From chemistry-request@server.ccl.net Wed Mar 19 14:05:40 2003 Received: from HQ-EXCHANGE-01.signaturebio.com ([65.219.36.67]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2JJ5cr17349 for ; Wed, 19 Mar 2003 14:05:40 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C2EE4A.8524749A" Subject: Call for speakers: Computational chemistry in drug discovery: Are high information content calculations better than low information content calculations? Date: Wed, 19 Mar 2003 11:05:34 -0800 Message-ID: <94CF80B100952D47ABB329579E6D1347311D89@hq-exchange-01.signaturebio.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Call for speakers: Computational chemistry in drug discovery: Are high information content calculations better than low information content calculations? Thread-Index: AcLuSoUKrrRAtUslR0e0ex9p+lZmzA== From: "Jennifer Miller" To: This is a multi-part message in MIME format. ------_=_NextPart_001_01C2EE4A.8524749A Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Symposium: Computational chemistry in drug discovery: Are high = information content calculations better than low information content = calculations? Conference: 226th National ACS Meeting COMP Division New York City, NY USA September 7-11, 2003 Description: In laboratories around the world, biologists carry out a variety of = assays to determine the potency and selectivity of potential drug = molecules. Each assay takes time to develop, validate and put into = production. These assays range from high-throughput, low information = content to low-throughput, high information content. The bottom line is = that there is a wide variety of assays employed every day in drug = discovery efforts and no single right answer for which assay to choose. = One can view the various computational drug design methods from the same = perspectives of "development time and cost" and "throughput vs. = information". For example, we select (filter) compounds on the basis of = their 2D graph, a process that is very high-throughput but arguably low = information content. At the other extreme, we evaluate compounds using = QM methods, or coupled QM/MM free energy calculations, that are very = low-throughput yet high information content. Moreover, much like assay = development, all of these methods take time to develop and validate = (and, like assays there are "kits" available for purchase). While a = direct comparison of the various approaches is difficult, this session = encourages submissions from researchers who can present a perspective on = the question: In drug discovery, are high information content = calculations better than low information content calculations? Topics = are not limited to the extremes of the methods, and talks are expected = to include success stories as well as failures. Organizer: Jennifer L. Miller, Signature BioScience, = jmilleracs@signaturebio.com Deadline: Abstracts for talks must be submitted to = http://oasys.acs.org/oasys.htm by 01 May 2003. ------_=_NextPart_001_01C2EE4A.8524749A Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Call for speakers: Computational chemistry in drug discovery: Are = high information content calculations better than low information = content calculations?

Symposium: Computational chemistry in = drug discovery: Are high information content calculations better than = low information content calculations?

Conference:       226th = National ACS Meeting
        =         COMP Division
         &nbs= p;      New York City, NY USA
         &nbs= p;      September 7-11, 2003

Description:

In laboratories around the world, = biologists carry out a variety of assays to determine the potency and = selectivity of potential drug molecules. Each assay takes time to = develop, validate and put into production. These assays range from = high-throughput, low information content to low-throughput, high = information content. The bottom line is that there is a wide variety of = assays employed every day in drug discovery efforts and no single right = answer for which assay to choose. One can view the various computational = drug design methods from the same perspectives of “development = time and cost” and “throughput vs. information”. For = example, we select (filter) compounds on the basis of their 2D graph, a = process that is very high-throughput but arguably low information = content. At the other extreme, we evaluate compounds using QM methods, = or coupled QM/MM free energy calculations, that are very low-throughput = yet high information content. Moreover, much like assay development, all = of these methods take time to develop and validate (and, like assays = there are “kits” available for purchase). While a direct = comparison of the various approaches is difficult, this session = encourages submissions from researchers who can present a perspective on = the question: In drug discovery, are high information content = calculations better than low information content calculations? Topics = are not limited to the extremes of the methods, and talks are expected = to include success stories as well as failures.

Organizer:  Jennifer L. Miller, = Signature BioScience, jmilleracs@signaturebio.com

Deadline:   Abstracts for = talks must be submitted to http://oasys.acs.org/oasys.htm by 01 May 2003.



------_=_NextPart_001_01C2EE4A.8524749A-- From chemistry-request@server.ccl.net Thu Mar 20 03:07:10 2003 Received: from salmon.maths.tcd.ie ([134.226.81.11]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h2K87Ar30361 for ; Thu, 20 Mar 2003 03:07:10 -0500 Received: from turing.maths.tcd.ie by salmon.maths.tcd.ie with SMTP id ; 20 Mar 2003 08:07:10 +0000 (GMT) Date: Thu, 20 Mar 2003 08:07:10 +0000 (GMT) From: Gemma Kinsella To: chemistry@ccl.net Subject: Helical Drift Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, I am interested in measuring the helical drift of a GPCR during a molecular dynamics simulation. At the moment I am using some RMSD code to determine how much they are moving but I would also like to know in which direction. Does anyone know of a centre of mass based piece of code, or some other way of measuring this?? Many thanks, Gemma Kinsella From chemistry-request@server.ccl.net Thu Mar 20 05:37:21 2003 Received: from dove2.cf.ac.uk ([131.251.1.170]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2KAbLr13361 for ; Thu, 20 Mar 2003 05:37:21 -0500 Received: from maincf2p.cf.ac.uk ([131.251.4.71] helo=pobox.cf.ac.uk) by dove2.cf.ac.uk with esmtp (Exim 4.05) id 18vxQD-0005wK-00 for chemistry@ccl.net; Thu, 20 Mar 2003 10:37:17 +0000 Received: from cardiff.ac.uk (m114.phrm.cf.ac.uk [131.251.35.246]) by pobox.cf.ac.uk; Thu, 20 Mar 2003 10:37:15 +0000 Date: Thu, 20 Mar 2003 10:36:28 +0000 Subject: Re: CCL:Receptor modeling Content-Type: text/plain; charset=US-ASCII; format=flowed Mime-Version: 1.0 (Apple Message framework v546) From: Dimitrios Vlachakis To: chemistry@ccl.net Content-Transfer-Encoding: 7bit In-Reply-To: <73564B8DE398D61180500008C75D7E4943895B@NTMAIL03> Message-Id: X-Mailer: Apple Mail (2.546) Dear Jaya, All you need to do is to download the homolog structure from NCBI onto your machine and ask modeller to include it in its database. There is an option on the menu of importing new PDB files to Modeller's database. Import the NCBI pdb file and the next time Modeller will do the seq alignment and look for homologues in its database it will pick it up for you... hope that helps.. Dimitrios Vlachakis PhD, Med Chem Cardiff University On Wednesday, March 19, 2003, at 12:15 am, Pandey, Jaya wrote: > Hi All, > > I am trying to use MODELLER for my receptor modeling. When I look into > it I > realise I do not have a strong PDB homolog to the structure. Very short > fragments (about 2) are available in PDB. Any clue how can I model my > receptor. I do have a very strong homolog in NCBI database. Please > help! > > Jaya > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To > Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Thu Mar 20 07:24:50 2003 Received: from uni-freiburg.de ([132.230.2.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2KCOor15625 for ; Thu, 20 Mar 2003 07:24:50 -0500 Received: from [132.230.171.124] (account ) by uni-freiburg.de (CommuniGate Pro WebUser 3.5.9) with HTTP id 16461336 for ; Thu, 20 Mar 2003 13:24:48 +0100 From: "Thomas Steinbrecher" Subject: DelphiLinux Segmentation Fault To: X-Mailer: CommuniGate Pro Web Mailer v.3.5.9 Date: Thu, 20 Mar 2003 13:24:48 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: 8bit Dear CCLers, I try to calculate the electrostatic contribution to the solvation energy of a protein-ligand-complex with the Delphi program (Version 4, release 1.1 for Linux-OS) as part of a MM-PBSA-calculation with the AMBER package. My complex consists of ~4000 atoms. When I increase the SCALE parameter in the Delphi input to 4 per A (default is 2) to get a higher grid resolution, the program fails with the (not very informative) message: "Segmentation fault". (It runs fine with SCALE=2 or 3) My delphi input file is: ----- bndcon=4 scale=4 exdi=80.0 indi=1.0 linit=1000 perfil=80.0 in(crg,file="./amber94_delphi.crg") in(siz,file="./parse_delphi.siz") in(pdb) energy(s) ----- Is it possible that my system is to big for such a fine grid resolution? Has anyone seen the same Delphi failure and/or possible clues/solutions? Thank you in advance for any comments, Thomas Steinbrecher From chemistry-request@server.ccl.net Thu Mar 20 02:59:58 2003 Received: from tungsten.chem.vu.nl ([130.37.144.65]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2K7xwr30232 for ; Thu, 20 Mar 2003 02:59:58 -0500 Received: from tungsten.chem.vu.nl ([127.0.0.1]) by tungsten.chem.vu.nl (8.10.0/8.10.0) with ESMTP id h2K7wit12792 for ; Thu, 20 Mar 2003 08:58:45 +0100 (MET) Message-Id: <200303200758.h2K7wit12792@tungsten.chem.vu.nl> X-Mailer: exmh version 2.0.2 2/24/98 To: chemistry@ccl.net From: Stan van Gisbergen Subject: DFT package ADF2003.01 available now Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Date: Thu, 20 Mar 2003 08:58:44 +0100 Sender: vgisberg@tungsten.chem.vu.nl Dear CCL members, SCM proudly announces the release of version 2003.01 of ADF, the complete density functional package for chemists. New functionality with respect to version 2002.02 includes: * ADFinput, the menu-based graphical input builder for ADF * Time-dependent DFT implementation for periodic structures * Improved performance for periodic structure calculations * AddRemove link model for QM/MM calculations * Improved basis sets For more information on ADF: * download the ADF Newsletter: http://www.scm.com/News/NL0303.pdf * visit booth 1913 at the ACS expo: http://www.scm.com/acs.html * contact us for an ADF brochure * get a free trial for ADF, BAND, and ADF-Graphical User Interface. Best regards, Stan van Gisbergen, on behalf of the SCM team. http://www.scm.com E-mail: info@scm.com From chemistry-request@server.ccl.net Thu Mar 20 02:40:47 2003 Received: from pado.krict.re.kr ([203.250.2.9]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2K7ekr29728 for ; Thu, 20 Mar 2003 02:40:46 -0500 Received: from anakin ([203.250.4.112]) by pado.krict.re.kr (v3smtp 8.11.6.7/8.11.2) with ESMTP id h2K7UVj29279 for ; Thu, 20 Mar 2003 16:30:31 +0900 From: =?ks_c_5601-1987?B?sejA5bno?= To: Subject: AMBER forcefield parameter for NADH Date: Thu, 20 Mar 2003 16:40:48 +0900 Message-ID: <000001c2eeb4$081fc920$7004facb@anakin> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0001_01C2EEFF.780A7E60" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 This is a multi-part message in MIME format. ------=_NextPart_000_0001_01C2EEFF.780A7E60 Content-Type: text/plain; charset="ks_c_5601-1987" Content-Transfer-Encoding: 7bit Dear all, Does anyone have or know of a reference (persons, article, book, etc.) where I can find AMBER forcefield parameters for NADH (nicotinamide adenine dinucleotide). Thanks for any information. Jangbae * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Jangbae Kim Researcher Bio-Organic Science Division Korea Research Institute of Chemical Technology (KRICT) P.O.Box 107, Yuseong, Taejeon, 305-600, Korea TEL : +82-42-860-7067 FAX : +82-42-861-0307 E-mail : jbkim@krict.re.kr * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ------=_NextPart_000_0001_01C2EEFF.780A7E60 Content-Type: text/html; charset="ks_c_5601-1987" Content-Transfer-Encoding: quoted-printable

Dear all,

 

Does anyone have or know of a reference (persons, article, = book, etc.)

where I can find AMBER forcefield = parameters for NADH (nicotinamide adenine dinucleotide).
   

Thanks for any information.

 

Jangbae

* * = * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *

Jangbae = Kim=

Researcher     &n= bsp;           &nb= sp;           &nbs= p;            = ;       

Bio-Organic Science = Division

Korea Research Institute of Chemical = Technology (KRICT)

 

P.O.Box = 107,  Yuseong, Taejeon,

305-600, = Korea=

TEL : = +82-42-860-7067

FAX : = +82-42-861-0307

E-mail : jbkim@krict.re.kr

* * = * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *

 

------=_NextPart_000_0001_01C2EEFF.780A7E60-- From chemistry-request@server.ccl.net Thu Mar 20 18:40:02 2003 Received: from mxout2.cac.washington.edu ([140.142.33.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2KNe2r03611 for ; Thu, 20 Mar 2003 18:40:02 -0500 Received: from smtp.washington.edu (smtp.washington.edu [140.142.33.9]) by mxout2.cac.washington.edu (8.12.1+UW03.03/8.12.1+UW02.12) with ESMTP id h2KNdqva019570; Thu, 20 Mar 2003 15:39:52 -0800 Received: from u.washington.edu (konga.chem.washington.edu [128.95.128.222]) (authenticated bits=0) by smtp.washington.edu (8.12.1+UW03.03/8.12.1+UW02.12) with ESMTP id h2KNdqwa006009 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT); Thu, 20 Mar 2003 15:39:52 -0800 Message-ID: <3E7A516D.8040300@u.washington.edu> Date: Thu, 20 Mar 2003 15:40:29 -0800 From: Carsten Detering User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry@ccl.net, autodock@scripps.edu Subject: Free energy of binding in AutoDock Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi all, I was posting a similar question a while ago, however never really having resolved the problem. Obviously, the calculated free energy of binding (with 'epdb' and AutoDock being in command mode (-c flag)) seems to be dependent on the atom types allowed for the receptor (specified in autocomm.h under ATOMTYPES and in gpf3gen.awk under PROTEIN_ATOMTYPES), without some actually being present in the molecule. For different sets of allowed atom types, I get different free energies of binding (for always the same ligand and receptor; the receptor is an RNA containing the atom types CNOPH), whether I allow also Fluorine and/or Iodine, or none of the latter. When I use only CNOPH, autogrid gives a segmentation fault. The first column gives the atom types that I specified in both autocomm.h and gpf3gen.awk, followed by the EFEB extracted from the .clg file: CNOPHXM Estimated Free Energy of Binding = -8.84 kcal/mol CNOPHXMFI Estimated Free Energy of Binding = -8.74 kcal/mol CNOPHXMI Estimated Free Energy of Binding = -8.56 kcal/mol CNOPHXMIF Estimated Free Energy of Binding = -9.03 kcal/mol CNOSHXMP Estimated Free Energy of Binding = -8.39 kcal/mol CNOSHXMPI Estimated Free Energy of Binding = -8.87 kcal/mol CNOSHXMPIF Estimated Free Energy of Binding = -8.87 kcal/mol It may have just a simple explanation, but I cannot explain that to me. Thanks for any help on this, Carsten -- Carsten Detering, Ph.D. University of Washington Seattle, WA 98195 Fon 206.543.5081 Fax 206.685.8665 From chemistry-request@server.ccl.net Thu Mar 20 14:40:14 2003 Received: from hisar.cc.boun.edu.tr ([193.140.192.229]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2KJe9r28535 for ; Thu, 20 Mar 2003 14:40:12 -0500 Received: by hisar.cc.boun.edu.tr (Postfix, from userid 4210) id A85F61346; Thu, 20 Mar 2003 21:40:29 +0200 (EET) Received: from localhost (localhost [127.0.0.1]) by hisar.cc.boun.edu.tr (Postfix) with ESMTP id 9D58BFCD for ; Thu, 20 Mar 2003 21:40:29 +0200 (EET) Date: Thu, 20 Mar 2003 21:40:29 +0200 (EET) From: "Alimet S. Ozen" X-Sender: ozensem@hisar.cc.boun.edu.tr To: chemistry@ccl.net Subject: pre-reaction complexes Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL Members, We are currently performing DFT calculations in order to elucidate the mechanism of some radical reactions. There are 6-7 pathways for each substituted molecule and I am just wondering if it is possible to compare only the transition states -setting the lowest energy TS as zero and scaling the others respectively- without having to calculate the pre-reaction complexes...(most of the TSs are lower in energy than the reactants) ... just thinking that any contribution due to a pre-reaction complex actually cancels out during the calculation of the activation energy though it is still important in calculating the tunneling correction...so, comparing only the TSs will at least give some qualitative info...? I will be so glad to hear your opinions about it... Kind Regards Alimet "Real value:is not the one whose presence fills an empty space but the one whose absence creats one" Ozdemir Asaf ozensem@boun.edu.tr alimetsema@yahoo.com http://www.geocities.com/alchemistrial