From chemistry-request@ccl.net Mon Sep 6 07:12:39 2004 Received: from smtp.dmbr.UGent.be (dmbr242.fvms.ugent.be [157.193.189.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i86CCbaG008201 for ; Mon, 6 Sep 2004 07:12:38 -0500 Received: from [157.193.200.22] (dmbr015.fvms.ugent.be [157.193.200.22]) by smtp.dmbr.UGent.be (Postfix) with ESMTP id 93E758003C; Mon, 6 Sep 2004 14:22:07 +0200 (CEST) Message-ID: <413C5672.5070701)at(dmbr.ugent.be> Date: Mon, 06 Sep 2004 14:22:10 +0200 From: Dominique Vlieghe User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.7.2) Gecko/20040803 X-Accept-Language: en-us, en MIME-Version: 1.0 To: "Dr. Csaba Hetenyi" Cc: chemistry)at(ccl.net Subject: Re: CCL:predict 3D structure from sequence (fwd) References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.9 required=7.5 tests=MY_BAD_DOT autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dr. Csaba Hetenyi wrote: >>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). > > Sadly, I must say from personal experience I agree with you, but the problem remains that one often has to homology model a given receptor, because a xray/nmr structure is lacking. We as end-users of docking algorithms cannot wait for the experimental structures, because it is almost always the case that the crystal structure is one of the last pieces of information that is available (i.e. an experimental validation of a certain protein-ligand interaction has been published before the structures are known). Does this mean that computational docking is not useful in a practical sense? And what do you think about high-throughput homology modeling set-ups (ModBase,...)? Regards Dominique >Sorry, if i was too negative concerning HM. >Best wishes, >Csaba > > > > >-= 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) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > -- ------------------------------------------------------------------------ Save the Hubble petition: http://www.savethehubble.org ------------------------------------------------------------------------ Dominique Vlieghe, Ph.D., Bioinformatics Core, Department for Molecular Biomedical Research (DMBR) VIB - Ghent University Technologiepark 927, B-9052 Ghent (Zwijnaarde), Belgium ------------------------------------------------------------------------ email: dominique.vlieghe)at(dmbr.ugent.be tel: +32-(0)9-33-13.693 www: http://www.dmbr.ugent.be/ fax: +32-(0)9-33-13.609 ------------------------------------------------------------------------ From chemistry-request@ccl.net Mon Sep 6 05:26:31 2004 Received: from jello277.jellocom.de (jello277.jellocom.de [217.17.194.152]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i86AQTaG026641 for ; Mon, 6 Sep 2004 05:26:30 -0500 Received: from imb-jena.de ([62.180.96.103]) (authenticated bits=0) by jello277.jellocom.de (8.12.11/8.12.9) with ESMTP id i86AZwB8013406 for ; Mon, 6 Sep 2004 12:35:59 +0200 Message-ID: <413C3D8E.AA214AED)at(imb-jena.de> Date: Mon, 06 Sep 2004 12:35:58 +0200 From: "Felipe Pineda, PhD" X-Mailer: Mozilla 4.73 [de] (Windows NT 5.0; U) X-Accept-Language: de MIME-Version: 1.0 To: chemistry)at(ccl.net Subject: Re: CCL:predict 3D structure from sequence (fwd) X-Priority: 1 (Highest) References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=4.4 required=7.5 tests=MY_BAD_DOT,NO_RDNS2, X_PRIORITY_HIGH autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear Csaba and all, "Dr. Csaba Hetenyi" wrote: > > 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. According to your own necessary/sufficient conditions this wouldn't be a good example, since the authors state that templates available for comparative modeling of CYP3A4 display just sequence identities < 30% with the target. On p. 684 you can read: "The most widely used templates for modeling CYP3A4 are the P450 structures from Bacillus megaterium (P450 BM3) and Saccharopolyspora erythraea (P450 EryF), both of which share less than 25% sequence identity with CYP3A4." Without the intension of self-advertising, I can refer you to our (Hillisch, A., Pineda, L.F. and Hilgenfeld, R.) recent paper published on DDT 9(2004)659-669 on the utility of homology models in the drug discovery process, wich contains a, in our opinion, balanced discussion on the performance of the comparative modeling method in different applications. Best regards Felipe From chemistry-request@ccl.net Mon Sep 6 07:00:27 2004 Received: from mailer.gwdg.de (mailer.gwdg.de [134.76.10.26]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i86C0QaG007547 for ; Mon, 6 Sep 2004 07:00:27 -0500 Received: from vrlab03.mpibpc.gwdg.de ([134.76.211.99] helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 4.42) id 1C4IJo-00080C-Fg for chemistry!at!ccl.net; Mon, 06 Sep 2004 14:09:56 +0200 Message-ID: <413C5391.7030102!at!mpi-bpc.mpg.de> Date: Mon, 06 Sep 2004 14:09:53 +0200 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CCL List Subject: Gaussian 03 termination Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: (clean) by exiscan+sophie X-Spam-Status: No, hits=1.9 required=7.5 tests=IMPRONONCABLE_1,MY_BAD_DOT autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCLers, Has anybody experience gaussian termination with the following error? Error termination request processed by link 9999. Error termination via Lnk1e in /usr/product/gaussian/g03/l9999.exe at Mon Sep 6 05:29:58 2004. Job cpu time: 0 days 5 hours 16 minutes 31.4 seconds. File lengths (MBytes): RWF= 30 Int= 0 D2E= 0 Chk= 11 Scr= 1 If yes could somebody tell me what can be the reason for this happening? My input is a Z-matrix file (I checked it and everything is fine with it) #P hf/6-31G* Opt=Tight SCF(Conver=8) Test Thank you very much in advance for advices vlad -- Vlad Cojocaru Max Planck Institute for Biophysical Chemistry Department: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1327 e-mail: Vlad.Cojocaru!at!mpi-bpc.mpg.de home tel: ++49-551-9963204 From chemistry-request@ccl.net Mon Sep 6 08:05:20 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 i86D5JaG013064 for ; Mon, 6 Sep 2004 08:05:19 -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 1C4JKV-0000aJ-BM for chemistry..at..ccl.net; Mon, 06 Sep 2004 15:14:43 +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 M2004090615144222462 for ; Mon, 06 Sep 2004 15:14:42 +0200 Received: from mail.szote.u-szeged.hu ([160.114.96.63]) by eos.fwall.u-szeged.hu with esmtp (Exim 4.34) id 1C4JKV-0000ae-89 for chemistry..at..ccl.net; Mon, 06 Sep 2004 15:14:43 +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 PAA01266 for ; Mon, 6 Sep 2004 15:14:38 +0200 Received: (qmail 8894 invoked by uid 525); 6 Sep 2004 13:14:38 -0000 Received: from localhost (sendmail-bs@127.0.0.1) by localhost with SMTP; 6 Sep 2004 13:14:38 -0000 Date: Mon, 6 Sep 2004 15:14:38 +0200 (CEST) From: "Dr. Csaba Hetenyi" To: Dominique Vlieghe cc: chemistry..at..ccl.net Subject: Re: CCL:predict 3D structure from sequence (fwd) In-Reply-To: <413C5672.5070701..at..dmbr.ugent.be> 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 > Does this mean that computational docking is not > useful in a practical sense? No, docking can be validated for a target and it is reliable if validated. I prefer using X-ray structures as targets during docking. If no measured structure is available, HM may be the way to get something like the real target could be. Of course, quality of the model depends on information used for building it. In some cases, e.g. in case of smaller, peptide-like targets spectroscopic methods (IR, NMR, CD) could provide some info on secondary structure or constraints, which could be used for HM or de novo model building. Similarity between biological activities of a known and HMed protein could also help. > And what do you think about high-throughput > homology modeling set-ups (ModBase,...)? However, there is no appropriate scheme for HM which could be used for any proteins and automated HM seems a dream for me. Validation is my central problem with HM. Proteins can be so different even within a family, that there is no surety of the precison of the model of an unknown protein. It would be interesting to collect more opinions on this topic to make a clear picture of HM. Best wishes, Csaba From chemistry-request@ccl.net Mon Sep 6 06:02:09 2004 Received: from apate.telenet-ops.be (apate.telenet-ops.be [195.130.132.57]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i86B27aG032132 for ; Mon, 6 Sep 2004 06:02:08 -0500 Received: from localhost (localhost.localdomain [127.0.0.1]) by apate.telenet-ops.be (Postfix) with SMTP id 97296248102 for ; Mon, 6 Sep 2004 13:11:37 +0200 (MEST) Received: from splashing.agr.kuleuven.ac.be (d51521AC4.kabel.telenet.be [81.82.26.196]) by apate.telenet-ops.be (Postfix) with ESMTP id 29B51248083 for ; Mon, 6 Sep 2004 13:11:36 +0200 (MEST) Message-Id: <6.0.1.1.2.20040906110727.025c3e98..at..ace.ulyssis.org> X-Sender: u0043641..at..u0043641.kuleuven.be (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 6.0.1.1 Date: Mon, 06 Sep 2004 13:11:35 +0200 To: chemistry..at..ccl.net From: eric breynaert Subject: g03 optimised geometry becomes unoptimised after freq calculation Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1"; format=flowed X-Spam-Status: No, hits=0.9 required=7.5 tests=MY_BAD_DOT autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i86B2AaG032142 dear ccl'ers, I'm doing dft (ub3lyp/lanl2dz) calculations on technetium compounds. After a geometry optimisation, i always run a stabe=(opt) and then a freq calculation. Item Value Threshold Converged? Maximum Force .000043 .000450 YES RMS Force .000007 .000300 YES Maximum Displacement .000646 .001800 YES RMS Displacement .000162 .001200 YES Predicted change in Energy=-3.998357D-08 Optimization completed. -- Stationary point found. Stable reports ->wavefunction stable under the perturbations considered At the end of the freq calculation the geom optimisation params become Item Value Threshold Converged? Maximum Force .004051 .000450 NO RMS Force .001202 .000300 NO Maximum Displacement .126525 .001800 NO RMS Displacement .018760 .001200 NO Predicted change in Energy=-1.029330D-03 Can anyone explain this ? What happens ? Thanks in advance, Eric Breynaert PS: How can i subscribe to this list. I tried mailing to both adresses listed on the website, but that didn't have any result. --------- * Eric Breynaert * Labo voor Colloodchemie * Departement Interfasechemie * K.U.Leuven * Kasteelpark Arenberg 23 * B-3001 Leuven * BELGIUM * * Tel: +3216321457 * Fax: +3216321998 --------- From chemistry-request@ccl.net Mon Sep 6 11:10:17 2004 Received: from mail.scs.uiuc.edu (mail.scs.uiuc.edu [130.126.231.250]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i86GAGaG001916 for ; Mon, 6 Sep 2004 11:10:16 -0500 Received: from localhost (localhost [127.0.0.1]) (uid 62) by mail.scs.uiuc.edu with local; Mon, 06 Sep 2004 11:19:46 -0500 References: In-Reply-To: From: jerome=at=scs.uiuc.edu To: "Dr. Csaba Hetenyi" Cc: Dominique Vlieghe , chemistry=at=ccl.net Subject: Re: CCL:predict 3D structure from sequence Date: Mon, 06 Sep 2004 11:19:46 -0500 Mime-Version: 1.0 Content-Type: text/plain; format=flowed; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Message-ID: X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear Dominique, Csaba, Felipe, and all Dominique Vlieghe writes: > Sadly, I must say from personal experience I agree with you, but the > problem remains that one often has to homology model a given receptor, > because a xray/nmr structure is lacking. I'd like to add that crystal structures themselves are not always exempt > from problems and may, when used as templates, induce problems in subsequent HM-based workflow. See for instance the discussions in the litterature about the use of the early CYP2C5 crystal structure and its consequences...In these cases, the origin of the problem may be a crystal structure rather than an 'homology modeling gone wild' Jerome ---------------------------------------------------------- Jerome Baudry, Ph.D. Senior Research Scientist, VizLab Manager. School of Chemical Sciences University of Illinois at Urbana-Champaign 505 S. Mathews Ave.; Box 2.1; Urbana, IL, 61801 Phone: (1) (217) 244 3210; Fax: (1) (217) 333 3120; e-mail: jerome=at=scs.uiuc.edu From chemistry-request@ccl.net Mon Sep 6 12:29:27 2004 Received: from mb2i1.ns.pitt.edu (mb2i1.ns.pitt.edu [136.142.11.140]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i86HTQaG010492 for ; Mon, 6 Sep 2004 12:29:26 -0500 Received: from CONVERSION-DAEMON by pitt.edu (PMDF V5.2-32 #41462) id <01LEJRST4Z3K001WF4..at..mb2i1.ns.pitt.edu> for chemistry..at..ccl.net; Mon, 6 Sep 2004 13:38:47 EDT Received: from [127.0.0.1] ([136.142.109.16]) by pitt.edu (PMDF V5.2-32 #41462) with ESMTP id <01LEJRSRDH7S002F7H..at..mb2i1.ns.pitt.edu>; Mon, 06 Sep 2004 13:38:45 -0400 (EDT) Date: Mon, 06 Sep 2004 13:38:40 -0400 From: Kadir Diri Subject: Re: CCL:Gaussian 03 termination In-reply-to: <413C5391.7030102..at..mpi-bpc.mpg.de> To: Vlad Cojocaru Cc: CCL List Message-id: <413CA0A0.5090207..at..visual1.chem.pitt.edu> MIME-version: 1.0 Content-type: text/plain; charset=ISO-8859-1; format=flowed Content-transfer-encoding: 7bit User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.7.2) Gecko/20040803 X-Accept-Language: en-us, en, tr References: <413C5391.7030102..at..mpi-bpc.mpg.de> X-Spam-Status: No, hits=4.0 required=7.5 tests=IMPRONONCABLE_1,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 Hi! It is not obvious from these error messages but I bet you got them because your calculation exceeded the default maximum number of cycles in the geometry optimization. You are using tight convergence criteria, which sometimes takes many cycles to converge. Check the end of the last cycle, it may tell you something like "number of steps exceeded, aborting optimization". If that is the case you can increase the number of cycles by putting a larger number for "N" in opt=(maxcycle=N,tight) Another possibility is that SCF did not converge, check your output also for that. kadir Vlad Cojocaru wrote: > Dear CCLers, > Has anybody experience gaussian termination with the following error? > > Error termination request processed by link 9999. > Error termination via Lnk1e in /usr/product/gaussian/g03/l9999.exe at > Mon Sep 6 05:29:58 2004. > Job cpu time: 0 days 5 hours 16 minutes 31.4 seconds. > File lengths (MBytes): RWF= 30 Int= 0 D2E= 0 Chk= > 11 Scr= 1 > > If yes could somebody tell me what can be the reason for this happening? > My input is a Z-matrix file (I checked it and everything is fine with it) > #P hf/6-31G* Opt=Tight SCF(Conver=8) Test > > Thank you very much in advance for advices > vlad > From chemistry-request@ccl.net Mon Sep 6 10:52:58 2004 Received: from mail.scs.uiuc.edu (mail.scs.uiuc.edu [130.126.231.250]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i86FqvaG000501 for ; Mon, 6 Sep 2004 10:52:57 -0500 Received: from localhost (localhost [127.0.0.1]) (uid 62) by mail.scs.uiuc.edu with local; Mon, 06 Sep 2004 11:02:26 -0500 References: In-Reply-To: From: jerome{at}scs.uiuc.edu To: "Dr. Csaba Hetenyi" Cc: Dominique Vlieghe , chemistry{at}ccl.net Subject: Re: CCL:predict 3D structure from sequence Date: Mon, 06 Sep 2004 11:02:26 -0500 Mime-Version: 1.0 Content-Type: text/plain; format=flowed; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Message-ID: X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net >> A "nice" example of failure of HM was recently mentioned in Williams et >> al. (...) 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). The definitive aspect of this statement sounds too ideological to me .. There *are* exemples of successsful HM/HTS using CYPs templates.. By sucessfull I mean either identification, confirmed experimentaly, of ligands through virtual screening or QSAR-like experimental/theoretical agreement on ligand/protein binding energies/Kd ... I agree that *uncontrolled* HM/docking is a plague, by I want to stress that the oposite is also true: successful HM/docking - in particular in the P450 world, contributes (to paraphrase) to "rising (and - in this case - right) confidence of experimental guys with modeling." As always when theory is involved, experiental confirmation is the key ...same old same old.. ---------------------------------------------------------- Jerome Baudry, Ph.D. Senior Research Scientist, VizLab Manager. School of Chemical Sciences University of Illinois at Urbana-Champaign 505 S. Mathews Ave.; Box 2.1; Urbana, IL, 61801 Phone: (1) (217) 244 3210; Fax: (1) (217) 333 3120; e-mail: jerome{at}scs.uiuc.edu From chemistry-request@ccl.net Mon Sep 6 11:08:52 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 i86G8paG001819 for ; Mon, 6 Sep 2004 11:08:51 -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 1C4MCE-0003su-CG for chemistry{at}ccl.net; Mon, 06 Sep 2004 18:18:22 +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 M2004090618182125727 for ; Mon, 06 Sep 2004 18:18:21 +0200 Received: from mail.szote.u-szeged.hu ([160.114.96.63]) by eos.fwall.u-szeged.hu with esmtp (Exim 4.34) id 1C4MCE-0003sn-5W for chemistry{at}ccl.net; Mon, 06 Sep 2004 18:18:22 +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 SAA04132 for ; Mon, 6 Sep 2004 18:18:21 +0200 Received: (qmail 11072 invoked by uid 525); 6 Sep 2004 16:18:20 -0000 Received: from localhost (sendmail-bs@127.0.0.1) by localhost with SMTP; 6 Sep 2004 16:18:20 -0000 Date: Mon, 6 Sep 2004 18:18:20 +0200 (CEST) From: "Dr. Csaba Hetenyi" To: jerome{at}scs.uiuc.edu cc: Dominique Vlieghe , chemistry{at}ccl.net Subject: Re: CCL:predict 3D structure from sequence In-Reply-To: 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 definitive aspect of this statement sounds too ideological to me .. Indeed, it was a bit ideological. In my view, the problem of homology modeling is very similar to e.g. genetic modification of plants. We do not know exactly what comes out of it... We cannot analyze/validate all of the results. Can we use it? Best wishes, Csaba From chemistry-request@ccl.net Mon Sep 6 09:27:03 2004 Received: from mailer.gwdg.de (mailer.gwdg.de [134.76.10.26]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i86ER2aG023484 for ; Mon, 6 Sep 2004 09:27:02 -0500 Received: from vrlab03.mpibpc.gwdg.de ([134.76.211.99] helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 4.42) id 1C4Kbh-0002br-0l for chemistry_at_ccl.net; Mon, 06 Sep 2004 16:36:33 +0200 Message-ID: <413C75F0.9040909_at_mpi-bpc.mpg.de> Date: Mon, 06 Sep 2004 16:36:32 +0200 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CCL List Subject: Gaussian logfile .. tomorrow Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: (clean) by exiscan+sophie X-Spam-Status: No, hits=0.9 required=7.5 tests=MY_BAD_DOT autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCLers, I thank everybody for the very fast replies to my question. You asked me to provide more of the output. The problem is that I deleted it and I started the job once more. In one case it proved useful and rerunning the job solved the problem. If the jobs will crash again in similar fashion, by tomorrow I will be able to send you more information on the output. Thanks again vlad -- Vlad Cojocaru Max Planck Institute for Biophysical Chemistry Department: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1327 e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de home tel: ++49-551-9963204 From chemistry-request@ccl.net Mon Sep 6 10:28:50 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 i86FSnaG030785 for ; Mon, 6 Sep 2004 10:28:49 -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 1C4LZQ-0001HO-JJ for chemistry_at_ccl.net; Mon, 06 Sep 2004 17:38:16 +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 M2004090617381625165 for ; Mon, 06 Sep 2004 17:38:16 +0200 Received: from mail.szote.u-szeged.hu ([160.114.96.63]) by eos.fwall.u-szeged.hu with esmtp (Exim 4.34) id 1C4LZQ-0001HL-DI for chemistry_at_ccl.net; Mon, 06 Sep 2004 17:38:16 +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 RAA03656 for ; Mon, 6 Sep 2004 17:38:16 +0200 Received: (qmail 10762 invoked by uid 525); 6 Sep 2004 15:38:12 -0000 Received: from localhost (sendmail-bs@127.0.0.1) by localhost with SMTP; 6 Sep 2004 15:38:12 -0000 Date: Mon, 6 Sep 2004 17:38:12 +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 > > 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. > > According to your own necessary/sufficient conditions this wouldn't be a good > example, since the authors state that templates available for comparative modeling > of CYP3A4 display just sequence identities < 30% with the target. On p. 684 you > can read: This example was used for demonstrating uncontrolled and failed HM. The authors refer to different homology models resulting structures far from their measured structure. The referred HMs were used for docking extensively, as i could follow from the literature. These HM->docking works caused pain for me...:) In my view, further clarification of general rules of HM and careful work would be necessary to avoid such mistakes... Best, Csaba From chemistry-request@ccl.net Mon Sep 6 11:16:23 2004 Received: from mserv6.dl.ac.uk (mail.dl.ac.uk [148.79.80.137]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i86GGMaG002252 for ; Mon, 6 Sep 2004 11:16:22 -0500 X-DL-MFrom: X-DL-Connect: Received: from dl.ac.uk (csevig6.dl.ac.uk [193.62.112.123]) by mserv6.dl.ac.uk (8.12.10/8.12.8/[ref postmaster_at_dl.ac.uk]) with ESMTP id i86GPm6A002716; Mon, 6 Sep 2004 17:25:48 +0100 Message-ID: <413C8F8C.7080605_at_dl.ac.uk> Date: Mon, 06 Sep 2004 17:25:48 +0100 From: Jens Thomas User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.6) Gecko/20040113 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Jeff C CC: chemistry_at_ccl.net Subject: CCL: Re: Queries: GAMESS-UK and 3D QSAR References: <20040902134700.61994.qmail_at_web25108.mail.ukl.yahoo.com> In-Reply-To: <20040902134700.61994.qmail_at_web25108.mail.ukl.yahoo.com> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-CCLRC-SPAM-report: 0 : X-Scanned-By: MIMEDefang 2.37 X-Spam-Status: No, hits=1.3 required=7.5 tests=FVGT_s_OBFU_Q1,IMPRONONCABLE_1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Jeff C wrote: >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. > Hi Jeff If you look through your output file, towards the end, you should see a line that reads: ********************** optimization converged ********************** This marks the start of the section where the information on convergence is printed. If you scroll down from this section, you should get to a bit that reads: =================== nuclear coordinates =================== x y z chg tag ============================================================ Each subsequent line under this table details the optimised x,y and z coordinates, charge and tag (label) of the nuceli. If you have any problems running the code, the quickest way to get help is to send an email to: gamess_uk_support_at_daresbury.ac.uk There is also a GAMESS-UK user list, which is described on the GAMESS-UK website at: http://www.cfs.dl.ac.uk/services/email.shtml Best wishes, Jens From chemistry-request@ccl.net Mon Sep 6 09:04:36 2004 Received: from host20 (host20.lctn.uhp-nancy.fr [193.50.239.24]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i86E4YaG021075 for ; Mon, 6 Sep 2004 09:04:35 -0500 Received: from lctn.uhp-nancy.fr (host5.lctn.uhp-nancy.fr [193.50.239.5]) by host20 (AIX4.3/8.9.3/8.9.3) with ESMTP id QAA33130; Mon, 6 Sep 2004 16:15:03 +0200 Sender: moreau@host20 Message-ID: <413C6FDD.8E6847F5:at:lctn.uhp-nancy.fr> Date: Mon, 06 Sep 2004 16:10:38 +0200 From: Yohann Moreau Organization: Equipe de Chimie et Biochimie =?iso-8859-1?Q?Th=E9oriques?= X-Mailer: Mozilla 4.7iC-CCK-MCD [en_US] (X11; I; AIX 4.3) X-Accept-Language: fr, en MIME-Version: 1.0 To: Vlad Cojocaru CC: CCL List Subject: Re: CCL:Gaussian 03 termination References: <413C5391.7030102:at:mpi-bpc.mpg.de> Content-Type: multipart/alternative; boundary="------------8E7A45DD6B424F836CED06F7" X-Spam-Status: No, hits=1.0 required=7.5 tests=HTML_MESSAGE,IMPRONONCABLE_1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --------------8E7A45DD6B424F836CED06F7 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi Vlad, I'm not sure but it seems that you exceeded the max. number of steps allowed for the geometry optimisation. Gaussian calculates this number of steps with the number of redundant internal redundant coordinates (the max. between 20 and twice the number of redundant internal redundant coodinates in case of default precedure) You can precise this value by yourself and if I take your input route, it can be : #P hf/6-31G* Opt=(Tight SCF(Conver=8),maxcycle=N) Test where N is the number of steps you want to allow. I hope this will help you, Yohann Vlad Cojocaru wrote: > Dear CCLers, > Has anybody experience gaussian termination with the following error? > > Error termination request processed by link 9999. > Error termination via Lnk1e in /usr/product/gaussian/g03/l9999.exe at > Mon Sep 6 05:29:58 2004. > Job cpu time: 0 days 5 hours 16 minutes 31.4 seconds. > File lengths (MBytes): RWF= 30 Int= 0 D2E= 0 Chk= 11 > Scr= 1 > > If yes could somebody tell me what can be the reason for this happening? > My input is a Z-matrix file (I checked it and everything is fine with it) > #P hf/6-31G* Opt=Tight SCF(Conver=8) Test > > Thank you very much in advance for advices > vlad > > -- > Vlad Cojocaru > Max Planck Institute for Biophysical Chemistry > Department: 060 > Am Fassberg 11, 37077 Goettingen, Germany > tel: ++49-551-201.1327 > e-mail: Vlad.Cojocaru:at:mpi-bpc.mpg.de > home tel: ++49-551-9963204 > > -= 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) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -- Yohann MOREAU, Doctorant Equipe de Chimie et Biochimie Thioriques UMR CNRS-UHP 7565 "SRMSC" BP 239, F-54506 Vandoeuvre-lhs-Nancy http://www.lctn.uhp-nancy.fr/Etudiants/Yohann.Moreau.html --------------8E7A45DD6B424F836CED06F7 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Vlad,

I'm not sure but it seems that  you exceeded the max. number of steps allowed for the geometry optimisation.
Gaussian calculates this number of steps with the number of redundant  internal redundant coordinates
(the max. between 20 and twice the number of redundant  internal redundant coodinates in case of default precedure)
You can precise this value by yourself and if I take your input route, it can be :

#P hf/6-31G* Opt=(Tight SCF(Conver=8),maxcycle=N)  Test
 

where N is the number of steps you want to allow.

I hope this will help you,

Yohann
 

Vlad Cojocaru wrote:

Dear CCLers,
  Has anybody experience gaussian termination with the following error?

Error termination request processed by link 9999.
 Error termination via Lnk1e in /usr/product/gaussian/g03/l9999.exe at
Mon Sep  6 05:29:58 2004.
 Job cpu time:  0 days  5 hours 16 minutes 31.4 seconds.
 File lengths (MBytes):  RWF=     30 Int=      0 D2E=      0 Chk=     11
Scr=      1

If yes could somebody tell me what can be the reason for this happening?
My input is a Z-matrix file (I checked it and everything is fine with it)
#P hf/6-31G* Opt=Tight SCF(Conver=8) Test

Thank you very much in advance for advices
vlad

--
Vlad Cojocaru
Max Planck Institute for Biophysical Chemistry
Department: 060
Am Fassberg 11, 37077 Goettingen, Germany
tel: ++49-551-201.1327
e-mail: Vlad.Cojocaru:at:mpi-bpc.mpg.de
home tel: ++49-551-9963204

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-- 

               Yohann MOREAU, Doctorant                 
       Equipe de Chimie et Biochimie Théoriques   
               UMR CNRS-UHP 7565 "SRMSC"        
          BP 239, F-54506 Vandoeuvre-lès-Nancy  
http://www.lctn.uhp-nancy.fr/Etudiants/Yohann.Moreau.html
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