in/outputted (even in polar coordinates). You can even copy/paste coordinates from e-mails and display them in Mol2Mol using the automatic recognition feature or using a format string. It can slice multiple structural files to single ones (such as PDB models or MDL SD files to single ones) and vice versa in several variations. Support for PDB Chime subformat (with 1-2-3 bonds). Many molecular utilities. Mol2mol is a very handy set of tools for everybody dealing with molecular modelling. It is impossible to write here all of the features of Mol2Mol, but have a look at its home page: http://www.gunda.hu/mol2mol e-mail: mol2mol {at} gunda {dot} hu POV-Ray fans may also have a look at the "desktop images" section at the above adress or: http://dragon.unideb.hu/~gundat/povraya.htm The program is available as 30 days unrestricted trial version or as shareware version. From owner-chemistry@ccl.net Fri Jan 9 08:14:01 2009 From: "Alberto Otero de la Roza alberto||carbono.quimica.uniovi.es" To: CCL Subject: CCL: CRITIC: program for QTAIM analysis in solids Message-Id: <-38405-090109041737-25158-5XbS3XDiYTqxKukhpZvAbw]-[server.ccl.net> X-Original-From: "Alberto Otero de la Roza" Date: Fri, 9 Jan 2009 04:17:31 -0500 Sent to CCL by: "Alberto Otero de la Roza" [alberto##carbono.quimica.uniovi.es] Dear CCL list, We have developed critic, a new code for the topological (QTAIM) analysis of the electron density in periodic solids. In this first version, we have tried to provide the basic capabilities for a full Atoms in Molecules study. A brief description of the features of critic is: * It can read the electron density from several sources, including WIEN2k calculations (http://www.wien2k.at/) and PI calculations (1). * Fast and completely automatic localization of the critical points (CPs) in the unit cell. Using the symmetry information provided in the struct file, the irreducible wedge of the Wigner-Seitz cell is calculated, and used to place the seeds for a Newton-Raphson algorithm. The complete list of CPs is presented in the output, along with their properties (density, laplacian,...). The localization of all the CPs is usually completed within seconds to minutes. * Atomic basin integration using a quadrature scheme plus a bisection strategy. * Lots of ways of representing the density, laplacian and gradient vector field: 1d, 2d, 3d, contour plots, basin plots, 2d and 3d maps of flux lines,... These capabilities are enhanced by the use of external graphical programs, with which critic interfaces: gnuplot, geomview (http://www.geomview.org/), tessel (http://web.uniovi.es/qcg/tessel/tessel.html),... * Critic is publicly available under the GPL licence. It has been published recently together with an article in Computer Physics Communications (2), and is downloadable from the CPC library or upon request to us. (1) M.A. Blanco, A. Martn-Pends, V. Luaa, Quantum mechanical cluster calculations of ionic materials: Revision 10 of the ab initio Perturbed Ion program, Comput. Phys. Comm. 103 (1997) 287--302. (2) A. Otero-de-la-Roza, M.A. Blanco, A. Martn-Pends and Vctor Luaa, Critic: a new program for the topological analysis of solid-state electron densities, Comput. Phys. Comm. 180 (2009) 157--166. We are currently working in a new version of critic (critic2) where we intend to implement lots of new features such as the use of different scalar fields (laplacian, ELF, electrostatic potential, etc.), the possibility of reading the electron density from a wider range of sources,... This new code is not ready for public distribution. If you are interested in the implementation of any particular feature, please contact with us. Therefore, the development of this first version of critic is frozen, limiting to bug fixes and small updates. However, we will gladly provide the users of critic with technical support, and we would appreciate very much any comment about the program. Best wishes, Alberto From owner-chemistry@ccl.net Fri Jan 9 09:53:01 2009 From: "amine amine m-22!A!hotmail.fr" To: CCL Subject: CCL: molecular mechanic in amber Message-Id: <-38406-090109095221-989-eJ9s/Mp8/sWLLLm7VN7KNw(!)server.ccl.net> X-Original-From: "amine amine" Date: Fri, 9 Jan 2009 09:52:17 -0500 Sent to CCL by: "amine amine" [m-22:+:hotmail.fr] Hi I want to do a MM Energy minimisation using amber: is it correct like this?? sander [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt with this sander.in initial minimisation prior to MD &cntrl imin = 1, maxcyc = 10000, ncyc = 5000, ntb = 0, igb = 0, ntc = 2, ntf = 2, cut = 12, / else? why i can do this? From owner-chemistry@ccl.net Fri Jan 9 16:29:00 2009 From: "Richard Tia richtiagh\a/gmail.com" To: CCL Subject: CCL: transition states Message-Id: <-38407-090109154016-8940-ZwLwkEEX84pIn/wNYsdY1A%a%server.ccl.net> X-Original-From: "Richard Tia" Date: Fri, 9 Jan 2009 15:40:13 -0500 Sent to CCL by: "Richard Tia" [richtiagh]|[gmail.com] Hi everybody, Does any one knows the best way(step by step instructions) as to how to compute transition states of cycloaddition reactions using spartan'06 (windows version)? Thanks Richard Tia Email: richtiagh~!~gmail.com Department of Chemistry KNUST, Kumasi Ghana From owner-chemistry@ccl.net Fri Jan 9 17:04:01 2009 From: "steinbrt===rci.rutgers.edu" To: CCL Subject: CCL: molecular mechanic in amber Message-Id: <-38408-090109115333-5133-7PsYfBPBEsHUvUKgHqKZRw*_*server.ccl.net> X-Original-From: steinbrt^rci.rutgers.edu Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Fri, 9 Jan 2009 11:02:23 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: steinbrt^rci.rutgers.edu Hi amine > sander [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt that is the correct command (leave out the brackets around -O) assuming sander is in your path. The minimized structure will appear as restrt and energy info in mdout > with this sander.in > > initial minimisation prior to MD > &cntrl > imin = 1, > maxcyc = 10000, > ncyc = 5000, > ntb = 0, > igb = 0, > ntc = 2, > ntf = 2, > cut = 12, > / > else? why i can do this? While this will do a minimization, in my opinion there is no need to do 5000 steps of steepest descent before CG. Any special reason you set ncyc to such a high value? Also, 10000 minimization steps are a lot, normally you dont see much change after say 500 or so even for biomolecules. If you really need such an extremely well minimized structure, look into the use of specialized minimizers such as implemented in ambers nmode program. Kind Regards, Dr. Thomas Steinbrecher BioMaps Institute Rutgers University 610 Taylor Rd. Piscataway, NJ 08854 From owner-chemistry@ccl.net Fri Jan 9 17:38:00 2009 From: "Gustavo L.C. Moura gustavo()mercury.chem.pitt.edu" To: CCL Subject: CCL: ECP Basis set for Europium Message-Id: <-38409-090109164235-20817-zwkDwrlmTdzbO2VyndkGsA-x-server.ccl.net> X-Original-From: "Gustavo L.C. Moura" Date: Fri, 9 Jan 2009 16:42:31 -0500 Sent to CCL by: "Gustavo L.C. Moura" [gustavo\a/mercury.chem.pitt.edu] Dear CCL Readers, I am looking for a very small ECP basis set for europium that includes the 4f electrons/orbitals in the core. I am aware of the MWB52 basis set, but it is too large for me (5s4p2d for the valence). I am looking for a smaller basis set for the valence. I found the CEP-4G basis set for europium but it includes the 4f electrons/orbitals in the valence and complicates the calculation (the system becomes multiconfigurational). The ideal for me would be a CEP-4G like basis set without the f electrons/orbitals in the valence. Thank you very much in advance. Sincerely yours, Dr. Gustavo L.C. Moura Gustavo _ mercury.chem.pitt.edu From owner-chemistry@ccl.net Fri Jan 9 18:14:00 2009 From: "Ross Walker ross=rosswalker.co.uk" To: CCL Subject: CCL: molecular mechanic in amber Message-Id: <-38410-090109132222-28139-+IUk4gajK2KHf0bqgDy4jw~!~server.ccl.net> X-Original-From: "Ross Walker" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="Windows-1252" Date: Fri, 9 Jan 2009 09:55:25 -0800 MIME-Version: 1.0 Sent to CCL by: "Ross Walker" [ross..rosswalker.co.uk] Hi You should probably take a look at the tutorials on the AMBER website: http://ambermd.org/tutorials/ Particularly the first one which explains how to setup simulations in sander, how to minimize and then how to run MD. It is also a good idea to sign up to the AMBER mailing list http://lists.ambermd.org/mailman/listinfo/amber and post questions specific to the AMBER software there. To answer your question you input file looks okay, assuming of course that you want to do a minimization in gas phase. Note, AMBER's standard minimizer works with SHAKE but will only take you so far towards a minimum before it will quit with a LINMIN failure error which essentially means it can go no further. All the best Ross > -----Original Message----- > From: owner-chemistry+ross==rosswalker.co.uk a ccl.net [mailto:owner- > chemistry+ross==rosswalker.co.uk a ccl.net] On Behalf Of amine amine m- > 22!A!hotmail.fr > Sent: Friday, January 09, 2009 6:52 AM > To: Walker, Ross > Subject: CCL: molecular mechanic in amber > > > Sent to CCL by: "amine amine" [m-22:+:hotmail.fr] > Hi > I want to do a MM Energy minimisation using amber: > is it correct like this?? > > > > sander [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt > > > with this sander.in > > initial minimisation prior to MD > &cntrl > imin = 1, > maxcyc = 10000, > ncyc = 5000, > ntb = 0, > igb = 0, > ntc = 2, > ntf = 2, > cut = 12, > / > else? why i can do this?