From owner-chemistry@ccl.net Mon Oct 15 03:19:00 2007 From: "Sina T reli sinatureli:_:gmail.com" To: CCL Subject: CCL: Large Computation Time Leap in Mopac and A Question About pm6 Message-Id: <-35381-071015031546-8853-y0BoHQIMTg6YJrjtnADDhQ~!~server.ccl.net> X-Original-From: "Sina T reli" Date: Mon, 15 Oct 2007 03:15:42 -0400 Sent to CCL by: "Sina T reli" [sinatureli!^!gmail.com] Hello, have two questions mainly regarding mopac. 1- Can mndo parameters in a molecular modelling program be replaced with mndo/d and pm6 parameters. Or in another words are the functions used in these three methods the same and only the parameters different? 2- I am using mopac2007 to do some geometry optimizations with mndod and pm6. My first subject was a molecule of size 141 which was handled quite nicely and fast and ended about in 30 minutes. However when I added a ligand that was about of 20 atoms in size, the calculation time leaped to like 2 days. The cycles werent even initiated before half a day passed... I used .mopac as the first output file and when I wanted to optimized the ligated one I used .xyz format with some atoms fixed to their coordinates. Is there something I am doing wrong or is this leap expected? And also I read that mopac 2007 isnt very practical for molecules of size above 600. Say if I use it for a molecule of size 400 atoms would it take too long on a 3.8 ghz 1gb ram machine? (I might plan to continue the work in a advanced computational center then...) Thanks From owner-chemistry@ccl.net Mon Oct 15 05:28:00 2007 From: "Konrad Hinsen hinsen_._cnrs-orleans.fr" To: CCL Subject: CCL: AminoAcid Rotamer Analysis Message-Id: <-35382-071015030855-8191-CM+jN/Zc8FaWSvYSsaUUrg..server.ccl.net> X-Original-From: "Konrad Hinsen" Date: Mon, 15 Oct 2007 03:08:50 -0400 Sent to CCL by: "Konrad Hinsen" [hinsen^^cnrs-orleans.fr] On 13.10.2007, at 01:57, Cesar Millan pachequin:-:gmail.com wrote: > Hi everyone! I have a couple of protein dynamics made by CHARMM (dcd format) > and I want to do a dihedral analysis of the aminoacids on my protein. I knew a > program called Dials and Windows that could this kind of analysis, but it only > runs on SGI machines. > Does anyone knows any free software that could realize this kind of > analysis on linux machines? The Molecular Modelling Toolkit, available freely at http://dirac.cnrs-orleans.fr/MMTK/ lets you write this kind of analysis programs in a few lines of Python code. What it does for you is reading the trajectory file and calculating the dihedral angles. What you have to do yourself is plug these two actions together and decide about the formatting of the output. Once you have some experience with MMTK, it will take you less time to write your analysis program than to search for an existing one. -- --------------------------------------------------------------------- Konrad Hinsen Centre de Biophysique Molculaire, CNRS Orlans Synchrotron Soleil - Division Expriences Saint Aubin - BP 48 91192 Gif sur Yvette Cedex, France Tel. +33-1 69 35 97 15 E-Mail: hinsen,+,cnrs-orleans.fr --------------------------------------------------------------------- From owner-chemistry@ccl.net Mon Oct 15 12:08:00 2007 From: "Schrodinger Announcements announce- -schrodinger.com" To: CCL Subject: CCL: Schrodinger Fall Webinars Message-Id: <-35383-071015120301-27780-eTV4VU/pEWHPZfJVxI97+A(_)server.ccl.net> X-Original-From: "Schrodinger Announcements" Date: Mon, 15 Oct 2007 12:02:58 -0400 Sent to CCL by: "Schrodinger Announcements" [announce---schrodinger.com] Schrodinger is pleased to announce a new series of webcast seminars for fall 2007. Featuring new talks highlighting recent research and development, the upcoming seminar series covers topics including: - Core hopping with CombiGlide - Shape-based searching using Phase - Workflow automation and data analysis using KNIME - Fragment docking and structure-based pharmacophores - Creating publication-quality images with Maestro - Flexible receptor docking - Protein crystal structure refinement using an all-atom force field and PrimeX Seminars begin Thursday, October 18th and run weekly through December 6th. The complete schedule, along with abstracts and registration details, is available on our website at: http://www.schrodinger.com/Fall2007Webinars.html The webcast seminars last approximately one hour, including time for question and answer sessions. The seminars are free of charge, and advance registration will ensure your participation. Sincerely, Mike Campbell Schrodinger Media Director From owner-chemistry@ccl.net Mon Oct 15 13:40:01 2007 From: "Gon alo Justino goncalo.justino-#-dq.fct.unl.pt" To: CCL Subject: CCL: How to mix input geometries Message-Id: <-35384-071015110425-23231-v6lGafrV6RatJ+nivftnTA+/-server.ccl.net> X-Original-From: "Gon alo Justino" Date: Mon, 15 Oct 2007 11:04:21 -0400 Sent to CCL by: "Gon alo Justino" [goncalo.justino]~[dq.fct.unl.pt] Dear all, I'd like to hear your opinion on the following trivial procedure: how would you build an input geometry combining a molecule with an undetermined geometry and a group with a known and fixed geometry? An example: taking the case of glucuronidea, I would like to use the pre-determined structure of the glucuronide moiety and fuse it with other geometries; besides the copy/paste procedure, are there any alternatives? Thanks in advance to all, Gonalo Justino From owner-chemistry@ccl.net Mon Oct 15 14:45:00 2007 From: "Wendy A Warr wendy..warr.com" To: CCL Subject: CCL: Symposium at the ACS meeting in New Orleans Message-Id: <-35385-071015144259-18516-j7A4aiQSQf5m3j+JOGBfoA##server.ccl.net> X-Original-From: "Wendy A Warr" Date: Mon, 15 Oct 2007 14:42:56 -0400 Sent to CCL by: "Wendy A Warr" [wendy/./warr.com] At the New Orleans ACS meeting, April 6-10, 2008, I am organizing a CINF/CSA Trust joint symposium on cheminformatics implications of collaborations between industry and academia. I want to take a broader approach than that of the safe exchange of structures symposium held two years ago, but I would not refuse one or two papers on that topic. I am also interested in covering IT, legal, business and cultural aspects of collaboration, so long as they are relevant to cheminformatics and to CINF division. If you think you have something useful to contribute, or you have a suggestion to make, please contact me before submitting an abstract on OASYS, as I have a very limited number of slots available. Wendy From owner-chemistry@ccl.net Mon Oct 15 18:30:01 2007 From: "Mustafa Hussein mustafa.hussein86^-^yahoo.com" To: CCL Subject: CCL:G: Electronic structure of carbon nanotubes Message-Id: <-35386-071015182610-23483-RwfKvVQGXEpiuB5zSlYXlw%server.ccl.net> X-Original-From: "Mustafa Hussein" Date: Mon, 15 Oct 2007 18:26:07 -0400 Sent to CCL by: "Mustafa Hussein" [mustafa.hussein86.**.yahoo.com] Hi CCLers, I have two questions: 1. How can carbon nanotubes be modeled? What are the available software to calculate their electronic structure? Can Gaussian 2003 be used for such job? 2. what are the limitations of the Z-matrix format for inputting molecular geometries? is their any alternative approach? how can a z-matrix be built for a large molecule? Please refer to any website that may be helpful in such topics Any help is appreciated cheers, Mustafa Hussein