From chemistry-request@ccl.net Mon Sep 29 08:54:59 2003 Received: from postoffice9.mail.cornell.edu (postoffice9.mail.cornell.edu [132.236.56.39]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8TCsQmK029575 for ; Mon, 29 Sep 2003 08:54:26 -0400 Received: from cornell.edu ([128.84.183.113]) by postoffice9.mail.cornell.edu (8.12.10/8.12.6) with ESMTP id h8TCrbw3011812; Mon, 29 Sep 2003 08:53:37 -0400 (EDT) Date: Mon, 29 Sep 2003 08:53:54 -0400 Subject: Re: CCL:Ring detection Content-Type: text/plain; charset=US-ASCII; format=flowed Mime-Version: 1.0 (Apple Message framework v552) Cc: John McKelvey , chemistry[at]ccl.net To: Geoff Hutchison From: Richard Gillilan In-Reply-To: <4E7963CE-F147-11D7-B4D7-000A95701B7A[at]chem.northwestern.edu> Message-Id: Content-Transfer-Encoding: 7bit X-Mailer: Apple Mail (2.552) X-Spam-Status: No, hits=-2.0 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, REPLY_WITH_QUOTES,USER_AGENT_APPLEMAIL version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Do you know if any of these codes have published their method? I have a paper somewhere (I think it was actually Journal of Mathematical Chemistry) that gives a method, but also gives me the impression that a fully-general algorithm is non-trivial task. I'll try to dig it up. In my OrderFour code, Ryan Lilien and I simply invented our own tree-search method for doing this, but I have no proof of how general it is ... certainly works on all the rings I have encountered so far and also can find arbitrarily large rings. Anyone is welcome to look at the code, it is C++. Just drop me an email. Richard On Saturday, September 27, 2003, at 08:04 PM, Geoff Hutchison wrote: >> Can anyone point me to a code [preferably fortran ,{I know}] for >> determining rings and size for atoms, given a connectivity list? > > I can't point you to a Fortran code for it, but I can point you to > several open source codes that do this: > > OpenBabel (C++): http://openbabel.sf.net/ > JOELib (Java): http://joelib.sf.net/ > CDK (Java): http://cdk.sf.net/ > > There are undoubtedly other codes, but I'm the most familiar with > these three. > > Cheers, > -Geoff > From chemistry-request@ccl.net Mon Sep 29 02:31:30 2003 Received: from nankai.edu.cn (sun.nankai.edu.cn [202.113.16.21]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8T6UrmK019318 for ; Mon, 29 Sep 2003 02:30:56 -0400 Received: (eyou send program); Mon, 29 Sep 2003 14:31:36 +0800 Received: from unknown (HELO 192.168.0.103) (unknown@128.195.87.184) by 202.113.16.21 with SMTP; Mon, 29 Sep 2003 14:31:36 +0800 Date: Sun, 28 Sep 2003 23:30:24 -0700 From: John Lee X-Mailer: The Bat! (v1.62r) Reply-To: John Lee X-Priority: 3 (Normal) Message-ID: <737846248.20030928233024[at]joyie.com> To: chemistry[at]ccl.net Subject: symmitric keyword and water cluster MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.7 required=7.0 tests=FROM_ENDS_IN_NUMS version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi CCL-ers I tried to optimize water cluster with 3 waters or even more (4,5..). In order to keep the symmetric structure, I used the symmetric input z-matrix as follow. But the result is not symmetric. The input keyword is like: # opt=(calcfc,gdiis,maxcycle=350) freq=noraman rb3lyp/6-311++g(d,p) #scf(maxcycle=350) Maybe I should use symmetric keyword, but I don't know how to use it. Does anyone could help me about this. How to get the optimized structure of water cluster. And how to use symmetric keyword. 0 1 O O 1 B1 O 2 B1 1 60.0 H 1 B2 3 A1 2 D1 H 1 B3 4 A2 3 D2 H 2 B2 1 A1 3 D1 H 2 B3 6 A2 1 D2 H 3 B2 2 A1 1 D1 H 3 B3 8 A2 2 D3 Variables: B1 2.53540324 B2 1.05113591 B2 1.05113591 B3 0.99000000 A1 16.89494000 A2 106.96310000 D1 173.74583000 D2 108.87723000 D3 -D2 -- Best regards, John Lee From chemistry-request@ccl.net Mon Sep 29 10:03:07 2003 Received: from compton.acpub.duke.edu (compton.acpub.duke.edu [152.3.233.74]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8TE2ZmK032339 for ; Mon, 29 Sep 2003 10:02:35 -0400 Received: from CONCORDIA (concordia.lib.duke.edu [152.3.237.233]) by compton.acpub.duke.edu (8.12.10/8.12.10/Duke-5.0.0) with SMTP id h8TE2VT3017697; Mon, 29 Sep 2003 10:02:31 -0400 (EDT) X-Originating-IP: 152.3.169.5 X-Mailer: MyDuke.com X-Originator-Info: jz7@acpub From: To: Subject: question about CIS excited states calculation Date: Mon, 29 Sep 2003 09:56:53 -0400 Message-ID: <008201c38691$89b890a0$eaed0398@CONCORDIA> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Thread-Index: AcOGkYm4SuOEc5oKRVi03ANRS6NoZA== 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, I just began to use CIS to calculate excited states properties, such as state dipole moment, transition dipole moment and energy. But I am confused about how many occupied and unoccupied orbitals to choose when using CIS to calculate excited states. I had expected that if I include more orbitals, I should get closer result to the "true value". And when the number of orbitals is greater than some certain number, the result should not change much. But the calculation results showed great fluctuation when I include more and more orbitals. So what is the problem? Really thanks a lot! Best, Jeny From chemistry-request@ccl.net Mon Sep 29 11:08:31 2003 Received: from yangtze.hku.hk (yangtze.hku.hk [147.8.148.244]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8TF7xmK002272 for ; Mon, 29 Sep 2003 11:08:00 -0400 Received: from localhost (lhhu@localhost) by yangtze.hku.hk (8.11.6/8.9.3) with ESMTP id h8TFQKh17307 for ; Mon, 29 Sep 2003 23:26:20 +0800 Date: Mon, 29 Sep 2003 23:26:19 +0800 (HKT) From: Hu LiHong To: chemistry/at/ccl.net Subject: CHARMM parameter 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) Dear all, I am running CHARMM. In the output file there are warnings 'MISS PARAMETER' and 'atom type does not match the mass'. Anyone has this kind of experience? I tried to find some parameter for some elements and put it in the rtf file, but it didn't work, i, e,, the warning can't be get rid of Who can tell me the solution of this problem? In addition, I'd like to know where I can find the detail explanation of BOMBLEVEL, WRNLEVEL, PRNLEVEL, etc. Thanks a lot in advance, Best Carol From chemistry-request@ccl.net Mon Sep 29 10:35:53 2003 Received: from cuces.unisi.it (cuces.unisi.it [193.205.4.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8TEZLmK000877 for ; Mon, 29 Sep 2003 10:35:22 -0400 Received: from CONVERSION-DAEMON.cuces.unisi.it by cuces.unisi.it (PMDF V6.2-X17 #30546) id <01L18RLKUISG000ATE$at$cuces.unisi.it> for CHEMISTRY$at$ccl.net; Mon, 29 Sep 2003 16:35:16 +0100 (MET) Received: from unisi.it (sgio2.ctf.unisi.it [172.16.52.81]) by cuces.unisi.it (PMDF V6.2-X17 #30546) with ESMTPA id <01L18RJEIB5Q000BE1$at$cuces.unisi.it> for CHEMISTRY$at$ccl.net; Mon, 29 Sep 2003 16:21:46 +0100 (MET) Date: Mon, 29 Sep 2003 16:19:14 +0200 From: Stefano Forli Subject: Compiling AutoDock 3.0 on IRIX... Sender: stefano$at$student.unisi.it To: CHEMISTRY$at$ccl.net Message-id: <3F783F62.3DE32B26$at$unisi.it> MIME-version: 1.0 X-Mailer: Mozilla 4.5 [en] (X11; I; IRIX 6.3 IP32) Content-type: text/plain; charset=UTF-7 Content-transfer-encoding: 7bit X-Accept-Language: en X-Spam-Status: No, hits=-0.3 required=7.0 tests=SIGNATURE_LONG_DENSE,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear all, I'm trying to compile some files in the $AUTODOCK/src directory on an Irix 6.5.16m machine, using the gcc compiler, but I get this error message: % gcc -o addsol addsol.c addsol.c: In function `main': addsol.c:13: warning: return type of `main' is not `int' The command line options are those suggested in the README file the $AUTODOCK/src/addsol directory. I tried the option "-O3" too, as suggested in a webpage, but the error is the same. The cc compiler, by other hand, says: cc-1174 cc: WARNING File = addsol.c, Line = 14 The variable "i" was declared but never referenced. int i, j; ^ However, compiled files are produced and are executable in both cases, but since this is first time I compile a code, I don't know if they are reliable, and if the error message is critical or not. Thank you in advice, Stefano -- *********************************** Dr. Forli Stefano Dip. Farmaco Chimico Tecnologico Universita' degli Studi di Siena Via Aldo Moro I-53100 Siena, Italy Phone: ++39 0577 234307 Fax: ++39 0577 234333 *********************************** From chemistry-request@ccl.net Mon Sep 29 11:05:32 2003 Received: from nihhubims3.hub.nih.gov (nihhubims3.hub.nih.gov [128.231.90.113]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8TF51mK002081 for ; Mon, 29 Sep 2003 11:05:01 -0400 Received: by nihhubims3.hub.nih.gov with Internet Mail Service (5.5.2657.46) id ; Mon, 29 Sep 2003 11:05:00 -0400 Message-ID: From: "Bienstock, Rachelle (NIH/NIEHS)" To: "'Peter Gannett'" , "'CHEMISTRY$at$ccl.net'" Subject: RE: 2C9 online website Date: Mon, 29 Sep 2003 11:04:59 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2657.46) Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=-0.5 required=7.0 tests=ORIGINAL_MESSAGE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Peter: The crystal structure of CYP 2C9 was published in Nature 424, 464 - 468 (24 July 2003) Crystal structure of human cytochrome P450 2C9 with bound warfarin PAMELA A. WILLIAMS*, JOSE COSME*, ALISON WARD?, HAYLEY C. ANGOVE, DIJANA MATAK VINKOVI & HARREN JHOTI Astex Technology, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, UK * These authors contributed equally to this work ? Present address: AstraZeneca, R&D Charnwood, Bakewell Road, Loughborough LE11 5RH, UK The coordinates have been deposited in the Protein Data Bank (http://www.rcsb.org) under accession codes 1OG2 and 1OG5, and are freely available for download. There are numerous free programs available for download, or that work within the browser (i.e Rasmol, Chime, etc..) to view the structure and potential mutations. Rachelle Dr. Rachelle J. Bienstock Molecular Modeling and Structural Biochemistry National Institutes of Health (NIH) National Institute of Environmental Health Sciences (NIEHS) ITSS P.O. Box 12233 MD F0-011 Research Triangle Park, NC 27709 Tel: (919) 541-3397 Fax: (919) 541-5737 -----Original Message----- From: Peter Gannett [mailto:pgannett$at$hsc.wvu.edu] Sent: Thursday, September 25, 2003 3:25 PM To: < Subject: CCL:2C9 online website All: I heard rumors of online modeling program where you can use the recently published 2C9 crystal structure and see the model on a desktop computer and then make mutations, etc. Does anyone know about this? Thanks. Pete Gannett -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY$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$ccl.net (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Mon Sep 29 11:09:40 2003 Received: from nihhubims3.hub.nih.gov (nihhubims3.hub.nih.gov [128.231.90.113]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8TF95mK002347 for ; Mon, 29 Sep 2003 11:09:08 -0400 Received: by nihhubims3.hub.nih.gov with Internet Mail Service (5.5.2657.46) id ; Mon, 29 Sep 2003 11:09:03 -0400 Message-ID: From: "Bienstock, Rachelle (NIH/NIEHS)" To: "'Peter Gannett'" , "'CHEMISTRY$at$ccl.net'" Subject: RE: 2C9 online website Date: Mon, 29 Sep 2003 11:08:30 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2657.46) Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=-0.5 required=7.0 tests=ORIGINAL_MESSAGE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Peter: There is also this website http://mutdb.org/AnnoSNP/data/EX/S0/RD/AC.nt.html: MutDB - Functionally Annotated Mutation Database MutDB is a resource created to provide a researchers with computational predictions of the underlying functional causes of disease-associated mutations. Here we provide three resources for understanding how mutations cause disease. First, we provide a server for the automatic prediction of the functional importance of uncharacterized, inputted disease-associated polymorphisms (Server). Second, we provide a database of mutations that have been annotated using comparative genomics and protein structural information, where available (Database). Finally, we also provide tools we've developed that we find useful (Tools). This web service was developed at Stanford University by Sean Mooney, PhD and was funded through an American Cancer Society Postdoctoral Fellowship. If you have any questions feel free to email Sean Mooney. Rachelle -----Original Message----- From: Peter Gannett [mailto:pgannett$at$hsc.wvu.edu] Sent: Thursday, September 25, 2003 3:25 PM To: < Subject: CCL:2C9 online website All: I heard rumors of online modeling program where you can use the recently published 2C9 crystal structure and see the model on a desktop computer and then make mutations, etc. Does anyone know about this? Thanks. Pete Gannett -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY$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) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Mon Sep 29 13:42:16 2003 Received: from prserv.net (asmtp1.prserv.net [32.97.166.51]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8THfhmK010125 for ; Mon, 29 Sep 2003 13:41:43 -0400 Received: from attglobal.net (dhcp065-029-082-127.indy.rr.com[65.29.82.127]) by prserv.net (asmtp1) with SMTP id <2003092917413925104n46uce> (Authid: usinet.jmmckel); Mon, 29 Sep 2003 17:41:41 +0000 Message-ID: <3F7826DE.37A1EA98!at!attglobal.net> Date: Mon, 29 Sep 2003 12:34:38 +0000 From: John McKelvey Reply-To: jmmckel!at!attglobal.net Organization: McKelvey Computational Chemistry X-Mailer: Mozilla 4.75 [en]C-CCK-MCD (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: jz7!at!duke.edu CC: chemistry!at!ccl.net Subject: Re: CCL:question about CIS excited states calculation References: <008201c38691$89b890a0$eaed0398@CONCORDIA> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-1.8 required=7.0 tests=DATE_IN_PAST_03_06,EMAIL_ATTRIBUTION,QUOTED_EMAIL_TEXT, REFERENCES,REPLY_WITH_QUOTES,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) Jeny, If this is for a semiempirical method I would use all possible excitations for CIS. For INDO/S, for example, the results can be strongly dependent on CI size, and accuracy is usually improved by increasing CI size to the limit for larger molecules. For ab initio I would include all the excitations I could afford. If there is a resource limit then one could correlate computed one electron propertied with CI size and see where things seem to converge to a constant value. Regards, John McKelvey jz7!at!duke.edu wrote: > Dear all, > > I just began to use CIS to calculate excited states properties, such as > state dipole moment, transition dipole moment and energy. But I am > confused about how many occupied and unoccupied orbitals to > choose when using CIS to calculate excited states. > > I had expected that if I include more orbitals, I should get closer > result to the "true value". And when the number of orbitals is greater > than some certain number, the result should not change much. But the > calculation results showed great fluctuation when I include more and > more orbitals. So what is the problem? > > Really thanks a lot! > > Best, > Jeny > > -= 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) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Mon Sep 29 11:54:53 2003 Received: from www.eyesopen.COM ([12.96.199.11]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8TFsKmK004688 for ; Mon, 29 Sep 2003 11:54:20 -0400 Received: from eyesopen.com ([10.1.245.3]) (authenticated) by www.eyesopen.com (8.11.6/8.11.6) with ESMTP id h8TFKUn27806; Mon, 29 Sep 2003 09:20:30 -0600 Message-ID: <3F785705.1070805!at!eyesopen.com> Date: Mon, 29 Sep 2003 10:00:05 -0600 From: Matthew Stahl User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.2.1) Gecko/20021204 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry!at!ccl.net, reg8!at!cornell.edu, jmmckel!at!attglobal.net Subject: Re: Ring Detection X-Enigmail-Version: 0.71.0.0 X-Enigmail-Supports: pgp-inline, pgp-mime Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-1.1 required=7.0 tests=EMAIL_ATTRIBUTION,QUOTED_EMAIL_TEXT,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) The following URL contains a number of references for (and a discussion about) SSSR methods (Section 12.7): http://www.eyesopen.com/oechem/doc/cplusprog/node123.html matt ---------- Forwarded message ---------- Date: Mon, 29 Sep 2003 08:53:54 -0400 From: Richard Gillilan To: Geoff Hutchison Cc: John McKelvey , chemistry!at!ccl.net Subject: CCL:Ring detection Do you know if any of these codes have published their method? I have a paper somewhere (I think it was actually Journal of Mathematical Chemistry) that gives a method, but also gives me the impression that a fully-general algorithm is non-trivial task. I'll try to dig it up. In my OrderFour code, Ryan Lilien and I simply invented our own tree-search method for doing this, but I have no proof of how general it is ... certainly works on all the rings I have encountered so far and also can find arbitrarily large rings. Anyone is welcome to look at the code, it is C++. Just drop me an email. Richard On Saturday, September 27, 2003, at 08:04 PM, Geoff Hutchison wrote: >>>> Can anyone point me to a code [preferably fortran ,{I know}] for >>>> determining rings and size for atoms, given a connectivity list? >> >> >> >> I can't point you to a Fortran code for it, but I can point you to >> several open source codes that do this: >> >> OpenBabel (C++): http://openbabel.sf.net/ >> JOELib (Java): http://joelib.sf.net/ >> CDK (Java): http://cdk.sf.net/ >> >> There are undoubtedly other codes, but I'm the most familiar with >> these three. >> >> Cheers, >> -Geoff > From chemistry-request@ccl.net Mon Sep 29 12:47:40 2003 Received: from Princeton.EDU (postoffice02.Princeton.EDU [128.112.130.38]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8TGl9mK007596 for ; Mon, 29 Sep 2003 12:47:09 -0400 Received: from smtpserver1.Princeton.EDU (smtpserver1.Princeton.EDU [128.112.129.65]) by Princeton.EDU (8.12.9/8.12.9) with ESMTP id h8TGl8ek000497 for ; Mon, 29 Sep 2003 12:47:08 -0400 (EDT) Received: from tucson.Princeton.EDU (tucson.Princeton.EDU [128.112.129.181]) by smtpserver1.Princeton.EDU (8.12.9/8.12.9) with ESMTP id h8TGl7UB007504 for ; Mon, 29 Sep 2003 12:47:07 -0400 (EDT) Received: from localhost (ccresson@localhost) by tucson.Princeton.EDU (8.9.1/8.9.1) with ESMTP id MAA08421 for ; Mon, 29 Sep 2003 12:47:07 -0400 (EDT) X-Authentication-Warning: tucson.Princeton.EDU: ccresson owned process doing -bs Date: Mon, 29 Sep 2003 12:47:07 -0400 (EDT) From: Catherine Cresson To: chemistry!at!ccl.net Subject: Force Fields & Torsion Parameters 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) Dear CCLers, I am working on a docking algorithm with a novel binding site representation. However, I do not wish to re-invent an intramolecular forcefield for the peptides I am docking into my protein. I am very familiar with InsightII, which unfortunately does not allow me to use my binding site model with their forcefields. Does anyone have any suggestions of free (or purchasable) software that might be more compatible with my needs? Also, to circumvent this problem, I tired to create a simple forcefield with minimal atom types and only terms for bond stretching, angle bending, torsion, and nonbonded interactions. The difficult portion of this task is finding the correct parameters for the torsion term. I've searched the literature and I seem to find either functional representations or rotamers libraries, but I am unsure exactly how to combine these two aspects to actually implement a working code. Can you give me any guidance and advice? Thanks so much for reading through my questions and I look forward to reading your responses. Catherine Cresson ************************************************** Catherine Cresson Department of Chemistry Princeton University Princeton, NJ 08544 lab: (609)258-2707 ************************************************** From chemistry-request@ccl.net Mon Sep 29 11:22:57 2003 Received: from mailhub1.shef.ac.uk (mailhub1.shef.ac.uk [143.167.1.9]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8TFMPmK003267 for ; Mon, 29 Sep 2003 11:22:26 -0400 Received: from stoat.shef.ac.uk ([143.167.2.1]) by mailhub1.shef.ac.uk with esmtp (Exim 3.22 #4) id 1A3zqz-0004ap-00 for chemistry!at!ccl.net; Mon, 29 Sep 2003 16:22:25 +0100 Received: from li1vg (helo=localhost) by stoat.shef.ac.uk with local-esmtp (Exim 3.14 #2) id 1A3zqy-000179-00 for chemistry!at!ccl.net; Mon, 29 Sep 2003 16:22:24 +0100 Date: Mon, 29 Sep 2003 16:22:24 +0100 (BST) From: Val Gillet X-Sender: li1vg@stoat To: chemistry!at!ccl.net Subject: CCL: Call for papers: Chemoinformatics Sheffield 2004 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) Call For Papers The Chemical Structure Association Trust and the Molecular Graphics and Modelling Society announce their Third Joint Sheffield Conference on Chemoinformatics. The conference will be held in The Octagon Centre and Tapton Hall of Residence, University of Sheffield, UK, > from 21st to 23rd April 2004. Offers of papers are welcomed in all aspects of chemoinformatics. Possible topics include (but are not limited to): * High-Throughput Screening including: assay QC and its influence on data mining; design of screening collections; systems based design * Virtual Screening including: docking and pharmacophore analysis; similarity methods; clustering * Computational Methods for Lead Identification and Optimisation including: structure-activity methods; structure-based design * New Algorithms and Technologies including: machine learning algorithms; data handling and visualisation * Case histories incorporating any of the above Authors wishing to submit a paper for consideration should send a title and abstract to Val Gillet (v.gillet!at!sheffield.ac.uk) by 31st October 2003. Submissions will be selected as either oral contributions or posters by the Organising Committee. In selecting papers for oral presentation we will seek to achieve a balance between new methodologies and successful applications of methods. Further details of the conference and registration information will follow later in the year and will be posted at cisrg.shef.ac.uk/shef2004. From ccl@ccl.net Mon Sep 29 13:55:38 2003 -0400 Return-Path: Reply-To: From: "Mark Thompson" To: Subject: CCL: Ring detection Date: Mon, 29 Sep 2003 09:07:17 -0700 Message-ID: <000901c386a3$c160e590$0200a8c0@planaria> Here is a very nice method to detect rings: "Efficient Exact Solution of the Ring Perception Problem" Renzo Balducci and Robert S. Pearlman J. Chem. Inf. Comput. Sci. 1994, 34, 822-831 I use this approach in ArgusLab and it's proven to be efficient and robust. Cheers, Mark *************************** Mark Thompson, PhD Planaria Software LLC PO Box 55207 Seattle, WA 98155 mark:at:arguslab.com http://www.arguslab.com *************************** -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request:at:ccl.net]On Behalf Of Richard Gillilan Sent: Monday, September 29, 2003 5:54 AM To: Geoff Hutchison Cc: John McKelvey; chemistry:at:ccl.net Subject: CCL:Ring detection Do you know if any of these codes have published their method? I have a paper somewhere (I think it was actually Journal of Mathematical Chemistry) that gives a method, but also gives me the impression that a fully-general algorithm is non-trivial task. I'll try to dig it up. In my OrderFour code, Ryan Lilien and I simply invented our own tree-search method for doing this, but I have no proof of how general it is ... certainly works on all the rings I have encountered so far and also can find arbitrarily large rings. Anyone is welcome to look at the code, it is C++. Just drop me an email. Richard On Saturday, September 27, 2003, at 08:04 PM, Geoff Hutchison wrote: >> Can anyone point me to a code [preferably fortran ,{I know}] for >> determining rings and size for atoms, given a connectivity list? > > I can't point you to a Fortran code for it, but I can point you to > several open source codes that do this: > > OpenBabel (C++): http://openbabel.sf.net/ > JOELib (Java): http://joelib.sf.net/ > CDK (Java): http://cdk.sf.net/ > > There are undoubtedly other codes, but I'm the most familiar with > these three. > > Cheers, > -Geoff > From chemistry-request@ccl.net Mon Sep 29 14:40:30 2003 Received: from bureau6.utcc.utoronto.ca (bureau6.utcc.utoronto.ca [128.100.132.16]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8TIdwmK012349 for ; Mon, 29 Sep 2003 14:39:58 -0400 Received: from mditdell.mdit.utoronto.ca ([128.100.251.12] HELO MditDell ident: IDENT-NOT-QUERIED [port 1128]) by bureau6.utcc.utoronto.ca with SMTP id <464399-25483>; Mon, 29 Sep 2003 14:39:42 -0400 From: "William Wei" To: "CCLers" Subject: Gaussian:Consistency failure #2 in CalDSu Date: Mon, 29 Sep 2003 14:43:26 -0500 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2727.1300 Importance: Normal X-Spam-Status: No, hits=-0.4 required=7.0 tests=MSGID_GOOD_EXCHANGE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, All, I was trying to do a Potential Energy Surface Scan with a carboxylate group rotation which is attached to a Phenol ring using Gaussian 98. I can not get through the calculation because the error:Consistency failure #2 in CalDSu. Input: #P B3LYP/6-31+G(d) Opt(Z-matrix) SCF(QC,MaxCycle=1000) .... D11= 0.00 S 14 12.00 Output: ................ Direct SCF. Tight linear equation convergence will be used. IExCor= 402 DFT=T Ex=B+HF Corr=LYP ScaHFX= 0.2000 ScaDFX= 0.8000 0.7200 1.0000 0.8100 IRadAn= 0 IRanWt= -1 IRanGd= 0 ICorTp=0 RB+HF-LYP wavefunction. Quadratic Convergence SCF Method. Line search only if initial step raises energy. Integral symmetry usage will be decided dynamically. Petite list used in FoFDir. MinBra= 0 MaxBra= 2 Meth= 1. IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 1 JSym2E=1. Iteration 1 EE=-1.412316206821171D+03 Rotation gradient= 1.101D+01 Gradient too large for Newton-Raphson or scaled steepest descent -- use steepest descent instead. ILin= 1 X=0.000D+00 Y=-1.412316206821D+03 DE= 0.00D+00 ILin= 2 X=1.883D-01 Y=-1.553750987307D+03 DE=-1.41D+02 ................. An expanding polynomial of degree 3 produced 0.0014 Iteration 3 EE=-3.853921411389580D+03 Rotation gradient= 1.913D+02 Gradient too large for Newton-Raphson or scaled steepest descent -- use steepest descent instead. ILin= 1 X=0.000D+00 Y=-3.853921411390D+03 DE= 0.00D+00 ILin= 2 X=9.159D-03 Y=-1.411316429667D+03 DE= 2.44D+03 ....................... ILin=10 X=5.725D-04 Y=-3.867590374611D+03 DE=-1.37D+01 Polynomial fit failed. ILin=11 X=4.048D-04 Y=-3.868980705028D+03 DE=-1.51D+01 Polynomial fit failed. ILin=12 X=2.862D-04 Y=-3.866325695930D+03 DE=-1.24D+01 Polynomial fit failed. ILin=13 X=2.024D-04 Y=-3.865204309062D+03 DE=-1.13D+01 Polynomial fit failed. .............. ILin=16 X=4.856D-07 Y=-3.871893814499D+03 DE= 2.52D-01 The polynomial fit failed. Using point 1. A contracting polynomial of degree 16 produced 0.0000 Search did not lower the energy significantly. No lower point found -- run aborted. Error termination via Lnk1e in /usr/people/tripos/g98/l508.exe. Job cpu time: 4 days 2 hours 0 minutes 41.5 seconds. File lengths (MBytes): RWF= 51 Int= 0 D2E= 0 Chk= 11 Scr= 1 Could anybody give me clue for what might be the problem? And how can I get through the scan? Thank you very much. Have a good day, William ------------------------- William Wei Molecular Design and Information Technology (MDIT) center Faculty of Pharmacy, University of Toronto 19 Russell Street, Toronto, ON. M5S 2S2 Tel: 1-416-946-8469 Fax: 1-416-978-8511 Email: william.wei{at}utoronto.ca william{at}phm.utoronto.ca From chemistry-request@ccl.net Mon Sep 29 15:12:11 2003 Received: from smtp.ice.mpg.de (smtp.ice.mpg.de [195.37.47.8]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8TJBemK013162 for ; Mon, 29 Sep 2003 15:11:40 -0400 Received: from uni-koeln.de (unknown [10.4.21.5]) by smtp.ice.mpg.de (GATE -1- /Central Mail System on MPI for Chemical Ecology) with ESMTP id E9A4E8794 for ; Mon, 29 Sep 2003 21:11:39 +0200 (CEST) Message-ID: <3F7883EA.6040805_at_uni-koeln.de> Date: Mon, 29 Sep 2003 21:11:38 +0200 From: Christoph Steinbeck User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.5b) Gecko/20030723 Thunderbird/0.1 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry_at_ccl.net Subject: Re: CCL:Ring detection References: <000901c386a3$c160e590$0200a8c0@planaria> In-Reply-To: <000901c386a3$c160e590$0200a8c0@planaria> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=-2.6 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,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) Me too, me too... I implemented the SSSR method by Figueras [1] as part of our Chemistry Development Kit (CDK), http://cdk.sourceforge.net, and it is even more efficient and robust :-) Cheers, Chris [1] Figueras, J. Ring Perception Using Breadth-First Search. J. Chem. Inf. Comput.Sci. 1996, 36, 986-991. -- Dr. Christoph Steinbeck (e-mail: c.steinbeck_at_uni-koeln.de) Groupleader Junior Research Group for Applied Bioinformatics Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Z|lpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. Mark Thompson wrote: > Here is a very nice method to detect rings: > > "Efficient Exact Solution of the Ring Perception Problem" > Renzo Balducci and Robert S. Pearlman > J. Chem. Inf. Comput. Sci. 1994, 34, 822-831 > > I use this approach in ArgusLab and it's proven to be efficient and robust. > > Cheers, > Mark > > *************************** > Mark Thompson, PhD > Planaria Software LLC > PO Box 55207 > Seattle, WA 98155 > > mark_at_arguslab.com > http://www.arguslab.com > *************************** > > -----Original Message----- > From: Computational Chemistry List [mailto:chemistry-request_at_ccl.net]On > Behalf Of Richard Gillilan > Sent: Monday, September 29, 2003 5:54 AM > To: Geoff Hutchison > Cc: John McKelvey; chemistry_at_ccl.net > Subject: CCL:Ring detection > > > Do you know if any of these codes have published their method? > I have a paper somewhere (I think it was actually Journal of > Mathematical Chemistry) that gives a method, but also gives me the > impression that a fully-general algorithm is non-trivial task. I'll > try to dig it up. In my OrderFour code, Ryan Lilien and I simply > invented our own > tree-search method for doing this, but I have no proof of how > general it is ... certainly works on all the rings I have > encountered so far and also can find arbitrarily large rings. > Anyone is welcome to look at the code, it is C++. Just drop > me an email. > > Richard > > On Saturday, September 27, 2003, at 08:04 PM, Geoff Hutchison wrote: > > >>>Can anyone point me to a code [preferably fortran ,{I know}] for >>>determining rings and size for atoms, given a connectivity list? >> >>I can't point you to a Fortran code for it, but I can point you to >>several open source codes that do this: >> >>OpenBabel (C++): http://openbabel.sf.net/ >>JOELib (Java): http://joelib.sf.net/ >>CDK (Java): http://cdk.sf.net/ >> >>There are undoubtedly other codes, but I'm the most familiar with >>these three. >> >>Cheers, >>-Geoff >> > > > > > > > > > > > > > > > -= 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) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > > From chemistry-request@ccl.net Mon Sep 29 18:53:20 2003 Received: from yakko.cimav.edu.mx (yakko.cimav.ecustomer.mx [148.223.46.2] (may be forged)) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8TMqnmK018295 for ; Mon, 29 Sep 2003 18:52:49 -0400 Received: from yakko (localhost [127.0.0.1]) by localhost.cimav.edu.mx (Postfix) with ESMTP id ABF961B8012 for ; Mon, 29 Sep 2003 15:52:36 -0700 (MST) Received: from localhost ([127.0.0.1]) by yakko.cimav.edu.mx (MailMonitor for SMTP v1.2.2 ) ; Mon, 29 Sep 2003 15:52:36 -0700 (MST) Received: from laquicom02 (byron.cimav.edu.mx [148.223.46.1]) by yakko.cimav.edu.mx (Postfix) with SMTP id 659331B8012 for ; Mon, 29 Sep 2003 15:52:36 -0700 (MST) Message-ID: <028a01c386dc$635b70d0$8400000a@laquicom02> From: "Dr. Daniel Glossman-Mitnik" To: Subject: DFT with 3-21G* Date: Mon, 29 Sep 2003 16:52:40 -0600 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0287_01C386AA.185100F0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 Disposition-Notification-To: "Dr. Daniel Glossman-Mitnik" X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=1.0 required=7.0 tests=HTML_30_40,HTML_MESSAGE version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------=_NextPart_000_0287_01C386AA.185100F0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear netters: It is very usual to find papers where geometry optimizations of medium and large molecules are performed with the=20 Hartree-Fock method using the 3-21G* basis set. And this is reported as giving almost as good geometries as HF/6-31G* in a fraction of time (see, for example, the excellent recent=20 book by Lewars). However, there are few examples in the=20 literature about doing DFT optimizations with 3-21G* (the same book quotes that they are very unsual, but doesn't state why). Is there any important reason for not using 3-21G* in DFT geometry optimizations, specially with large molecules?=20 I have performed some calculations (very limited, of course) and found that PBE1PBE/3-21G* gives geometries of similar quality as PBE1PBE/6-31G*, in a third of CPU time. Thanks in advance Dr. Daniel Glossman-Mitnik =20 ********************************************************************** Dr. Daniel Glossman-Mitnik Centro de Investigaci=F3n en Materiales Avanzados (CIMAV) LAQUICOM - Laboratorio de Qu=EDmica Computacional Miguel de Cervantes 120 - Comp. Ind. Chihuahua Chihuahua, Chih. 31109 - MEXICO Tel.: (52) 614 4391151 FAX: (52) 614 4391112 E-mail: daniel.glossman$at$cimav.edu.mx glossman$at$hotmail.com dglossman$at$yahoo.com ********************************************************************** ------=_NextPart_000_0287_01C386AA.185100F0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear netters:
 
It is very usual to find papers where = geometry=20 optimizations
of medium and large molecules are = performed with=20 the
Hartree-Fock method using the 3-21G* = basis set. And=20 this is
reported as giving almost as good = geometries as=20 HF/6-31G*
in a fraction of time (see, for = example, the=20 excellent recent
book by Lewars). However, there are few = examples in=20 the
literature about doing DFT = optimizations with=20 3-21G* (the same
book quotes that they are very unsual, = but doesn't=20 state why).
Is there any important reason for not = using 3-21G*=20 in DFT
geometry optimizations, specially with = large=20 molecules?
I have performed some calculations = (very limited,=20 of course)
and found that PBE1PBE/3-21G* gives = geometries of=20 similar
quality as PBE1PBE/6-31G*, in a third = of CPU=20 time.
 
Thanks in advance
 
          &nbs= p;            = ;            =    =20 Dr. Daniel Glossman-Mitnik   
 
 
****************************************************************= ******
Dr.=20 Daniel Glossman-Mitnik
Centro de Investigaci=F3n en Materiales = Avanzados=20 (CIMAV)
LAQUICOM - Laboratorio de Qu=EDmica Computacional
Miguel = de=20 Cervantes 120 - Comp. Ind. Chihuahua
Chihuahua, Chih. 31109 - = MEXICO
Tel.:=20 (52) 614 4391151
FAX: (52) 614 4391112
E-mail: daniel.glossman$at$cimav.edu.mx=
           = ;=20 glossman$at$hotmail.com
 &n= bsp;         =20 dglossman$at$yahoo.com
**********= ************************************************************
= ------=_NextPart_000_0287_01C386AA.185100F0--