From chemistry-request@ccl.net Fri Sep 3 09:04:36 2004 Received: from gamma.dou.dk (gamma.dou.dk [130.225.156.12]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i83E4YcI009069 for ; Fri, 3 Sep 2004 09:04:35 -0500 Received: from webmail (webmail.sdu.dk [130.226.194.3]) by gamma.dou.dk (8.9.3/8.9.3) with ESMTP id QAA04574; Fri, 3 Sep 2004 16:13:45 +0200 (METDST) X-WebMail-UserID: hjj)at(chem.sdu.dk Date: Fri, 3 Sep 2004 16:19:08 +0200 Sender: "Hans J=?ISO-8859-1?Q?=F8rgen?= Aa. Jensen" From: "Hans J=?ISO-8859-1?Q?=F8rgen?= Aa. Jensen" To: chemistry)at(ccl.net X-EXP32-SerialNo: 00002380 Subject: Release of DIRAC04 Message-ID: <413545F4@webmail> Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: 7bit X-Mailer: WebMail (Hydra) SMTP v3.61 X-Spam-Status: No, hits=0.0 required=7.5 tests=RM_ft_Iso8859 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net It is a pleasure to announce that DIRAC04, the new release of "Dirac, a relativistic ab initio electronic structure program" is now ready for download. The new release has been tested on various architectures and will run significantly faster than the 3.2 release. Some of the most important features are listed below. Methods available: - Hartree-Fock - Density Functional Theory - Coupled Cluster - Configuration Interaction - Moeller-Plesset Perturbation Theory Hamiltionians available: - Dirac-Coulomb (includes all spin-orbit coupling and scalar relativistic effects) - spinfree Dirac-Coulomb (scalar relativistic effects only) - Levy-Leblond (nonrelativistic) Molecular properties: - Up to quadratic response properties at the Hartree-Fock level of theory - First order properties with DFT and MP2 Efficiency: - Full symmetry handling for linear molecules (otherwise up to D2h) - Parallelization using MPI library calls (MPI should be preinstalled) Users who would like to obtain DIRAC04 can download and complete the new licence agreement that is now available at our website, http://dirac.chem.sdu.dk. On behalf of the Dirac author group, H. J. Aa. Jensen T. Saue L. Visscher From chemistry-request@ccl.net Fri Sep 3 04:43:19 2004 Received: from eos.fwall.u-szeged.hu (eos.fwall.u-szeged.hu [160.114.120.248]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i839hHcI024379 for ; Fri, 3 Sep 2004 04:43:18 -0500 Received: from localhost ([127.0.0.1] helo=eos.fwall.u-szeged.hu) by eos.fwall.u-szeged.hu with smtp (Exim 4.34) id 1C3AkF-0007EC-S5 for chemistry(at)ccl.net; Fri, 03 Sep 2004 11:52:35 +0200 Received: from eos.fwall.u-szeged.hu ([127.0.0.1]) by eos.fwall.u-szeged.hu (SAVSMTP 3.1.0.29) with SMTP id M2004090311523501729 for ; Fri, 03 Sep 2004 11:52:35 +0200 Received: from mail.szote.u-szeged.hu ([160.114.96.63]) by eos.fwall.u-szeged.hu with esmtp (Exim 4.34) id 1C3AkF-0007E9-Lo for chemistry(at)ccl.net; Fri, 03 Sep 2004 11:52:35 +0200 Received: from ovrisc.mdche.u-szeged.hu (IDENT:qmailr(at)ovrisc.mdche.u-szeged.hu [160.114.101.224]) by mail.szote.u-szeged.hu (8.9.3/8.8.7) with SMTP id LAA24723 for ; Fri, 3 Sep 2004 11:52:34 +0200 Received: (qmail 18489 invoked by uid 525); 3 Sep 2004 09:52:35 -0000 Received: from localhost (sendmail-bs@127.0.0.1) by localhost with SMTP; 3 Sep 2004 09:52:35 -0000 Date: Fri, 3 Sep 2004 11:52:35 +0200 (CEST) From: "Dr. Csaba Hetenyi" To: chemistry(at)ccl.net Subject: Re: CCL:predict 3D structure from sequence (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-SZTE-local: YES X-SZTE-AVcheck: YES X-Spam-Status: No, hits=5.0 required=7.5 tests=COMBINED_FROM,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net > The first one called Camparative Protein Modeling, which requires a 3d > structure of a protein, which has >30% sequence Similarity comparing to > target. It's pretty reliable. The second approach has lower success > rate.. I'd rather not say "it is pretty reliable". In my view, sequence similarity (30 % or above) is not a sufficient only a necessary requirement of possible homology modeling (HM). A "nice" example of failure of HM was recently mentioned in Williams et al. Science 305 (2004) 683-686. E.g. CYPs are "excellent" examples of proteins not appropriate for HM. Extensive, uncontrolled use of HM (or - horribile dictu - HM and consecutive docking on a HMed target contributes to rising (and - in this case - right) scepticism of experimental guys against modeling (against us). Sorry, if i was too negative concerning HM. Best wishes, Csaba From chemistry-request@ccl.net Thu Sep 2 12:31:06 2004 Received: from mx1.tripos.com (mx1.tripos.com [192.160.145.7]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i82HV59C007341 for ; Thu, 2 Sep 2004 12:31:05 -0500 Message-ID: From: "Paul Hawkins" To: "'LEDM \(Leonardo De Maria\)'" , Date: Thu, 2 Sep 2004 13:40:18 -0400 Subject: RE: octanol-water partition coefficient calculations for peptides/small proteins MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="--=_NextPart_ST_12_39_54_Thursday_September_02_2004_356" X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4925.2800 In-Reply-To: <76F96CFE2AA2114C886B028A065A7FC4023DE626*at*exdkba020.novo.dk> Thread-Index: AcSQ6XI1UowADAeHTSCRMoB1lDMc9gAKls2Q X-eShield-AntiVirus: Passed X-eShield-AntiVirus-Message: Scanned by http://www.bluecoat.com/eShield X-Spam-Status: No, hits=4.3 required=7.5 tests=HTML_60_70,HTML_FONTCOLOR_BLUE, HTML_FONT_BIG,HTML_MESSAGE,MIME_BOUND_NEXTPART,MK_BAD_HTML_16, YM_USELESS_U autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ----=_NextPart_ST_12_39_54_Thursday_September_02_2004_356 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Leonardo, Try HINT! from Glen Kellogg at VCU .http://www.eslc.vabiotech.com/hint/ Paul. _____ From: Computational Chemistry List [mailto:chemistry-request*at*ccl.net] On Behalf Of LEDM (Leonardo De Maria) Sent: Thursday, September 02, 2004 8:36 AM To: CHEMISTRY*at*ccl.net Subject: CCL:octanol-water partition coefficient calculations for peptides/small proteins Hi out there, can anyone point my attention to software to calculate the octanol-water partition coefficient calculations of peptides/small proteins (10-40 amino acids) besides PLOGP? It will be appreciated if they use 3D information for that purpose. Regards, Leonardo De Maria, PhD Novozymes A/S Research Scientist Brudelysvej 26 Bygning 1U.S25 Protein Design 2880 Bagsveard Molecular Biotechnology Denmark +45 44421890 direct +45 44980246 fax LeDM*at*novozymes.com www.novozymes.com ----=_NextPart_ST_12_39_54_Thursday_September_02_2004_356 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable CCL: octanol-water partition coefficient calculations fo= r peptides/small proteins
Leonardo,
 
Try HINT! from Glen Kellogg at VCU
 
 
·http://www.eslc.vabiotech.com/= hint/=20
 
 
Paul.

From: Computational Chemistry List=20 [mailto:chemistry-request*at*ccl.net] On Behalf Of LEDM (Leonardo De Maria)
Sent: Thursday, September 02, 2004 8:36 AM
To: CHEMISTRY*at*ccl.net
Subject: CCL:octanol-water partition coefficien= t=20 calculations for peptides/small proteins

Hi out there,

can anyone point my attention to sof= tware to=20 calculate the
octanol-water = partition=20 coefficient calculations of
peptides/small proteins (10-40 amino acids) besides PLOGP? =

It will be appreciated if they use 3= D=20 information for that
purpose= =2E=20

Regards,

Leonardo De Maria,= PhD =20 Novozymes A/S
Research Scientist
Brudelysvej 26 =20        =20         Bygning 1U.S25=20
P= rotein=20 Design         =20         2880 Bagsveard
Molecular Biotechnology=20         Denmark        =20        
        +45 44421890 direct
        +45 44980246 fax     &nbs= p; =20
LeDM*at*novozymes.com     =20         www.novozymes.com

----=_NextPart_ST_12_39_54_Thursday_September_02_2004_356-- From chemistry-request@ccl.net Thu Sep 2 22:35:01 2004 Received: from mx.seanet.com (mx.seanet.com [199.181.164.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i833Yx9C030991 for ; Thu, 2 Sep 2004 22:34:59 -0500 Received: from pepeketua.seanet.com (pepeketua.seanet.com [199.181.164.73]) by milkyway.seanet.com (8.12.11/8.12.11) with ESMTP id i833iDHJ053960 for ; Thu, 2 Sep 2004 20:44:17 -0700 (PDT) Received: from planaria (c-24-18-170-25.client.comcast.net [24.18.170.25]) by pepeketua.seanet.com (Postfix) with ESMTP id 478CED7 for ; Thu, 2 Sep 2004 20:44:13 -0700 (PDT) Reply-To: From: "Mark Thompson" To: Subject: Limits on number of rotatable bonds in ArgusDock? Date: Thu, 2 Sep 2004 20:44:11 -0700 Message-ID: <003901c49168$46672e50$0200a8c0@planaria> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.6604 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 Importance: Normal X-Spam-Status: No, hits=2.6 required=7.5 tests=RCVD_IN_DYNABLOCK, RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I've been asked by more than one user if there is a limit on the number of rotatable bonds for docking molecules using the ArgusDock engine. The short answer is : no There is no fundamental limit in the program for max torsions, or the like. However, I have not extensively tested drugs with numbers of rotatable bonds > 30. There may be some combinations of these ultra large drugs with large shallow binding sites on the surfaces of proteins that make ArgusDock choke....let me know if you find any. This is one reason I put the GADock code into ArgusLab alongside the ArgusDock engine. GADock is pretty robust and you might find it works well for some cases. The ArgusDock engine has been rung-out extensively on hundreds of test cases, but I would still classify it as a work in progress simply because it's not yet had widespread use from the general community. Cheers, Mark ********************************* Mark Thompson Planaria PO Box 55207 Seattle, WA 98155 voice: 206.240.4769 FAX: 206.440.3305 mark*at*planaria-software.com http://www.planaria-software.com ********************************* From chemistry-request@ccl.net Thu Sep 2 17:22:43 2004 Received: from MM01SNLNTO.son.sandia.gov (mm01snlnto.sandia.gov [132.175.109.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i82MMf9C019537 for ; Thu, 2 Sep 2004 17:22:42 -0500 Received: from 132.175.109.1 by MM01SNLNTO.son.sandia.gov with ESMTP ( Tumbleweed MMS SMTP Relay 01 (MMS v5.6.1)); Thu, 02 Sep 2004 16:31:49 -0600 X-Server-Uuid: C223CCCD-D7BD-4D0E-A874-9ACF7D7E7905 Received: from singsing.sandia.gov (sadl17668.sandia.gov [134.253.242.21]) by sass165.sandia.gov (8.12.10/8.12.10) with ESMTP id i82MVkf2003669; Thu, 2 Sep 2004 16:31:47 -0600 (MDT) Received: from singsing.sandia.gov (localhost.localdomain [127.0.0.1]) by singsing.sandia.gov (8.12.11/8.12.11) with ESMTP id i82MRrH1027540; Thu, 2 Sep 2004 16:27:53 -0600 Received: (from sjplimp@localhost) by singsing.sandia.gov ( 8.12.11/8.12.11/Submit) id i82MRrQZ027536; Thu, 2 Sep 2004 16:27:53 -0600 Date: Thu, 2 Sep 2004 16:27:53 -0600 Message-ID: <200409022227.i82MRrQZ027536-.at.-singsing.sandia.gov> From: "Steven J. Plimpton" To: chemistry-.at.-ccl.net Subject: LAMMPS, an open-source molecular dynamics code cc: sjplimp-.at.-sandia.gov X-PMX-Version: 4.6.1.107272, Antispam-Core: 4.6.1.106808, Antispam-Data: 2004.9.2.2 MIME-Version: 1.0 X-WSS-ID: 6D2940DF14K4664169-01-01 Content-Type: text/plain Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net For those interested in classical molecular dynamics (MD) simulation, we've released a new version of LAMMPS, our open-source parallel MD code, which is available for download on the WWW. It has several features which may be of interest to you: (1) It combines the force fields and features of several of our previous parallel MD codes. Thus it can simulate atomic systems, polymers, metals, proteins or other biomolecules, granular materials, etc. (2) It's written in C++, and is designed to allow for easy modification and extension, yet preserves the speed and scalability of the earlier F77 & F90 versions. (3) It's portable to any parallel platform that uses MPI. It also runs on single-processor boxes. Here are the relevant URLs: www.cs.sandia.gov/~sjplimp/lammps.html (LAMMPS WWW site) www.cs.sandia.gov/~sjplimp/download.html (download page) www.cs.sandia.gov/~sjplimp/lammps/doc/Manual.html (on-line documentation) Thanks, Steve Plimpton Sandia National Labs sjplimp-.at.-sandia.gov From chemistry-request@ccl.net Thu Sep 2 15:42:29 2004 Received: from smtp.goldrush.com (smtp.goldrush.com [206.171.171.11]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i82KgS9C016217 for ; Thu, 2 Sep 2004 15:42:28 -0500 Received: from COMPAQ1800T (x2-04-40.goldrush.com [64.162.10.40]) by smtp.goldrush.com (8.12.8/8.12.8) with SMTP id i82KpWZj030603; Thu, 2 Sep 2004 13:51:33 -0700 From: "Steve Bowlus" To: "Jeff C" , Subject: RE: Queries: GAMESS-UK and 3D QSAR Date: Thu, 2 Sep 2004 13:51:28 -0700 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4927.1200 Importance: Normal In-Reply-To: <20040902134700.61994.qmail.-at-.web25108.mail.ukl.yahoo.com> X-MailScanner: Found to be clean X-MailScanner-SpamCheck: X-MailScanner-From: chezbowlus.-at-.goldrush.com X-Spam-Status: No, hits=0.3 required=7.5 tests=FVGT_s_OBFU_Q1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net SOMFA2 is free, but I don't know how efficient: http://bellatrix.pcl.ox.ac.uk/Downloads/ Commercial programs which may be affordable to academics, but pricey to industry are CoMFA (Tripos), MFA and/or Catalyst (Accelrys). Both programs are widely used and there is a good literature base determine whether they may be useful to you. Hopfinger's 4D-QSAR (www.SeascapeLearning.com) is also available for IRIX, maybe Linux. A bit more compute-intensive but worth it for some problems. sb > -----Original Message----- > From: Computational Chemistry List [mailto:chemistry-request.-at-.ccl.net]On > Behalf Of Jeff C > Sent: Thursday, September 02, 2004 6:47 AM > To: chemistry.-at-.ccl.net > Subject: CCL:Queries: GAMESS-UK and 3D QSAR > > > Dear CCL scientists, > > I am a novice who is currently learning GAMESS-UK. Can > someone please tell me what is the silly mistake I am > making when after my calculation is completed, I can t > find the optimised atomic coordinates. I know this > must be trivial to most of you but your input would > really help me tremendously. In addition, can any one > also please kindly tell me what is the most affordable > (yet efficient) 3D QSAR software used in drug design. > > > Much appreciated. > > Best regards > > Jeff > > > > > > > ___________________________________________________________ALL-NEW > Yahoo! Messenger - all new features - even more fun! http://uk.messenger.yahoo.com -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY.-at-.ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST.-at-.ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow.-at-.nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Fri Sep 3 09:38:33 2004 Received: from chemaxon.hu (90.156-228-195.hosting.adatpark.hu [195.228.156.90]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i83EcTcI012662 for ; Fri, 3 Sep 2004 09:38:30 -0500 Received: from [10.0.0.149] (246.124-182-adsl-pool.axelero.hu [81.182.124.246]) by chemaxon.hu (8.12.8/8.12.8) with ESMTP id i83Ellmd009357; Fri, 3 Sep 2004 16:47:48 +0200 Message-ID: <4138840C.5090407-.at.-chemaxon.com> Date: Fri, 03 Sep 2004 16:47:40 +0200 From: Alex Allardyce Reply-To: aa-.at.-chemaxon.com User-Agent: Mozilla Thunderbird 0.7 (Windows/20040616) X-Accept-Language: en-us, en MIME-Version: 1.0 To: CHEMISTRY-.at.-ccl.net, chemweb-.at.-ic.ac.uk Subject: ChemAxon free chemistry software via Academic Package - Instructions, conditions and online application area is opened Content-Type: multipart/alternative; boundary="------------000107060905090909030500" X-Spam-Status: No, hits=4.3 required=7.5 tests=HTML_MESSAGE,HTML_TITLE_EMPTY, MY_DSL,RCVD_IN_DYNABLOCK,RCVD_IN_SORBS,YM_USELESS_B autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. --------------000107060905090909030500 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Good day, Further to our previous communication "ChemAxon announces free software for the academic community via the JChem and Marvin Academic Package", I write to announce that the online application area has been opened. Instructions, conditions, online application form as well as a questions and comments forum are available. *Links:* Instructions, conditions and online application form : http://www.chemaxon.hu/forum/ftopic193.html Academic Package license forum topic: http://www.chemaxon.hu/forum/forum20.html *Software tools covered in the Academic Package;* * *Marvin *for editing and viewing chemical structures, reactions and queries, * *Calculator Plugins* for prediction of various properties based on structure (pKa, logP, logD, H-bond aceptor/donor, etc), * *JChem Base* for structure and reaction searching and database handling, * *JChem Cartridge* for Oracle. database integration, * *Standardiser* for structure canonisation, * *Reactor *for structure transformations and virtual synthesis, * *Screen *for pharmacophore and structure based screening, * *JKlustor* for clustering and diversity analysis, * we are also currently completing our toolkit for *drug design*. **Please circulate this information to relevant colleagues and online/print communities. Thank you -- Alex Allardyce Communications Director Chemaxon Ltd Maramaros kvz 3/a Budapest, 1037 Hungary Tel.: +361 4532658 Fax.: +361 4532659 e-mail: aa-.at.-chemaxon.com --------------000107060905090909030500 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Good day,

Further to our previous communication "ChemAxon announces free software for the academic community via the JChem and Marvin Academic Package", I write to announce that the online application area has been opened. Instructions, conditions, online application form as well as a questions and comments forum are available.

Links:
Instructions, conditions and online application form : http://www.chemaxon.hu/forum/ftopic193.html
Academic Package license forum topic: http://www.chemaxon.hu/forum/forum20.html

Software tools covered in the Academic Package;
  • Marvin for editing and viewing chemical structures, reactions and queries,
  • Calculator Plugins for prediction of various properties based on structure (pKa, logP, logD, H-bond aceptor/donor, etc),
  • JChem Base for structure and reaction searching and database handling,
  • JChem Cartridge for Oracle® database integration,
  • Standardiser for structure canonisation,
  • Reactor for structure transformations and virtual synthesis,
  • Screen for pharmacophore and structure based screening,
  • JKlustor for clustering and diversity analysis,
  • we are also currently completing our toolkit for drug design.
Please circulate this information to relevant colleagues and online/print communities.

Thank you
-- 
Alex Allardyce
Communications Director

Chemaxon Ltd
Máramaros köz 3/a
Budapest, 1037 Hungary
Tel.: +361 4532658
Fax.: +361 4532659

e-mail: aa-.at.-chemaxon.com
--------------000107060905090909030500--