From chemistry-request@ccl.net Thu Nov 13 20:11:25 2003 Received: from imo-d01.mx.aol.com (imo-d01.mx.aol.com [205.188.157.33]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAE1Ap9c029895 for ; Thu, 13 Nov 2003 20:10:52 -0500 Received: from uccajgo7^at^netscape.net by imo-d01.mx.aol.com (mail_out_v36_r1.1.) id g.2c.b493ce3 (16238) for ; Thu, 13 Nov 2003 20:10:46 -0500 (EST) Received: from netscape.net ([128.192.9.210]) by air-in03.mx.aol.com (v97.8) with ESMTP id MAILININ32-3f6e3fb42b9520c; Thu, 13 Nov 2003 20:10:45 -0500 Message-ID: <3FB42C1D.6080600^at^netscape.net> Date: Thu, 13 Nov 2003 20:13:01 -0500 From: Jorge Gonzalez User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: CHEMISTRY^at^ccl.net Subject: CCL: ACS Computational Chemistry of Carbohydrates Symposium Content-Type: multipart/alternative; boundary="------------020903010705090700050409" X-AOL-IP: 128.192.9.210 X-Mailer: Unknown (No Version) X-Spam-Status: No, hits=0.9 required=7.0 tests=HTML_30_40,HTML_MESSAGE,USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) --------------020903010705090700050409 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear Colleagues, This note is to let you know that December 2 is the deadline for abstracts for the spring 2004 ACS meeting in Anaheim CA, March 28 - Apr 1. If you wish to present a poster or make an oral presentation at the "Computational Chemistry of Carbohydrates Symposium" please submit an abstract on the ACS webpage http://oasys.acs.org/ as soon as possible. My intention is to use this symposium as a platform to illustrate not only advances in computational methods, but also to illustrate the application of these methods in experimental structural analysis. This meeting is jointly sponsored by the COMP and CARB divisions and so it should provide an excellent opportunity for experimentalists and theoreticians to discuss issues of common interest. Invited speakers have not yet been selected or contacted as that will depend heavily on the funding. So please go ahead and submit an abstract before it is past the deadline. Feel free to circulate this email among your colleagues and to contact me with requests for specific topics or speakers. Offers to contribute to funding the travel expenses for invited speakers, as well as suggestions for sources of funding are of course very welcome! During these symposia scientists present their results and of course discuss their computing needs. Sponsorship is a very good opportunity for hardware vendors to influence a significant number of active research scientists. I hope to see you there. Best wishes, Rob Woods Robert J. Woods, Ph.D. Associate Professor of Biochemistry Voice: (706) 542-4454 and Molecular Biology FAX: (706) 542-4412 University of Georgia http://glycam.ccrc.uga.edu Complex Carbohydrate Research Center 315 Riverbend Road "One small step for Man, Athens, GA 30602 one giant leap for Man-9" --------------020903010705090700050409 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit

Dear Colleagues,
 
 This note is to let you know that December 2 is the deadline for abstracts
 for the spring 2004 ACS meeting in Anaheim CA, March 28 - Apr 1.  If you
 wish to present a poster or make an oral presentation at the
 "Computational Chemistry of Carbohydrates Symposium" please submit an
 abstract on the ACS webpage http://oasys.acs.org/ as soon as possible.
 
 My intention is to use this symposium as a platform to illustrate not only
 advances in computational methods, but also to illustrate the application
 of these methods in experimental structural analysis.  This meeting is
 jointly sponsored by the COMP and CARB divisions and so it should provide
 an excellent opportunity for experimentalists and theoreticians to discuss
 issues of common interest.
 
 Invited speakers have not yet been selected or contacted as that will
 depend heavily on the funding. So please go ahead and submit an abstract
 before it is past the deadline.  
 
 Feel free to circulate this email among your colleagues and to contact me
 with requests for specific topics or speakers.
 
 Offers to contribute to funding the travel expenses for invited speakers,
 as well as suggestions for sources of funding are of course very welcome!
 During these symposia scientists present their results and of
 course discuss their computing needs.  Sponsorship is a very good
 opportunity for hardware vendors to influence a significant number of
 active research scientists.  
 
 I hope to see you there.
 
 Best wishes,
 
 Rob Woods
 
 
 Robert J. Woods, Ph.D.
 
 Associate Professor of Biochemistry          Voice: (706) 542-4454
  and Molecular Biology                     FAX: (706) 542-4412
 
 University of Georgia                http://glycam.ccrc.uga.edu
 Complex Carbohydrate Research Center      
 315 Riverbend Road                  "One small step for Man,
 Athens, GA 30602                      one giant leap for
 Man-9"

--------------020903010705090700050409-- From chemistry-request@ccl.net Thu Nov 13 15:59:03 2003 Received: from sal.ahpcrc.org (sal.ahpcrc.org [144.34.1.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hADKwW9c023454 for ; Thu, 13 Nov 2003 15:58:32 -0500 Received: from mycroft.ahpcrc.org (mycroft.ahpcrc.org [144.34.9.34]) by sal.ahpcrc.org (8.11.6/8.11.6) with ESMTP id hADKwX616436 for ; Thu, 13 Nov 2003 14:58:33 -0600 Received: from ahpcrc.org (GULL.dhcp.famu.ahpcrc.org [144.34.131.114]) by mycroft.ahpcrc.org (8.11.6/8.11.6) with ESMTP id hADKwRU30169 for ; Thu, 13 Nov 2003 14:58:27 -0600 Message-ID: <3FB3F06F.895961C8^at^ahpcrc.org> Date: Thu, 13 Nov 2003 15:58:23 -0500 From: Genzo Tanaka X-Mailer: Mozilla 4.79 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry^at^ccl.net Subject: Scanning Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-0.1 required=7.0 tests=USER_AGENT_MOZILLA_XM,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, I have a problem for relaxed scanning of torsion using PM3 in Gaussian98. My molecule has about 90 atoms. A single torsion scanning was successful. Scanning with two torsions has hardly optimized even at the first point. More specifically, the first point, which should be the starting structure since it had optimized before, could be obtained occasionally, but then an error "incomplete coordinate system" occurred: Incomplete coordinate system. Try restarting with Geom=Check Guess=Read Opt=(ReadFC,NewRedundant) Restart could optimize only a single point. I have tried both cartesian and Z-matrix input format, and loosening the convergence criteria, nothing helped at all. A similar job with 50 atoms completed scanning all assigned combinations. Does anybody give me any suggestions how to overcome this problem? My input file is attached below Thanks, Genzo *** my input file *** %nprocl=8 %Chk=conj1opttorscan #P RHF/PM3 Opt=(ModRedundant,Loose) NoSymm GFINPUT IOP(6/7=3) IOP(2/16=1) conj1 Torsion Scanning 32-42-53-76-68 (120,180 original) 0 1 C -5.629806 0.277667 0.815136 C -6.673190 -0.814308 0.915021 C -8.103200 -0.395261 1.056532 .... O 9.155696 -0.234578 2.974792 N 5.137230 1.557668 -6.584475 H 6.699645 -2.635203 0.905287 H 7.066098 -2.208875 2.588433 H 8.376042 -2.670414 1.489473 * 42 53 * R 32 42 53 76 S 5 60.0 * 53 76 * R 42 53 76 68 S 5 60.0 From chemistry-request@ccl.net Thu Nov 13 20:19:35 2003 Received: from eddings.acpub.duke.edu (eddings.acpub.duke.edu [152.3.233.76]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAE1J49c030124 for ; Thu, 13 Nov 2003 20:19:04 -0500 Received: from minerva (minerva2.lib.duke.edu [152.3.237.232]) by eddings.acpub.duke.edu (8.12.10/8.12.10/Duke-5.0.0) with SMTP id hAE1J3le015740; Thu, 13 Nov 2003 20:19:03 -0500 (EST) X-Originating-IP: 152.3.169.5 X-Mailer: MyDuke.com X-Originator-Info: jz7@acpub From: To: Subject: how to get overlap matrix in output file Date: Thu, 13 Nov 2003 20:15:24 -0500 Message-ID: <000401c3aa4c$c7e1db50$e8ed0398..at..myduke.lib.duke.edu> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Thread-Index: AcOqTMffxBVFRSI/QdKlvgTfV581+g== Content-Class: urn:content-classes:message X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=1.4 required=7.0 tests=MISSING_OUTLOOK_NAME,NO_REAL_NAME version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear all, Does anyone know how can I let Gaussian write the overlap matrix to the output file? What kind of command should I add to the input file? Urgent, please help! Thanks a lot! From chemistry-request@ccl.net Thu Nov 13 22:41:40 2003 Received: from wilson.acpub.duke.edu (wilson.acpub.duke.edu [152.3.233.69]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAE3f89c001599 for ; Thu, 13 Nov 2003 22:41:08 -0500 Received: from CONCORDIA (concordia.lib.duke.edu [152.3.237.233]) by wilson.acpub.duke.edu (8.12.10/8.12.10/Duke-5.0.0) with SMTP id hAE3f7GX012013; Thu, 13 Nov 2003 22:41:07 -0500 (EST) X-Originating-IP: 68.18.13.69 X-Mailer: MyDuke.com X-Originator-Info: jz7@acpub From: To: Subject: how to get overlap matrix in Gaussian output file Date: Thu, 13 Nov 2003 22:37:27 -0500 Message-ID: <003401c3aa60$a00d14a0$eaed0398@CONCORDIA> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Thread-Index: AcOqYKANCPakppjgR92Y2TPTqaifsQ== Content-Class: urn:content-classes:message X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=1.4 required=7.0 tests=MISSING_OUTLOOK_NAME,NO_REAL_NAME version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear all, Does anyone know how can I let Gaussian write the overlap matrix to the output file? What kind of command should I add to the input file? Urgent, please help! Thanks a lot! From chemistry-request@ccl.net Thu Nov 13 09:39:19 2003 Received: from mail.fescomail.net ([202.94.7.253]) by server.ccl.net (8.12.8/8.12.8) with SMTP id hADEch9c010233 for ; Thu, 13 Nov 2003 09:38:46 -0500 Received: (qmail 96528 invoked by uid 2000); 13 Nov 2003 22:38:56 -0000 Message-ID: <20031113223856.96527.qmail-.at.-mail.fescomail.net> From: "xiongying99" To: "CCL" Subject: CCL:about generating NAMD PSF file Date: Thu, 13 Nov 2003 22:38:56 +0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed; charset="gb2312" Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=3.3 required=7.0 tests=DEAR_SOMETHING,FROM_ENDS_IN_NUMS version=2.55 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear Sir, I tried to use NAMD program to do a MD with an enzyme. When I generate the PSF file(run a command: vmd -dispdev text -e *.pgn), I get the following error information: ----------------------------------------------------------------- ding coordinates from pdb file dpma2p.pdb for segment U Warning: failed to set coordinate for atom O ARG:363 U Warning: failed to set coordinate for atom OXT ARG:363 U Warning: failed to set coordinate for atom O1 CBX:169 U Warning: failed to set coordinate for atom O2 CBX:169 U Info: guessing coordinates for 2549 atoms (2 non-hydrogen) Warning: poorly guessed coordinates for 5 atoms (2 non-hydrogen): Warning: poorly guessed coordinate for atom HT1 ALA:35 U Warning: poorly guessed coordinate for atom HT2 ALA:35 U Warning: poorly guessed coordinate for atom HT3 ALA:35 U Warning: poorly guessed coordinate for atom OT1 ARG:363 U Warning: poorly guessed coordinate for atom OT2 ARG:363 U write: dpma.pdb is not logged in child process exited abnormally write: dpma.psf is not logged in child process exited abnormally ------------------------------------------------------------------ The program implied that it failed to set coordinate for atom O1 and O2 of CBX, OXT and O of ARG. Maybe CBX is not a residue, so I need make topology and parameter files by myself. However I am surprised why fail to set coordinate for O of ARG? The relevant data in pdb file are as follows: ------------------------------------------------------------------- ATOM 2504 N ARG A 363 41.396 15.455 11.857 1.00 48.54 ATOM 2505 CA ARG A 363 42.465 16.448 11.632 1.00100.00 ATOM 2506 C ARG A 363 42.189 17.560 10.606 1.00100.00 ATOM 2507 O ARG A 363 41.746 17.235 9.491 1.00 91.41 ATOM 2508 CB ARG A 363 43.810 15.791 11.367 1.00100.00 ATOM 2509 CG ARG A 363 44.961 16.745 11.606 1.00100.00 ATOM 2510 CD ARG A 363 46.290 16.228 11.087 1.00 99.83 ATOM 2511 NE ARG A 363 47.418 16.656 11.939 1.00100.00 ATOM 2512 CZ ARG A 363 48.684 16.372 11.632 1.00100.00 ATOM 2513 NH1 ARG A 363 49.011 15.651 10.514 1.00100.00 ATOM 2514 NH2 ARG A 363 49.680 16.805 12.467 1.00100.00 ATOM 2515 OXT ARG A 363 42.443 18.761 10.918 1.00100.00 ATOM 2516 C CBX A 169 46.148 -4.112 26.276 1.00 23.92 ATOM 2517 O1 CBX A 169 47.170 -3.732 26.821 1.00 13.49 ATOM 2518 O2 CBX A 169 45.286 -4.887 26.831 1.00 15.89 ------------------------------------------------------------------- Thank you very much! ---------------------------------------------------------------- FESCOmail.net From chemistry-request@ccl.net Fri Nov 14 07:44:52 2003 Received: from hotmail.com (bay2-dav21.bay2.hotmail.com [65.54.246.125]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAECiL9c025263 for ; Fri, 14 Nov 2003 07:44:21 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Fri, 14 Nov 2003 04:44:20 -0800 Received: from 210.22.76.10 by bay2-dav21.bay2.hotmail.com with DAV; Fri, 14 Nov 2003 12:44:20 +0000 X-Originating-IP: [210.22.76.10] X-Originating-Email: [li_zhenhua(at)hotmail.com] From: "Zhenhua Li" To: "CCL" Subject: gamess compilation Date: Fri, 14 Nov 2003 20:43:33 +0800 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_00C8_01C3AAEF.F8657450" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced 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------=_NextPart_000_00C8_01C3AAEF.F8657450-- From chemistry-request@ccl.net Fri Nov 14 01:59:12 2003 Received: from mail.fescomail.net ([202.94.7.253]) by server.ccl.net (8.12.8/8.12.8) with SMTP id hAE6wa9c009484 for ; Fri, 14 Nov 2003 01:58:38 -0500 Received: (qmail 22723 invoked by uid 2000); 14 Nov 2003 14:58:37 -0000 Message-ID: <20031114145837.22722.qmail(at)mail.fescomail.net> From: "xiongying99" To: "CCL" Subject: the problem with running the configuration of NAMD program Date: Fri, 14 Nov 2003 14:58:37 +0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed; charset="gb2312" Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=3.3 required=7.0 tests=DEAR_SOMETHING,FROM_ENDS_IN_NUMS version=2.55 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear sir, I have another question. When I run a minimization, the program stopped abnormally: REINITIALIZING VELOCITIES AT STEP 100 TO 310 KELVIN. TCL: Running for 100 steps ERROR: Constraint failure in RATTLE algorithm for atom 1551! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 1193! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 2102! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 3254! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 3120! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 3575! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 4624! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 3069! ERROR: Constraint failure; simulation has become unstable. ERROR: Exiting prematurely. ========================================== WallClock: 25.321195 CPUTime: 25.270000 Memory: 16074 kB Program finished. ============================================================================ What's wrong with my configuration? Thank you very much! YIng Xiong ---------------------------------------------------------------- FESCOmail.net From chemistry-request@ccl.net Fri Nov 14 04:19:50 2003 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAE9JD9c015756 for ; Fri, 14 Nov 2003 04:19:17 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailserver.unimi.it (iPlanet Messaging Server 5.2 Patch 1 (built Aug 19 2002)) with ESMTP id <0HOC00A1A4K2GX*at*mailserver.unimi.it> for chemistry*at*ccl.net; Fri, 14 Nov 2003 10:19:14 +0100 (MET) Received: from villa (villa.farma.unimi.it [159.149.79.66]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with SMTP id <0HOC00IM74JZ24*at*smtp.unimi.it> for chemistry*at*ccl.net; Fri, 14 Nov 2003 10:19:12 +0100 (MET) Date: Fri, 14 Nov 2003 10:21:18 +0100 From: Giulio Vistoli Subject: Re: CCL:about generating NAMD PSF file To: xiongying99 , CCL Message-id: <001301c3aa90$a8f13b20$424f959f@villa> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Mailer: Microsoft Outlook Express 6.00.2800.1158 Content-type: multipart/alternative; boundary="Boundary_(ID_p90DLk/Nv9VM+KrXSXsPFQ)" X-Priority: 3 X-MSMail-priority: Normal References: <20031113223856.96527.qmail*at*mail.fescomail.net> X-Spam-Status: No, hits=0.7 required=7.0 tests=HTML_40_50,HTML_MESSAGE,REFERENCES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. --Boundary_(ID_p90DLk/Nv9VM+KrXSXsPFQ) Content-type: text/plain; charset=gb2312 Content-transfer-encoding: 7BIT You can generate the .psf file for namd program for protein as well as small organic compounds using VEGA (www.ddl.unimi.it) Giulio Vistoli _________________________ Giulio Vistoli Istituto di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano Italia Tel. +39-02-50317545 Fax +39-02-50317565 giulio.vistoli*at*unimi.it http://www.ddl.unimi.it --Boundary_(ID_p90DLk/Nv9VM+KrXSXsPFQ) Content-type: text/html; charset=gb2312 Content-transfer-encoding: 7BIT

You can generate the .psf file for namd program for protein as well as small organic compounds using VEGA (www.ddl.unimi.it)

Giulio Vistoli

_________________________
Giulio Vistoli
Istituto di Chimica Farmaceutica e Tossicologica
Viale Abruzzi, 42
I-20131 Milano
Italia
Tel. +39-02-50317545
Fax +39-02-50317565
giulio.vistoli*at*unimi.it
http://www.ddl.unimi.it

--Boundary_(ID_p90DLk/Nv9VM+KrXSXsPFQ)-- From chemistry-request@ccl.net Fri Nov 14 02:55:28 2003 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAE7su9c011679 for ; Fri, 14 Nov 2003 02:54:57 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailserver.unimi.it (iPlanet Messaging Server 5.2 Patch 1 (built Aug 19 2002)) with ESMTP id <0HOC00A7P0NKGX*at*mailserver.unimi.it> for chemistry*at*ccl.net; Fri, 14 Nov 2003 08:54:56 +0100 (MET) Received: from heisenberg.chimica.unimi.it (heisenberg.chimica.unimi.it [159.149.240.30]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0HOC00H6N0NJL3*at*smtp.unimi.it> for chemistry*at*ccl.net; Fri, 14 Nov 2003 08:54:55 +0100 (MET) Received: by heisenberg.chimica.unimi.it (Postfix, from userid 500) id 9907B2F34C; Fri, 14 Nov 2003 09:07:01 +0100 (CET) Received: from localhost (localhost [127.0.0.1]) by heisenberg.chimica.unimi.it (Postfix) with ESMTP id 5519713B95 for ; Fri, 14 Nov 2003 09:07:01 +0100 (CET) Date: Fri, 14 Nov 2003 09:06:59 +0100 (CET) From: Alessandro Contini Subject: summary in converting .cif files To: chemistry*at*ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=ISO-8859-1 X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id hAE7tS9c011699 Hi, I'd like to thanks Rudolf Herrmann, for suggesting the program Platon http://www.cryst.chem.uu.nl/platon/pl000000.html Roberto Forlani, who suggest ViewerLite, from Accelerys. Noel O'Boyle, Jacco van de Stree, Donna Bassolino-Kl and Stephen Bowlus for their suggestions in trying mercury, from Cambridge Cryst. Database http://www.ccdc.cam.ac.uk/prods/mercury/index.html and last but not least Dimitri G. Goussev who suggest Ortep http://www.chem.gla.ac.uk/~louis/software/ortep3/index.html and thank you all for this excellent mailing list Alessandro Contini Alessandro Contini, Ph.D. Istituto di Chimica Organica "Alessandro Marchesini" Universit` degli Studi di Milano, Facolt` di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini*at*unimi.it From chemistry-request@ccl.net Fri Nov 14 15:31:42 2003 Received: from research.neu.edu (research.neu.edu [129.10.1.80]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAEKVA9c012116 for ; Fri, 14 Nov 2003 15:31:10 -0500 Received: from localhost (maryjo@localhost) by research.neu.edu with ESMTP id PAA05892 for ; Fri, 14 Nov 2003 15:31:10 -0500 (EST) X-Authentication-Warning: research.neu.edu: maryjo owned process doing -bs Date: Fri, 14 Nov 2003 15:31:10 -0500 (EST) From: Maryjo Ondrechen To: chemistry^at^ccl.net Subject: protein potential programs Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-0.4 required=7.0 tests=USER_AGENT_PINE,X_AUTH_WARNING version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello. I am making a list of programs that compute the electrical potential functions of proteins, such as finite difference or finite element Poisson- Boltzmann solvers. Please let me know of available programs. Is it commercial? Free? Available at cost? Downloadable from the web? Any comments on ease of use? Is a license required? There are many such programs out there, but I am trying to make a comprehensive list of them. Please help. I will compile the list of programs and share it with the CCL list. Thanks, Mary j.o. From chemistry-request@ccl.net Fri Nov 14 11:28:36 2003 Received: from youkai.llnl.gov (youkai.llnl.gov [134.9.187.176]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAEGS49c003200 for ; Fri, 14 Nov 2003 11:28:05 -0500 Received: from youkai.llnl.gov (localhost.localdomain [127.0.0.1]) by youkai.llnl.gov (8.12.8/8.12.5) with ESMTP id hAEGS48o014536; Fri, 14 Nov 2003 08:28:04 -0800 Received: from localhost (brian@localhost) by youkai.llnl.gov (8.12.8/8.12.5/Submit) with ESMTP id hAEGS4OG014532; Fri, 14 Nov 2003 08:28:04 -0800 Date: Fri, 14 Nov 2003 08:28:04 -0800 (PST) From: Brian Bennion To: xiongying99 cc: CCL Subject: Re: CCL:the problem with running the configuration of NAMD program In-Reply-To: <20031114145837.22722.qmail)at(mail.fescomail.net> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.4 required=7.0 tests=DEAR_SOMETHING,EMAIL_ATTRIBUTION,IN_REP_TO, QUOTED_EMAIL_TEXT,REPLY_WITH_QUOTES,SIGNATURE_LONG_DENSE, USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello you are heating the protein too fast!! Did you add the tcl libraries to your namd installation? What does your config file look like? Then I can tell you if there is something wrong with your config. I will bet that you have an unkown command error in your log file just above the errors you list below. Brian On Fri, 14 Nov 2003, xiongying99 wrote: > Dear sir, > I have another question. When I run a minimization, the program stopped > abnormally: > REINITIALIZING VELOCITIES AT STEP 100 TO 310 KELVIN. > TCL: Running for 100 steps > ERROR: Constraint failure in RATTLE algorithm for atom 1551! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1193! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 2102! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3254! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3120! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3575! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 4624! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3069! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Exiting prematurely. > ========================================== > WallClock: 25.321195 CPUTime: 25.270000 Memory: 16074 kB > Program finished. > > ============================================================================ > What's wrong with my configuration? > Thank you very much! > > YIng Xiong > > ---------------------------------------------------------------- > FESCOmail.net > > > -= 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, jkl)at(ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > -- ***************************************************************** **Brian Bennion, Ph.D. ** **Computational and Systems Biology Division ** **Biology and Biotechnology Research Program ** **Lawrence Livermore National Laboratory ** **P.O. Box 808, L-448 bennion1)at(llnl.gov ** **7000 East Avenue phone: (925) 422-5722 ** **Livermore, CA 94550 fax: (925) 422-6605 ** ***************************************************************** From chemistry-request@ccl.net Fri Nov 14 16:03:54 2003 Received: from cornell.edu (cornell.edu [132.236.56.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAEL3L9c013205 for ; Fri, 14 Nov 2003 16:03:22 -0500 Received: from dopey (dopey.ccmr.cornell.edu [128.84.241.121]) by cornell.edu (8.9.3p2/8.9.3) with SMTP id QAA26336 for ; Fri, 14 Nov 2003 16:03:22 -0500 (EST) Message-ID: <000801c3aaf2$bc786440$6400000a..at..ccmr.cornell.edu> From: "Connie Chang" To: Subject: CCL: Restarting a Freq job in Gaussian03 Date: Fri, 14 Nov 2003 16:03:21 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0005_01C3AAC8.D3836290" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=1.7 required=7.0 tests=FROM_ENDS_IN_NUMS,HTML_30_40,HTML_MESSAGE version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------=_NextPart_000_0005_01C3AAC8.D3836290 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi -- My freq job in G03 was interrupted and I tried to restart it, but when I = did, the job completed really quickly (too quicky) and didn't give any = meaningful numbers (meaning, it gave me nan's) for the frequency. Why = is this happening? Isn't it possible to restart frequency jobs? My = original route looks like: #PM3 SCF=3D(MaxCyc=3D2000) SCF=3DQC IOp(4/21=3D20,4/21=3D200) = Geom=3DCheck Guess=3DRead Freq Test And my job was interrupted by someone turning rebooting the computer at = this point: =20 SE2nd: IAtom=3D 44 IXYZ=3D2 IS=3D2. SE2nd: IAtom=3D 44 IXYZ=3D3 IS=3D1. SE2nd: IAtom=3D 44 IXYZ=3D3 IS=3D2. SE2nd: IAtom=3D 45 IXYZ=3D1 IS=3D1. SE2nd: IAtom=3D 45 IXYZ=3D1 IS=3D2. SE2nd: IAtom=3D 45 IXYZ=3D2 IS=3D1. SE2nd: IAtom=3D 45 IXYZ=3D2 IS=3D2. SE2nd: IAtom=3D 45 which I believe are the last steps in the PM3 Freq calculation. =20 Then I tried restarting the job using Freq=3Drestart and the calculation = finishes within 5 minutes whereas I know the calculation needs more time = than that and the output doesn't give me any real frequencies... Any help would be appreciated... Thanks, Connie ------=_NextPart_000_0005_01C3AAC8.D3836290 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi --

My freq job in G03 was interrupted and = I tried to=20 restart it, but when I did, the job completed really quickly (too = quicky) and=20 didn't give any meaningful numbers (meaning, it gave me nan's) for the=20 frequency. Why is this happening? Isn't it possible to = restart=20 frequency jobs? My original route looks like:

#PM3 SCF=3D(MaxCyc=3D2000) SCF=3DQC = IOp(4/21=3D20,4/21=3D200)=20 Geom=3DCheck Guess=3DRead Freq Test

And my job was interrupted by someone = turning=20 rebooting the computer at this point:

SE2nd: IAtom=3D 44 IXYZ=3D2 = IS=3D2.
SE2nd:=20 IAtom=3D 44 IXYZ=3D3 IS=3D1.
SE2nd: IAtom=3D 44 IXYZ=3D3 = IS=3D2.
SE2nd:=20 IAtom=3D 45 IXYZ=3D1 IS=3D1.
SE2nd: IAtom=3D 45 IXYZ=3D1 = IS=3D2.
SE2nd:=20 IAtom=3D 45 IXYZ=3D2 IS=3D1.
SE2nd: IAtom=3D 45 IXYZ=3D2 = IS=3D2.
SE2nd:=20 IAtom=3D 45

which I believe are the last steps in = the PM3 Freq=20 calculation.

Then I tried restarting the job using = Freq=3Drestart=20 and the calculation finishes within 5 minutes whereas I know the = calculation=20 needs more time than that and the output doesn't give me any real=20 frequencies...

Any help would be = appreciated...

Thanks,

Connie

------=_NextPart_000_0005_01C3AAC8.D3836290-- From chemistry-request@ccl.net Fri Nov 14 15:17:56 2003 Received: from adenine.cgl.ucsf.edu (socrates.cgl.ucsf.edu [169.230.27.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAEKHP9c011538 for ; Fri, 14 Nov 2003 15:17:25 -0500 Received: from localhost (socrates.cgl.ucsf.edu [169.230.27.3]) by adenine.cgl.ucsf.edu (8.12.10/8.12.10/GSC1.16) with ESMTP id hAEKHJhH968293 for ; Fri, 14 Nov 2003 12:17:24 -0800 (PST) Date: Fri, 14 Nov 2003 12:17:19 -0800 (PST) From: Pradipta Bandyopadhyay To: chemistry..at..ccl.net Subject: MD code with potential truncation!! Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, Does anyone have a simple Molecular dynamics code which truncates the potential and shifts (ideally for a three point rigid molecule, e.g. TIP3P)? I know it exists in various large programs - but I am looking for just an illustrative code. Any help would be appreciated. Pradipta From chemistry-request@ccl.net Fri Nov 14 11:47:12 2003 Received: from lgdx04.lg.ehu.es (lgdx04.lg.ehu.es [158.227.1.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAEGkd9c003932 for ; Fri, 14 Nov 2003 11:46:41 -0500 Received: by lgdx04.lg.ehu.es id RAA0000026077; Fri, 14 Nov 2003 17:46:28 +0100 (MET) Message-ID: <01a201c3aace$d951afa0$222fe39e=at=lc.ehu.es> From: "Pablo Vitoria" To: "Zhenhua Li" , "CCL" References: Subject: Re: CCL:gamess compilation Date: Fri, 14 Nov 2003 17:46:27 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_019F_01C3AAD7.3AEB5E20" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=1.9 required=7.0 tests=HTML_40_50,HTML_MESSAGE,REFERENCES,UPPERCASE_25_50 version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------=_NextPart_000_019F_01C3AAD7.3AEB5E20 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: quoted-printable Hi, I compiled Gamess (version 3July2003R2) with ifc 7.1 and did not observe = that behaviour. Which optimization flags did you use? In my dual Xeon I = either '-tpp7 -O2 -xW' or '-tpp7 -O3' worked fine, but '-tpp7 -O3 -xW' = although much faster gave wrong results with some of the exam files. Besides, if you want to get rid of the 'FLUSH--FAILED:: Bad address' = messages, you should change line 428 of the file unport.src from '*F2C = CALL FLUSH(LUNIT)' to 'C---*F2C CALL FLUSH(LUNIT)'. Best regards Pablo -------------------------------------------------------- Pablo Vitoria Garcia Dpto. Qu=A8=AAmica Inorg=A8=A2nica, Facultad de Ciencias Universidad del Pa=A8=AAs Vasco (UPV/EHU) Aptdo. 644 48080 Bilbao (Bizkaia) Tfno. 94 6015992 Fax. 94 4648500 ----- Original Message -----=20 From: Zhenhua Li=20 To: CCL=20 Sent: Friday, November 14, 2003 1:43 PM Subject: CCL:gamess compilation Dear Listers, I am compiling the gamess(US) under Redhat 8.0 with intel fortran = compiler 7.1. I successfully compiled it. It runs well for HF = calculations. But when I tried to run CI jobs, such as the exam09 and = exam33 provided by gamess source. The job failed with error message: STEP CPU TIME =3D 0.12 TOTAL CPU TIME =3D 0.2 ( 0.0 = MIN) TOTAL WALL CLOCK TIME=3D 0.6 SECONDS, CPU UTILIZATION IS = 42.86% FLUSH--FAILED:: Bad address FLUSH--FAILED:: Bad address 170758 WORDS OF DYNAMIC MEMORY USED FLUSH--FAILED:: Bad address FLUSH--FAILED:: Bad address EXECUTION OF GAMESS TERMINATED NORMALLY Fri Nov 14 20:36:58 2003 FLUSH--FAILED:: Bad address FLUSH--FAILED:: Bad address = = =20 DATA SERVER STATS: TOTAL DISTRIBUTED MEMORY USED (MEMDDI)=3D 0 = MWORDS. FIRST DATA SERVER'S MAXIMUM MEMORY=3D 0 WORDS, CPU=3D = 0.0 SECONDS. = = =20 ddikick: all processes have ended gracefully. Seems the problem is with the dynamic memory allocation.=20 Have anyone met such problems before?=20 Zhenhua Li Chem. Dept. of Fudan University Shanghai, China ------=_NextPart_000_019F_01C3AAD7.3AEB5E20 Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: quoted-printable

Hi,

I compiled Gamess (version = 3July2003R2) with=20 ifc 7.1 and did not observe that behaviour. Which optimization flags did = you=20 use? In my dual Xeon I either '-tpp7 -O2 -xW' or '-tpp7 -O3' worked = fine, but=20 '-tpp7 -O3 -xW' although much faster gave wrong results with some of the = exam=20 files.

Besides, if you want to get rid of the=20 'FLUSH--FAILED:: Bad address' messages, you should change line 428 of = the file=20 unport.src from '*F2C CALL FLUSH(LUNIT)' to 'C---*F2C CALL=20 FLUSH(LUNIT)'.

Best regards

Pablo

--------------------------------------------------------
Pablo = Vitoria=20 Garcia
Dpto. Qu=A8=AAmica Inorg=A8=A2nica, Facultad de = Ciencias
Universidad del Pa=A8=AAs=20 Vasco (UPV/EHU)
Aptdo. 644
48080 Bilbao (Bizkaia)

Tfno. 94 6015992
Fax. 94 4648500

----- Original Message -----
From:=20 Zhenhua=20 Li
To: CCL

Sent: Friday, November 14, 2003 = 1:43=20 PM

Subject: CCL:gamess = compilation

Dear Listers,

I am compiling the gamess(US) under Redhat 8.0 = with intel=20 fortran compiler 7.1. I successfully compiled it. It runs well for HF=20 calculations. But when I tried to run CI jobs, such as the exam09=20 and exam33 provided by gamess source. The job failed with = error=20 message:

STEP CPU TIME =3D     = 0.12 TOTAL CPU=20 TIME =3D        0.2 = (    0.0=20 MIN)
TOTAL WALL CLOCK = TIME=3D       =20 0.6 SECONDS, CPU UTILIZATION IS 42.86%
FLUSH--FAILED:: Bad=20 address
FLUSH--FAILED:: Bad = address
     =20 170758 WORDS OF DYNAMIC MEMORY USED
FLUSH--FAILED:: Bad=20 address
FLUSH--FAILED:: Bad address
EXECUTION OF GAMESS = TERMINATED=20 NORMALLY Fri Nov 14 20:36:58 2003
FLUSH--FAILED:: Bad=20 address
FLUSH--FAILED:: Bad=20 = address
          &n= bsp;           &nb= sp;           &nbs= p;            = ;            =             &= nbsp;           &n= bsp;           &nb= sp;           &nbs= p;            = ;            =             &= nbsp;          =20
DATA SERVER STATS: TOTAL DISTRIBUTED MEMORY USED=20 (MEMDDI)=3D       0 MWORDS.
FIRST = DATA SERVER'S=20 MAXIMUM=20 = MEMORY=3D          &nbs= p; =20 0 WORDS, CPU=3D     0.0=20 = SECONDS.
          &= nbsp;           &n= bsp;           &nb= sp;           &nbs= p;            = ;            =             &= nbsp;           &n= bsp;           &nb= sp;           &nbs= p;            = ;            =            =20
ddikick: all processes have ended gracefully.

Seems the problem is with the dynamic memory = allocation.=20

Have anyone met such problems before? =

Zhenhua Li

Chem. Dept. of Fudan University

Shanghai, China

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