From chemistry-request@server.ccl.net Thu Jan 2 08:49:28 2003 Received: from typhoeus.chem.york.ac.uk ([144.32.72.225]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h02DnR900361 for ; Thu, 2 Jan 2003 08:49:27 -0500 Received: from ysbl.york.ac.uk (rasher [144.32.20.17]) by typhoeus.chem.york.ac.uk (8.11.6+Sun/8.11.6) with ESMTP id h02DnRm14573 for ; Thu, 2 Jan 2003 13:49:28 GMT Sender: greaves@ysbl.york.ac.uk Message-ID: <3E144367.1821EAED@ysbl.york.ac.uk> Date: Thu, 02 Jan 2003 13:49:27 +0000 From: Richard Greaves Reply-To: greaves@ysbl.york.ac.uk Organization: York Structural Biology Laboratory X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: buried waters in UHBD calculations Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I am trying to run UHBD pKa calculations on a protein structure that contains several buried water molecules. Whereabouts in the input coordinates should these waters appear if I do not want to explicitly titrate them? Should they be considered as being part of the polypeptide chain with which they are associated? When I run these calculations UHBD outputs core files but continues to execute ( but doesn't terminate correctly ). Could this be caused by the waters being incorrectly set up in the calculation? (I also get some error messages about using a non-standard floating point mode which I have been unable to resolve) Richard Greaves. From chemistry-request@server.ccl.net Thu Jan 2 10:07:42 2003 Received: from mail.mersin.edu.tr ([193.255.128.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h02F7c901924 for ; Thu, 2 Jan 2003 10:07:41 -0500 Received: from localhost (localhost.mersin.edu.tr [127.0.0.1]) by mail.mersin.edu.tr (Postfix) with ESMTP id 95B4A1DE for ; Thu, 2 Jan 2003 17:24:17 +0200 (EET) Received: from 10.0.6.34 (localhost.mersin.edu.tr [127.0.0.1]) by mail.mersin.edu.tr (Postfix) with SMTP id D651C197 for ; Thu, 2 Jan 2003 17:24:16 +0200 (EET) Message-ID: X-Mailer: BasiliX 1.1.0 -- http://basilix.org X-SenderIP: 10.0.6.34 Date: Thu, 02 Jan 2003 17:24:16 EET From: Reply-To: haticecan@mersin.edu.tr Subject: Restart to CASSCF-MP2 To: chemistry@ccl.net X-Virus-Scanned: by AMaViS perl-11 Dear CCL Members, How can I restart to CASSCF (Nroot= 2) with MP2=Full calculations by using G98? When I used the following route line, it seems that it is not restart . My route line is like below: #T CAS(16,12,NRoot=2)/3-21G* Guess=Read MP2=Full # SCF=Restart Geom=Check Charge Many thanks and kind regards, Hatice From chemistry-request@server.ccl.net Thu Jan 2 09:27:00 2003 Received: from mailstudenti.unimi.it ([159.149.10.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h02ER0901142 for ; Thu, 2 Jan 2003 09:27:00 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailstudenti.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0H8300HNXC4TWR@mailstudenti.unimi.it> for chemistry@ccl.net; Thu, 02 Jan 2003 15:26:54 +0100 (MET) Received: from heisenberg (heisenberg.chimica.unimi.it [159.149.240.30]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0H83002DKC4UWP@smtp.unimi.it> for chemistry@ccl.net; Thu, 02 Jan 2003 15:26:54 +0100 (MET) Date: Thu, 02 Jan 2003 15:29:36 +0100 From: Alessandro Contini Subject: Phosphotyrosyne Parameters for Amber To: CCL Message-id: <200301021529.36276.alessandro.contini@unimi.it> Organization: Istituto di Chimica Organica "Alessandro Marchesini" MIME-version: 1.0 Content-type: text/plain; charset=iso-8859-15 User-Agent: KMail/1.4.3 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h02ER0901143 Hi, does anybody knows if Phosphotyrosine has been parametrized for using it as a modified residue in amber? Thanks for the Help Alessandro -- Dott. Alessandro Contini Istituto di Chimica Organica "Alessandro Marchesini" Facoltà di Farmacia Università degli Studi di Milano Via Venezian, 21 20133 Milano Tel. +390250314480 Fax +390250314476 http://users.unimi.it/istchimorg/pagconthtm.htm From chemistry-request@server.ccl.net Wed Jan 1 23:57:09 2003 Received: from yangtze.hku.hk ([147.8.148.244]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h024v8913280 for ; Wed, 1 Jan 2003 23:57:08 -0500 Received: from localhost (lhhu@localhost) by yangtze.hku.hk (8.11.6/8.9.3) with ESMTP id h0259hJ12928 for ; Thu, 2 Jan 2003 13:09:51 +0800 Date: Thu, 2 Jan 2003 13:09:43 +0800 (HKT) From: Hu LiHong To: chemistry@ccl.net Subject: Calculate Heat of formation by Guassian98 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all, Happy new year! I'd like to use Guassian to calculate the heat of formation of some compounds. I am using DFT method and basis set 6-311G(d,p) to optimize the structures and calculate the frequency. After checking the website of www.gaussion.com, I used the formula for calculating the enthalpy of formation, it is a little complicated but I found the result of enthalpy of formation have large difference from experimental values. I don't know what's wrong with it? Who can tell me 1) whether I can use the formula in the website 2) what should be noticed when I am using it 3) if there is other easier method to calculate the enthalpy of formation by using the energy calculated by Guassian 98? I'll appreciate you very much Cheer, Yours, Carol From chemistry-request@server.ccl.net Thu Jan 2 11:10:55 2003 Received: from smtp01.sohu.com ([61.135.132.105]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h02GAr903578 for ; Thu, 2 Jan 2003 11:10:54 -0500 Received: from pak3 (unknown [140.232.202.227]) by smtp01.sohu.com (Postfix) with ESMTP id 863945367A for ; Thu, 2 Jan 2003 23:43:38 +0800 (CST) Message-ID: <031e01c2b279$5d1bb8c0$e3cae88c@pak3> From: "Alan Leo" To: References: <3E144367.1821EAED@ysbl.york.ac.uk> Subject: FLEXX error message from ligand MOL2 read Date: Thu, 2 Jan 2003 11:09:27 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Hi, All: I am using FLEXX evalution now, but when I input the ligand minimization mol2 file, the following error messgae is appeared: _____________________________________________ FLEXX> lig FLEXX/LIGAND> read TSB_min >> DATA ERROR: No molecules found. [occured in line 126 of file TSB_min] Segmentation fault (core dumped) _____________________________________________ I have three question: 1. I don't know if there is any newsgroup related to FLEXX except chemweb newsgroup. 2. The error message above point out the error of my sybyl mol2 file error, or maybe it is because of other reasons. 3. Should I minimize the ligand structure before I generate the *_min.mol2 file? Which software I should use? Don't peng me, I am a newbie. :) Your help is much appreciated.. Best, Alan From chemistry-request@server.ccl.net Thu Jan 2 14:03:11 2003 Received: from smtp01.sohu.com ([61.135.132.105]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h02J37906592 for ; Thu, 2 Jan 2003 14:03:09 -0500 Received: from pak3 (unknown [140.232.202.227]) by smtp01.sohu.com (Postfix) with ESMTP id BE7E25352B for ; Fri, 3 Jan 2003 02:35:53 +0800 (CST) Message-ID: <033a01c2b291$6c173ee0$e3cae88c@pak3> From: "Alan Leo" To: Subject: FLEXX error message from ligand MOL2 read Date: Thu, 2 Jan 2003 14:01:49 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Hi, All: I am using FLEXX evalution now, but when I input the ligand minimization mol2 file, the following error messgae is appeared: _____________________________________________ FLEXX> lig FLEXX/LIGAND> read TSB_min >> DATA ERROR: No molecules found. [occured in line 126 of file TSB_min] Segmentation fault (core dumped) _____________________________________________ I have three question: 1. I don't know if there is any newsgroup related to FLEXX except chemweb newsgroup. 2. The error message above point out the error of my sybyl mol2 file error, or maybe it is because of other reasons. 3. Should I minimize the ligand structure before I generate the *_min.mol2 file? Which software I should use? Don't peng me, I am a newbie. :) Your help is much appreciated.. Best, Alan From chemistry-request@server.ccl.net Thu Jan 2 16:21:22 2003 Received: from pilsener.srv.ualberta.ca ([129.128.5.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h02LLM909438 for ; Thu, 2 Jan 2003 16:21:22 -0500 Received: from webmail.ualberta.ca (webmail.srv.ualberta.ca [129.128.5.105]) by pilsener.srv.ualberta.ca (8.12.6/8.12.6) with ESMTP id h02LLLSE028353 for ; Thu, 2 Jan 2003 14:21:21 -0700 (MST) X-WebMail-UserID: tluchko Date: Thu, 2 Jan 2003 14:22:07 -0700 Sender: tluchko From: tluchko To: chemistry@ccl.net X-EXP32-SerialNo: 00003228 Subject: CHARMM: GTP and GDP parameters Message-ID: <3E165239@webmail.ualberta.ca> Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: 7bit X-Mailer: WebMail (Hydra) SMTP v3.61.08 Hello, I am trying to come up with some parameters for GTP and GDP bound to tubulin for the CHARMM27 parameter set. My hope is to use ATP and ADP as a starting point, however, I have run into two problems. The first is that CHARMM does not seem to like the ATP/ADP parameters themselves. I get errors such as : No angle parameters for 5 ( ON6B CN7 CN8 ) : A TOTAL OF 5 MISSING PARAMETERS ***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( -2) IS NOT REACHED. WRNLEV IS 5 CHECKDH> dihedral : 1 28 31 32 will NOT be generated Is there something wrong with the parameters? If these parameters are supposed to be missing for ADP/ATP why is this correct? The second problem is with the charge distribution. GTP/GDP binds to tubulin in two places in each monomer (according to the pdb). This means removing four hydrogens per dimer and gives a non-integer net charge for the system. what methods/tools can I use to redistribute the correct charge among the remaining atoms? Thank you, Tyler -- ############################################################################## >< Tyler Luchko Masters Student >< >< Deparment of Physics 780-492-5519 >< >< University of Alberta tluchko@ualberta.ca >< >< Edmonton, Alberta, Canada p442a >< ############################################################################## From chemistry-request@server.ccl.net Thu Jan 2 19:09:24 2003 Received: from mailrelay1.lanl.gov ([128.165.4.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0309N912478 for ; Thu, 2 Jan 2003 19:09:24 -0500 Received: from swan.lanl.gov (localhost.localdomain [127.0.0.1]) by mailrelay1.lanl.gov (8.12.3/8.12.3/(ccn-5)) with ESMTP id h0309N9i023136; Thu, 2 Jan 2003 17:09:23 -0700 Received: from heron.lanl.gov (heron.lanl.gov [128.165.96.39]) by swan.lanl.gov (8.12.1/8.12.1) with ESMTP id h0307roR016115; Thu, 2 Jan 2003 17:07:53 -0700 Received: from localhost (tamulis@localhost) by heron.lanl.gov (8.12.1/8.12.1) with ESMTP id h02H1p3t008161; Thu, 2 Jan 2003 10:01:51 -0700 Date: Thu, 2 Jan 2003 10:01:51 -0700 (MST) From: "Temporary Guest Account;CNLS;7-1444;9999999" To: cc: Subject: Coordinates of fullerene C68 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, Would you please to send me coordinates of few more stable isomers of fullerene C68 or say where I can find these coordinates. Thanking your in advance, Arvydas Tamulis Temporal address until 28 February 2003: Los Alamos National Laboratory Center for Nonlinear Studies P.O. Box 1663, Mail Stop B258 Los Alamos, New Mexico 87545 Work Phone: (505) 667-7278 Fax: (505) 665-2659 e-mail: tamulis@cnls.lanl.gov From chemistry-request@server.ccl.net Thu Jan 2 20:13:15 2003 Received: from TheWorld.com ([199.172.62.103]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h031DF913206 for ; Thu, 2 Jan 2003 20:13:15 -0500 Received: from vaio.theworld.com (1Cust221.tnt12.bos10.da.uu.net [63.17.121.221]) by TheWorld.com (8.9.3/8.9.3) with ESMTP id UAA04363 for ; Thu, 2 Jan 2003 20:13:10 -0500 Message-Id: <5.1.0.14.1.20030102202556.026005d0@pop.theworld.com> X-Sender: jle@pop.theworld.com X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Thu, 02 Jan 2003 20:27:24 -0500 To: chemistry@ccl.net From: Joe Leonard Subject: Single vs. Double precision/forcefields Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Folks, Has anybody done, or does anybody have pointers to a study on the effect of precision on forcefield energies and/or gradients? This would be most interesting on Intel and/or AMD chipsets (which seem to prefer single-precision up through P-III's)... Note to language bigots, please replace single/double precision with float/doubles as necessary :-). Happy new year to all! Joe P.S. I would also be interested in learning of any groups doing work on internal data representations of chemical entites, and how this would relate to how codes are written in the future... From chemistry-request@server.ccl.net Thu Jan 2 22:17:24 2003 Received: from web20414.mail.yahoo.com (web20402.mail.yahoo.com [66.163.169.90]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with SMTP id h0317gj12984 for ; Thu, 2 Jan 2003 20:07:42 -0500 (EST) Message-ID: <20030103010741.80283.qmail@web20414.mail.yahoo.com> Received: from [202.185.66.42] by web20402.mail.yahoo.com via HTTP; Thu, 02 Jan 2003 17:07:41 PST Date: Thu, 2 Jan 2003 17:07:41 -0800 (PST) From: Juraina Jamil Subject: Autodoc: ERROR - energy is infinite To: chemistry@ccl.net I received an error saying "eval.cc: ERROR! energy is infinite" and another saying "eval.cc: ERROR! energy is not a number" in the autodock output file that's followed by a list of atoms in the ligand designated as INF or NaN. Why is this so? Though the errors are there, autodock is running fine. Someone asked on sidechains flexibility of protein during docking before and I understood that it's not possible with autodock but is it possible to have only a certain range of residues to have such flexibility? And if not, what other available docking softwares that would be able to do just that? Best wishes for 2003, Juraina __________________________________________________ Do you Yahoo!? Yahoo! Mail Plus - Powerful. Affordable. Sign up now. http://mailplus.yahoo.com