From owner-chemistry@ccl.net Wed Jul 18 03:00:00 2007 From: "sangeeth subramaniam srdshigella---gmail.com" To: CCL Subject: CCL: Batch mode minimisation in AMBER Message-Id: <-34759-070718024559-26122-3N+Rz/PhseLY8N3FOGsKWg|a|server.ccl.net> X-Original-From: "sangeeth subramaniam" Date: Wed, 18 Jul 2007 02:45:56 -0400 Sent to CCL by: "sangeeth subramaniam" [srdshigella**gmail.com] Hi, Has anyone tried minimising large number of structures in AMBER. I would like to know how to automate the process of minimisation in AMBER for more than 500 strutcures. Thanks Sangeetha. From owner-chemistry@ccl.net Wed Jul 18 04:51:01 2007 From: "marcel.swart/./icrea.es" To: CCL Subject: CCL: total energy : adf Message-Id: <-34760-070717184559-14341-CGPFO8wZmGzeJLkDWbCDdg=server.ccl.net> X-Original-From: marcel.swart .. icrea.es Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Tue, 17 Jul 2007 23:45:48 +0200 MIME-Version: 1.0 Sent to CCL by: marcel.swart^^icrea.es Dear Shrinwantu, the total bonding energy in ADF is calculated relative to atomic or molecular fragments; more information can be found in the "Chemistry with ADF" paper that appeared in J.Comput.Chem. in 2001: JCC 2001, 22, 931-967. Given in the ADF output is (apart from the Bonding Energy that can be decomposed into physical components like Pauli Repulsion, Electrostatics, and Orbital Interactions) also the total energy of the fragments, which is given as "Total XC:". However, the total energy is generally not necessary when you always use the same atomic fragments. The interaction energy can of course be corrected for BSSE, although with the Slater-type orbitals, these corrections are usually much smaller than with GTO's (ca. 0.5-1.0 kcal/mol using TZ2P basis sets). Again, see the "Chemistry with ADF" paper. NB. I don't understand what you mean with "there is a problem..", as far as I can see there is no problem; for more details, visit the SCM website, look for the Forum, and the JCC paper mentioned above. If you still have questions, please send a mail to support,,scm.com. Quoting "Shrinwantu Pal paul**jncasr.ac.in" : > I DO NOT SEEM TO FIGURE OUT HOW TO USE ADF IN FINDING OUT THE TOTAL > ENERGY OF A SYSTEM. > > I WOULD LIKE TO STRESS THAT I HAVE USED ADF TO GET INTERACTION > ENERGIES BETWEEN FRAGMENTS, BUT AS IN THIS CASE I NEED THE TOTAL > ENERGY. > > IS THERE A WAY WHERE ONE CAN DEFINE EACH ATOM AS A FRAGMENT AND > CALCULATE INTERACTION ENERGY? > > BUT THEN THERE IS A PROBLEM ABOUT THE ATOM NOT BEING CONSIDERED > PROPERLY AS THE ATOM WHILE IN BONDING, IS NO LONGER SPHERICAL. > > DO WE THEN CORRECT THE INTERACTION ENERGY SUPPORTED BY 'BSSE' ? > > ANY HELP FROM YOU ALL WOULD BE HUMBLY APPRECIATED. > > ~Shrinwantu Pal > TSU > JNCASR > INDIA From owner-chemistry@ccl.net Wed Jul 18 12:11:01 2007 From: "Conley, Michael mconley() leadscope.com" To: CCL Subject: CCL: Where to find FDA drug database Message-Id: <-34761-070718120932-17654-GlsgmZP61MsfsHAvndXyEw**server.ccl.net> X-Original-From: "Conley, Michael" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 18 Jul 2007 11:37:00 -0400 MIME-Version: 1.0 Sent to CCL by: "Conley, Michael" [mconley(-)leadscope.com] Leadscope through our Cooperative Research and Development Agreement (CRADA) with the U.S. FDA distributes toxicity databases for data harvested from the FDA files by the FDA and Leadscope. These databases contain structures and related toxicity information for compounds of both drugs and food additives. The structures can be exported as SD Files and the toxicity data can be exported as XML files. The FDA toxicity databases containing non-proprietary information for the following endpoints (each endpoint is a separate database): # of structures # of studies FDA CDER 2007 Genetox 239 4,600 FDA CDER 2007 Chronic 112 550 FDA CFSAN 2007 Genetox 527 6,590 FDA CFSAN 2007 Chronic 646 1,714 FDA CFSAN 2007 Repro-Developmental 309 1,051 While these databases are not all inclusive of the data held by the FDA, they represent the toxicity information that has been captured to date. Efforts are ongoing to capture all of the FDA toxicity information. These databases will be updated annually. Additional endpoints will be released in the future. For a brief overview of the databases please visit www.leadscope.com/demos for a short pre-recorded demonstration. If you have any questions or for further information regarding these FDA toxicity databases, please contact Leadscope at info:+:leadscope.com. Mike Conley ************************************** Michael Conley Leadscope, Inc. 1393 Dublin Road Columbus, Ohio 43215 614-675-3768 614-675-3732 fax mconley:+:leadscope.com -----Original Message----- > From: owner-chemistry:+:ccl.net [mailto:owner-chemistry:+:ccl.net] Sent: Wednesday, July 11, 2007 1:08 PM To: Conley, Michael Subject: CCL: Where to find FDA drug database Sent to CCL by: [DSprous*redpointbio.com] In reply to "Yuan Zhao" [ccl=-=mail.sioc.ac.cn] query summarized as: "I wonder how many drugs FDA have approved till now or this year?" To my knowledge: The FDA Orange Book (http://www.fda.gov/cder/ob/) is closest publicly available answer to this question. It is a list of approved drug formulations and does not have structures. Further, since it is a list of approved formulations, children's motrin is distinct from adult strength which is different from extra strength. The FDA apparently simply does not seem to be interested in an actual molecular database of approved active ingredients. You would need to download a copy of the list, develop a script to generate a unique list of active ingredients and then use something like LexiChem to convert the chemical and trade names to SMILES. This gives one about 1300 to 1400 compounds. An alternative which is easier to work with is the DrugBank (http://redpoll.pharmacy.ualberta.ca/drugbank/) datasets maintained by Wishart [University of Alberta]. This too is a list of ~1300 to 1400 compounds. If anyone knows better public sources, please post. Dennis G. Sprous, PhD Chemoinformatics/Computational Chemistry RedPointBio Inc. 7 Graphics Drive Ewing NJ 08628 609-637-9700 -----Original Message----- > From: owner-chemistry],[ccl.net [mailto:owner-chemistry],[ccl.net] Sent: Wednesday, July 11, 2007 10:40 AM To: Dennis Sprous Subject: CCL: Where to find FDA drug database Sent to CCL by: "Yuan Zhao" [ccl=-=mail.sioc.ac.cn] Hi all, I wonder how many drugs FDA have approved till now or this year. If possible, where can I download the FDA drug database in sd, mol or other chemical formats? Does anyone know how many drugs in FDA are fit for Lipinski rule of five? Any clue will be appreciate. Thanks. Stevenhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/ chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Jul 18 21:39:01 2007 From: "David A. Case case++scripps.edu" To: CCL Subject: CCL: Batch mode minimisation in AMBER Message-Id: <-34762-070718142204-23555-iQxPgXDRzfKlGSZdoJwfMA:+:server.ccl.net> X-Original-From: "David A. Case" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 18 Jul 2007 11:21:55 -0700 Mime-Version: 1.0 Sent to CCL by: "David A. Case" [case/a\scripps.edu] On Wed, Jul 18, 2007, sangeeth subramaniam srdshigella---gmail.com wrote: > > Has anyone tried minimising large number of structures in AMBER. > I would like to know how to automate the process of minimisation in AMBER > for more than 500 strutcures. I think most Amber users would write a shell script (or a perl script) to handle a task like this. There is also nice support for this sort of thing in the MMTSB toolkit (http://mmtsb.scripps.edu). There's a learning curve involved in both of these approaches, but dividends as well once you learn how to do it. ...good luck...dave case