From chemistry-request@ccl.net Mon Jul 21 20:26:35 2003 Received: from upstate.edu (gw4.upstate.edu [139.127.9.87]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6M0QZjq028728 for ; Mon, 21 Jul 2003 20:26:35 -0400 Received: from HSCHOSP-MTA by upstate.edu with Novell_GroupWise; Mon, 21 Jul 2003 20:26:20 -0400 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.4 Beta Date: Mon, 21 Jul 2003 20:25:49 -0400 From: "Michael Chen" To: Subject: SHAKE problem. Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi, guys, I ran a multi-processor job in use of SHAKE, and I got tons of bizzar messages like this: ERROR in SHAKEA. Contraints spanning parallel partition ignored. Would someone please tell me what was going on? Was this because of hardware things or software things? My CHARMM still kept running, but those messages were so annoying. Thank you very much. Have a nice day. ***************************************************** Michael Chen Department of Biochemistry & Pharmacology SUNY Upstate Medical University 750 East Adams Street Syracuse, NY 13210 USA ***************************************************** From chemistry-request@ccl.net Tue Jul 22 03:55:59 2003 Received: from iris.chimfarm.unipg.it (iris.chimfarm.unipg.it [141.250.13.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6M7tsjq011459 for ; Tue, 22 Jul 2003 03:55:57 -0400 Received: from apollo.chimfarm.unipg.it ([141.250.13.72] helo=apollo) by iris.chimfarm.unipg.it with esmtp (Exim 2.04 #2) id 19f0QQ-0000FB-00 for chemistry~at~ccl.net; Tue, 22 Jul 2003 09:55:42 -0700 From: "Daniele Bellocchi" To: Subject: ONIOM calculation Date: Tue, 22 Jul 2003 09:55:55 +0200 Message-ID: <000001c35026$aeaf9df0$480dfa8d@apollo> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0001_01C35037.72386DF0" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0001_01C35037.72386DF0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear All, i performed a two layers ONIOM calculation (AM1:amber) on a complex enzyme-substrate. The problem that i have is that AMBER requires all the parameters for the ligand, even though the ligand belongs to the QM shell. Is there any ways to circonvent this problem? Thanks in advance. Daniele Bellocchi, PhD Student Molecular Modeling Section Istituto di Chimica e Tecnologia del Farmaco University of Perugia Italy bellocks~at~chimfarm.unipg.it ------=_NextPart_000_0001_01C35037.72386DF0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear = All,

i performed a two = layers ONIOM calculation (AM1:amber) on a complex enzyme-substrate. The problem = that i have is that AMBER requires all the parameters for the ligand, even = though the ligand belongs to the QM shell.

 Is there any ways to circonvent = this problem?

Thanks<= font size=3D2 face=3DArial> in advance.

 

 

Daniele Bellocchi, PhD = Student

Molecular Modeling Section

Istituto di Chimica e Tecnologia del Farmaco

University of = Perugia

Italy

bellocks~at~chimfarm.unipg.it

 

------=_NextPart_000_0001_01C35037.72386DF0-- From chemistry-request@ccl.net Mon Jul 21 17:45:09 2003 Received: from red.CACheSoftware.com ([12.17.172.66]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6LLj9jq023961; Mon, 21 Jul 2003 17:45:09 -0400 Received: from DAVEG-LIFEBOOK.cachesoftware.com (netscreen.cachesoftware.com [12.17.172.74]) by red.CACheSoftware.com (8.11.6/8.9.3/3) with ESMTP id h6LLjCk06025; Mon, 21 Jul 2003 14:45:12 -0700 Message-Id: <5.2.1.1.0.20030721142733.015f3ac8~at~mail.cachesoftware.com> X-Sender: daveg~at~mail.cachesoftware.com (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.2.1 Date: Mon, 21 Jul 2003 14:41:48 -0700 To: chemistry~at~ccl.net From: David Gallagher Subject: CCL:Structure Guided Drug Discovery Seminars Cc: chemistry-request~at~ccl.net Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_23181633==.ALT" --=====================_23181633==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Seminar Announcement (2nd notice): Structure Guided Drug Discovery with Molecular Modeling 1. Discovering Asparagine Synthetase Inhibitors using Molecular Modeling 2. Active-Site Identification, Ligand Design, Docking, & QSAR 3. Demonstration of new BioMedCAChe 6.0 for Windows Abstracts & further info: http://www.cachesoftware.com/sem/ Venues and Dates (August 2003): San Diego, CA Monday, August 4th, pm San Francisco, CA Tuesday, August 5th, am Cincinnati, OH Wednesday, August 6th, am Philadelphia, PA Thursday, August 7th, am Princeton, NJ Thursday, August 7th, pm Boston, MA Friday, August 8th, am Sponsored by CAChe Group, Fujitsu For free registration contact Kristin at sales~at~cachesoftware.com (1 503 746 3602) --=====================_23181633==.ALT Content-Type: text/html; charset="us-ascii"             Seminar  Announcement (2nd notice):

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1. Discovering Asparagine Synthetase Inhibitors using Molecular Modeling
2. Active-Site Identification, Ligand Design, Docking, & QSAR
3. Demonstration of new BioMedCAChe 6.0 for Windows

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(1 503 746 3602)




--=====================_23181633==.ALT-- From chemistry-request@ccl.net Tue Jul 22 08:59:44 2003 Received: from webmail.mta.ca (rash.mta.ca [138.73.1.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6MCxhjq023501 for ; Tue, 22 Jul 2003 08:59:43 -0400 Received: from nobody by webmail.mta.ca with local (Exim 4.04) id 19ewkI-0004WA-00 for chemistry|at|ccl.net; Tue, 22 Jul 2003 09:59:58 -0300 Received: from 138.73.24.161 ( [138.73.24.161]) as user srwhttl|at|mailserv.mta.ca by webmail.mta.ca with HTTP; Tue, 22 Jul 2003 09:59:58 -0300 Message-ID: <1058878798.3f1d354ebe024|at|webmail.mta.ca> Date: Tue, 22 Jul 2003 09:59:58 -0300 From: srwhttl|at|mta.ca To: chemistry|at|ccl.net Subject: Unknown ONIOM error. MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Originating-IP: 138.73.24.161 CCL, I am trying to run an two layered ONIOM calculation on an emzyme using B3LYP 6- 31+G(d,p):PM3. However, the calculation dies after is has read in the input and the error message is the following: GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. Initialization pass. Optmz1 allocation failure: iend,mxcore=1294987819 16252928 Error termination via Lnk1e in /usr/local/gaussian/g03/l103.exe at Mon Jul 21 18:11:33 2003. Job cpu time: 0 days 0 hours 3 minutes 16.6 seconds. File lengths (MBytes): RWF= 12 Int= 0 D2E= 0 Chk= 1 Scr= 1 Thanking in advance for any feedback, Sarah Whittleton Mount Allison University, New Brunswick, Canada From chemistry-request@ccl.net Tue Jul 22 12:29:23 2003 Received: from kafka.net.nih.gov (mailfwd.nih.gov [165.112.130.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6MGTNjq032685 for ; Tue, 22 Jul 2003 12:29:23 -0400 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by kafka.net.nih.gov (8.12.9/8.12.9) with ESMTP id h6MGTMx9006729; Tue, 22 Jul 2003 12:29:22 -0400 (EDT) Date: Tue, 22 Jul 2003 11:52:47 -0400 From: Rick Venable To: Michael Chen cc: chemistry(at)ccl.net Subject: Re: CCL:SHAKE problem. In-Reply-To: Message-ID: References: ReplyTo: Rick_Venable(at)nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 21 Jul 2003, Michael Chen wrote: > I ran a multi-processor job in use of SHAKE, and I got tons of > bizzar messages like this: > > ERROR in SHAKEA. Contraints spanning parallel partition ignored. > > Would someone please tell me what was going on? Was this because of > hardware things or software things? My CHARMM still kept running, but > those messages were so annoying. It means you are attempting to apply SHAKE to bonds between heavy atoms, e.g. C-C bonds, which is a problem for parallel usage. The constraint is not applied (ignored) for any case where the 2 atoms have been partitioned onto separate processors. A more typical usage of SHAKE is SHAKE BONH PARAM where only bonds to H atoms are constrained (to their parameter length); the atom partioning scheme always keeps H atoms in the same partition as the heavy atom they are bonded to, so the above error message should not occur. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable(at)nih.gov ALT email: rvenable(at)speakeasy.org ------------------------------------- "Don't blame me, I voted for Kang." Homer =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@ccl.net Tue Jul 22 11:23:04 2003 Received: from mail.uvigo.es (mail.uvigo.es [193.146.32.91]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6MFN3jq029485 for ; Tue, 22 Jul 2003 11:23:04 -0400 Received: from mail.uvigo.es (localhost [127.0.0.1]) by mail.uvigo.es (8.12.9/8.12.1) with ESMTP id h6MFMwej015875 for ; Tue, 22 Jul 2003 17:22:58 +0200 Received: from correo.uvigo.es (correo.uvigo.es [193.146.32.68]) by mail.uvigo.es (8.12.9/8.12.1) with ESMTP id h6MFMv0T015869 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Tue, 22 Jul 2003 17:22:58 +0200 Received: from correo (correo [193.146.32.68]) by correo.uvigo.es (8.12.9/8.12.5) with ESMTP id h6MFMv6B019592 for ; Tue, 22 Jul 2003 17:22:57 +0200 Date: Tue, 22 Jul 2003 17:22:57 +0200 (CEST) From: Faza Olalla Nieto X-X-Sender: To: Subject: Gaussian error Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, Anyone knows what the following error message mean? "Inverted reduced A of dimension 334 with in-core refinement. Not enough memory in AlgDDF. Error termination via Lnk1e in /usr/local//g98/linda-exe/l1002.exel." And what can I do to eliminate it, of course. Thank you in advance. Regards, Olalla Nieto Faza Dpto. Quimica Organica Universidade de Vigo Lagoas-Marcosende 36200 Vigo (Spain) e-mail: faza_at_uvigo.es From chemistry-request@ccl.net Tue Jul 22 11:19:55 2003 Received: from hpserv.imim.es (hpserv.imim.es [193.144.6.104]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6MFJsjq029370 for ; Tue, 22 Jul 2003 11:19:55 -0400 Received: by hpserv.imim.es with Internet Mail Service (5.5.2656.59) id ; Tue, 22 Jul 2003 17:24:10 +0200 Message-ID: <10708933FD0CD511BCFE000102BE5F72761222_at_hpserv.imim.es> From: =?iso-8859-1?Q?=22Teran_Casta=F1on=2C_Hugo_Gutierrez_de=22?= To: "'Peter Zwart '" , "'Pedro Antonio Reche '" Cc: "'ccp4bb_at_dl.ac.uk '" , "'chemistry_at_ccl.net '" Subject: RE: [ccp4bb]: modeling inhibitor in groove Date: Tue, 22 Jul 2003 17:24:03 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2656.59) Content-Type: text/plain; charset="iso-8859-1" Hi Peter, You can overlay the proposed inhibitor to the crystallographic inhibitor on the basis of molecular electrostatic potential (MEP) or GRID generated molecular interaction fields (MIF) with the software MIPSIM (http://www1.imim.es/modeling/mipsim/index.html). With the best superposition choosen, you can simply replace one inhibitor with the other one and carry on your simmulations. Good luck, Hugo -----Original Message----- From: Peter Zwart To: Pedro Antonio Reche Cc: ccp4bb_at_dl.ac.uk; chemistry_at_ccl.net Sent: 21/07/2003 3:14 Subject: CCL:[ccp4bb]: modeling inhibitor in groove > > Hi, I have a PDB of a kinase in complex with a inhibitor, and I would > like to replace that inhibitor with a related compound. I have > already generated a PDB file for this compound but I do not I have > to proceed, and thereby any input about the software (better if unix > open source), and strategy to replace the original inhibitor with > this related compound will be greatly appreciated. Also, does anyone > know of a software to overlay 3D structures of small molecules? I am > thinking that overlaying the derivative compound with the inhibitor > in the 3D structure of the kinase would be a possibility, but what > software to use?! > Anyway, any idea, or suggestion about best way to solve this problem > will be greatly appreciated. > Cheers You could give MOLREP a try, the manual says: ------------------------------------------------------------------------ ----------------------------------------- Fitting two models (FM) The idea is to fit the electron densities instead of the atomic models, trying to find the best overlap. Advantages are: * can be used for cases with very low homology; * can be used when amino acid sequence is absent; * no need to use the list of equivalent atoms. If you define only two files of models (searching model and model_2), without a file of structure factors (Fobs), the program will fit the search model (keyword FILE_M ) to the second model (keyword MODEL_2 ). The search model must be smaller or equal to the second model. ------------------------------------------------------------------------ ----------------------------------------- No clue how to handle (large) conformational differences though. Or soak and solve maybe ? Peter Zwart This e-mail was scanned by RAV Antivirus. (www.ravantivirus.com) -= This is automatically added to each message by 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, jkl_at_ccl.net (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Tue Jul 22 11:08:12 2003 Received: from ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6MF87jq028865 for ; Tue, 22 Jul 2003 11:08:12 -0400 Received: from mumbai.ks.uiuc.edu (mumbai.ks.uiuc.edu [130.126.120.104]) by ks.uiuc.edu (8.12.9/8.11.2) with ESMTP id h6MF87Vn009689 for ; Tue, 22 Jul 2003 10:08:07 -0500 (CDT) Received: from localhost (emad@localhost) by mumbai.ks.uiuc.edu (8.11.6/8.9.3) with ESMTP id h6MF87417518 for ; Tue, 22 Jul 2003 10:08:07 -0500 X-Authentication-Warning: mumbai.ks.uiuc.edu: emad owned process doing -bs Date: Tue, 22 Jul 2003 10:08:07 -0500 (CDT) From: Emad Tajkhorshid To: computational Chemistry List Subject: Spartan ESP charge calculation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Does anybody know what scheme (Merz-Kollman, Chelp, ChelpG, ...) is used by Spartan to choose points at which the electrostatic potential will be calculated and used for generating ESP charges? I could not find any explanation for such details in the help of the program. Thanx Emad ------------------ Emad Tajkhorshid, Ph.D. http://www.ks.uiuc.edu/~emad Assistant Director of Research NIH Resource for Macromolecular Modeling and Bioinformatics Theoretical and Computational Biophysics Group Beckman Institute, 405 N. Mathews, Urbana, IL 61801, USA Tel:(217)244-4361 Fax:(217)244-6078 Email: emad_at_ks.uiuc.edu From chemistry-request@ccl.net Tue Jul 22 13:34:22 2003 Received: from exasp.biogeo.uw.edu.pl (gate.biogeo.uw.edu.pl [212.87.8.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6MHYGjq003744 for ; Tue, 22 Jul 2003 13:34:20 -0400 Received: from localhost (localhost.localdomain [127.0.0.1]) by exasp.biogeo.uw.edu.pl (Postfix) with ESMTP id E969C15E3C for ; Tue, 22 Jul 2003 19:34:24 +0200 (CEST) Received: by exasp.biogeo.uw.edu.pl (Postfix, from userid 526) id 41CDD15E1D; Tue, 22 Jul 2003 19:34:23 +0200 (CEST) Date: Tue, 22 Jul 2003 19:34:23 +0200 From: Grzegorz Bakalarski To: CHEMISTRY|at|ccl.net Subject: CCL: g03 and opteron Message-ID: <20030722173423.GA32261|at|exasp.biogeo.uw.edu.pl> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4i X-Virus-Scanned: by AMaViS snapshot-20020300 Dear All, Has anybody tried to compile g03 on opteron machine either 32 bit or 64 bit using pgf77 (32 or 64 bit) or intel (32 bit) ? Any suggestions and maybe some benchmarks or comparisions to xeon based machine ? Kind regards, GB From chemistry-request@ccl.net Tue Jul 22 14:21:51 2003 Received: from sentinel.ucr.edu (sentinel.ucr.edu [138.23.226.228]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6MILpjq006973 for ; Tue, 22 Jul 2003 14:21:51 -0400 Received: from dopetec (dunn4470.ucr.edu [138.23.156.82]) by sentinel.ucr.edu (Mirapoint Messaging Server MOS 3.2.1-GA) with ESMTP id ANV07807; Tue, 22 Jul 2003 11:21:46 -0700 (PDT) Reply-To: From: "Donald Keidel" To: Cc: Subject: CCL: Summary of pka database for carboxylic acids Date: Tue, 22 Jul 2003 11:21:44 -0700 Organization: UCR Message-ID: <000001c3507e$1ae62e60$529c178a@dopetec> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.3416 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 I want to thank everyone for their responses and suggestions. I ended up using ACD Labs prediction software and I am currently developing a binding affinity prediction equation with this information and other data. Sorry that the summary took so long to post, but I noticed today that I never did it and had all the e-mails marked as unread. Thank you again. Don ------------------------------------------------------------------------ --------------------------------------- Donald J. Keidel University of California, Riverside Department of Biochemistry and Molecular Biology Riverside, CA 92521 phone: (909) 787-5493 fax: (909) 787-4434 dopetec~at~dslextreme.com webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm