From chemistry-request@server.ccl.net Thu Jun 7 04:35:10 2001 Received: from tigris.klte.hu ([193.6.138.33]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f578Z9517922 for ; Thu, 7 Jun 2001 04:35:09 -0400 Received: from anti07 (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP; Thu, 7 Jun 2001 10:32:29 +0200 Message-ID: <008b01c0ef2c$c4260780$3b8506c1@chem.klte.hu> From: "Tamas E. Gunda" To: "Dr. Wolfgang Utz" , References: Subject: Re: CCL:Software for mopac7 Date: Thu, 7 Jun 2001 10:35:10 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-2" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f578ZA517935 Hi, Mol2Mol can do, it has an option to capture coordinates from MOPAC-type output files, and associate the structure with charges or other computed data, with a very little user editing of the original file. Have a look at http://www.compuchem.com/mol2mol for a general overlook or http://www.klte.hu/~gundat/m2m/ and navigate here to Molfiles -> Z matrix etc Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 512 900/2472 fax: (+36-52) 512 914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm ----- Original Message ----- From: "Dr. Wolfgang Utz" To: Sent: Friday, June 01, 2001 5:33 PM Subject: CCL:Software for mopac7 > Hi, > > I'm looking for NT software which is able to read output files from mopac7. > We are using Webmo on a linux box and would like to load the .out file > together with atomic charges into the program. Furthermore we would like to > graph MEPs from the charges. > We have tested raswin, molekel, weblabviewer and we screened the ccl page > also. > Could some of you give us some links? > > Thankyou in advance > > Wolfgang > *********************************************************************** > Dr. Wolfgang Utz > Department of Medicinal Chemistry > Emil Fischer Center > Friedrich-Alexander University > Schuhstr. 19 > D-91052 Erlangen > Germany > Tel. 09131/8524100 > Fax 09131/8522585 > E-mail:utz@pharmazie.uni-erlangen.de > http://www.medchem.uni-erlangen.de/personel/utz.htm > *********************************************************************** > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Thu Jun 7 04:14:08 2001 Received: from xena.oai.co.uk ([195.172.92.249]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f578E7516971 for ; Thu, 7 Jun 2001 04:14:08 -0400 Received: by XENA with Internet Mail Service (5.5.2650.21) id ; Thu, 7 Jun 2001 09:14:06 +0100 Message-ID: <5FD8C12EECBBD4119DD10002B3027B9A667C3F@GABRIELLE> From: "Robinson, James" To: "'Sofia Godinho'" Cc: "'CCL'" Subject: RE: nth-order saddle point, n>1 Date: Thu, 7 Jun 2001 09:13:56 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" A transition state should have only ONE imaginary frequency. It would be odd if a single TS could lead to different products. How would the TS distinguish between paths to follow. I suspect that attempting to rationalise some mathematical result will be academic. I doubt if it has any physio/chemical meaning and is probably just the result of computation. Simple finding some computational result does not mean anything. Results should be reconciled with real-world problems. James -----Original Message----- From: Sofia Godinho [mailto:sgodinho@itqb.unl.pt] Sent: Wednesday, June 06, 2001 6:43 PM To: CCL Subject: CCL:nth-order saddle point, n>1 Dear CCLers, I wonder what is the chemical/physical meaning of a nth-order saddle point (n>1)? That is...for instance, when I get four immaginary frequencies does it mean that I have to "pass through" four vibrational modes to arrive to a minimum? (Or to three to get to a transition state?) Or it simply has nothing to do with it and it is only a mathematical definition of a saddle point? Or...? May I thank you in advance for any help, Sofia Sofia Godinho Ph-D student ITQB-UNL-Portugal email: sgodinho@itqb.unl.pt -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Thu Jun 7 06:55:14 2001 Received: from theo1.theochem.tu-muenchen.de ([129.187.157.20]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f57AtD508395 for ; Thu, 7 Jun 2001 06:55:14 -0400 Received: from theochem.tu-muenchen.de (theox210.theochem.tu-muenchen.de [129.187.157.71]) by theo1.theochem.tu-muenchen.de (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id MAA14833 for ; Thu, 7 Jun 2001 12:55:11 +0200 Sender: matveev@theochem.tu-muenchen.de Message-ID: <3B1F5D8D.2B2FBB15@theochem.tu-muenchen.de> Date: Thu, 07 Jun 2001 12:55:09 +0200 From: Alexei Matveev X-Mailer: Mozilla 4.51 [en] (X11; I; Linux 2.2.10 i586) X-Accept-Language: en, de-DE, ru MIME-Version: 1.0 To: chemistry@ccl.net Subject: latex bib-style for IJQC Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Dear CCLers, Not really related to Computational Chemistry: Anybody knows of a bibliography style (.bst file) for Int. J. Of Quantum Chemistry. What could I use instead? References there look like (no bold, no italics): Journal article: 1. Fletcher, T. R.; Rosenfeld, R. N. J Am Chem Soc 1985, 107, 2203-2212. Book: 2. Stothers, J. B. Carbon-13 NMR Spectroscopy; Academic: New York, 1972; Chapter 2. Sorted in order of appearance. ( http://www.interscience.wiley.com/jpages/0020-7608/authors.html ) Thanks in anticipation. Alexei Matveev From chemistry-request@server.ccl.net Thu Jun 7 08:29:52 2001 Received: from mail2.zrz.tu-berlin.de ([130.149.4.14]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f57CTq509328 for ; Thu, 7 Jun 2001 08:29:52 -0400 Received: from mailszrz.zrz.tu-berlin.de ([130.149.4.11]) by mail2.zrz.tu-berlin.de with esmtp (exim-3.22) id 157yv4-0004TH-00; Thu, 07 Jun 2001 14:29:46 +0200 Received: from natrium.chem.tu-berlin.de ([130.149.42.210]) by mailszrz.zrz.tu-berlin.de with esmtp (exim-3.22) id 157yv3-0003O4-00; Thu, 07 Jun 2001 14:29:45 +0200 Mime-Version: 1.0 X-Sender: chwu0531@mailszrz.zrz.tu-berlin.de Message-Id: In-Reply-To: <5FD8C12EECBBD4119DD10002B3027B9A667C3F@GABRIELLE> References: <5FD8C12EECBBD4119DD10002B3027B9A667C3F@GABRIELLE> Date: Thu, 7 Jun 2001 14:29:45 +0200 To: "Robinson, James" From: Christoph van =?iso-8859-1?Q?W=FCllen?= Subject: Re: CCL:nth-order saddle point, n>1 Cc: chemistry@ccl.net Content-Type: text/plain; charset="us-ascii" ; format="flowed" >A transition state should have only ONE imaginary frequency. > the reason is that if it is a higher-order TS, there will be another one with lower energy, and molecules are sharp enough to take that one. -- +---------------------------------+-------------------------------------+ | Prof. Christoph van Wullen | Tele-Phone (+49) (0)30 314 27870 | | Technische Universitat Sekr. C3 | Tele-Fax (+49) (0)30 314 23727 | | Strasse des 17. Juni 135 | eMail | | D-10623 Berlin, Germany | Christoph.vanWullen@TU-Berlin.De | +---------------------------------+-------------------------------------+ From chemistry-request@server.ccl.net Thu Jun 7 06:50:46 2001 Received: from mail.fqspl.com.pl ([212.244.147.7]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f57Aog508295 for ; Thu, 7 Jun 2001 06:50:44 -0400 Received: (qmail 13832 invoked from network); 7 Jun 2001 12:52:54 -0000 Received: from test.fqspl.com.pl (HELO test) (10.10.10.50) by mail.fqspl.com.pl with SMTP; 7 Jun 2001 12:52:54 -0000 Message-ID: <00e301c0ef40$0ff65080$320a0a0a@fqspl.com.pl> From: "Victor Anisimov" To: References: <00c301c0e768$a3d56460$320a0a0a@fqspl.com.pl> Subject: Summary: Protein structures Date: Thu, 7 Jun 2001 12:53:18 +0200 X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Dear Netters, A week ago I asked a question regarding existence of reliable automatic assignment of hydrogen atoms to large proteins with possible structure verification. The short answer is NO. There are many powerful and smart graphical user interfaces but all of them require a posteriori expert's check. You know well all these brand names therefore I will not repeat them. I may guess that the best program for adding hydrogen atoms to relatively small proteins is AMPAC graphical interface. The situation with large proteins is less favourive. It means, if one decide running QM calculation on 100 000 atoms protein the guy should be ready to spend few months on atom by atom manual check. Hope the situation will change in future but now we can rely on our selves only. I'm very grateful to Deepak, Jeremy Greenwood, Wayne Steinmetz, Denys Bashtovyy, and Andy Holder for valuable suggestions. With kind regards, Victor. ================================================== Victor Anisimov, PhD, Senior Software Researcher - Computational Chemist FQS Poland, a Fujitsu company ul. Starowislna 13-15, 31-038 Krakow, Poland Email: victor@fqspl.com.pl Tel.(+48 12) 429-4345 Fax(+48 12) 429-6124 ================================================== From: "Deepak" > > In my experience, there is no better way of handling > the hydrogen issue than using a program with good, > well-parameterized forcefield (such as CHARMM or > AMBER). This is how I have always handled the pre-QM > treatment. Although I know people who will use > something like CHEM-3D and the MM2 module inherent in > that to treat the hydrogens, but I am not sure that > works as well. > > Regards > > Deepak. From: "Jeremy Greenwood" > > One little trick for repairing protein structures: build a homology > model with 100% homology, using e.g. Swissprot, which fixes up the > residues. Then you can put back the non-residue atoms (waters etc.) > from the original file, and start working on the protons. > > The site has all kinds of nifty features. > > http://www.expasy.ch/sprot/sprot-top.html > > Hope this helps a little, > > Jeremy > ---------------------------------------------------------------------- > Jeremy Greenwood jeremy.greenwood@i.am > Department of Medicinal Chemistry bh +45 35306117 > Royal Danish School of Pharmacy fx +45 35306040 > Universitetsparken 2, DK-2100 Copenhagen, Denmark ah +45 32598030 > ---------------------------------------------------------------------- From: "Wayne Steinmetz" > > I have learned that the Richardson's at Duke University > have been addressing the problem of ferreting incorrect > X-ray structures out of the literature. I suggest that you > contact Jane Richardson. From: "Denys Bashtovyy" > > similar question was asked once at PDB mailing list, maybe that thread will > be of interest to you: > http://www.rcsb.org/pdb/lists/pdb-l/199902/msg00023.html > and > http://www.rcsb.org/pdb/lists/pdb-l/199902/msg00025.html > > I think you should repeat your question at that list, could be that some new > soft appeared since 1999 (also, Dr.Vriend could give a good advice again) > > I had similar problem, trying to assign atom types and bond orders for the > molecule of ~60000 atoms. InsightII's Biopolymer module worked more or less > well for that (it assigns protonation states based on pH, recognizes bond > orders etc). But if you do it regularly with many different molecules, I am not > sure Biopolymer is a best automated tool. > > Best wishes, > > Denys > > -- > Denys Bashtovyy > http://www.brc.hu/~tpali/group/index.html From: "Andy Holder @ UMKC" > > Our AMPAC graphical user interface has an excellent algorithm for adding Hs > to pdb structures. Several users have told us that it is better than any > other available method. We would be happy to provide a demo version. > > Best regards, Andy Holder > > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > DR. ANDREW HOLDER > President > > Semichem, Inc. || Email: andy@semichem.com > PO Box 1649 || Web: http://www.semichem.com > Shawnee Mission, KS 66222 || Phone Number: (913) 268-3271 > || Fax Number: (913) 268-3445 > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Thu Jun 7 08:10:12 2001 Received: from mail.fqspl.com.pl ([212.244.147.7]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f57C9h509088 for ; Thu, 7 Jun 2001 08:10:03 -0400 Received: (qmail 14997 invoked from network); 7 Jun 2001 14:12:07 -0000 Received: from test.fqspl.com.pl (HELO test) (10.10.10.50) by fqspl.com.pl with SMTP; 7 Jun 2001 14:12:07 -0000 Message-ID: <011d01c0ef4b$20a3b840$320a0a0a@fqspl.com.pl> From: "Victor Anisimov" To: References: <00e401c0e827$3d6ce850$320a0a0a@fqspl.com.pl> Subject: Summary: protein ionization Date: Thu, 7 Jun 2001 14:12:31 +0200 X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Dear CCLers, Some time ago I asked references on research papers modelling protein ionization as a reaction on the solvent environment. Here are the responses. Many thanks to Stanislaw Oldziej, Jordi Villa, and Paul Beroza. With kind regards, Victor. ================================================== Victor Anisimov, PhD, Senior Software Researcher - Computational Chemist FQS Poland, a Fujitsu company ul. Starowislna 13-15, 31-038 Krakow, Poland Email: victor@fqspl.com.pl Tel.(+48 12) 429-4345 Fax(+48 12) 429-6124 ================================================== From: "Stanislaw Oldziej (Wizytator Nowej Francji)" > > Have look at reference from our group. > > D.R. Ripoll, Yu. Vorobjev, A. Liwo, J.A. Vila and H.A. Scheraga. > Coupling between folding and ionization equilibrium. Effects of pH on the > conformational preferences of oligopeptides. > {\it J. Mol. Biol.}, {\bf 1996}, 264, 779-783. > > > Best regards from Gdansk > > Stanislaw Oldziej > > =============================================================================== > Dr Stanislaw Oldziej > Faculty of Chemistry, > University of Gdansk, "Plucie to nie to samo co wolnosc wypowiedzi" > Molecular Modelling Group > Sobieskiego 18, 80-952 Gdansk > POLAND > tel:(048-58)-345-0361 > fax:(048-58)-341-0357 > =============================================================================== From: "Jordi Villa" > > Check > > Consistent Calculations of pKa's of Ionizable Residues in Proteins: Semi-Microscopic and > Macroscopic Approaches, Y. Y. Sham, Z. T. Chu and A. Warshel, J. Phys. > Chem. B 101, 4458-4472 (1997). > > Jordi > > -- > Jordi Villa i Freixa > jorgevil@usc.edu http://laetro.usc.edu/wgroup/people/jorgevil > Department of Chemistry, University of Southern California > Los Angeles, CA, USA, 90089-1062 > Tlf: 1-(213)-740 7671 Fax: 1-(213)-740 2701 From: "Paul Beroza" > > Here's a reference for you: > > W.H. Richardson, C. Peng, D. Bashford, L. Noodleman and D.A. Case. > Incorporating solvation effects into density functional theory: > Calculation of absolute acidities. Int. J. Quant. Chem. 61, 207-217 (1997) > > Paul Beroza > Telik, Inc. > pberoza@telik.com From chemistry-request@server.ccl.net Thu Jun 7 10:20:51 2001 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f57EKp511159 for ; Thu, 7 Jun 2001 10:20:51 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id KAA00635; Thu, 7 Jun 2001 10:20:51 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Thu, 07 Jun 2001 10:21:18 -0400 (Eastern Daylight Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GEK00DKNCZDM2@lvlmail.unitedcatalysts.com> for chemistry@ccl.net; Thu, 07 Jun 2001 10:16:25 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Thu, 07 Jun 2001 10:21:03 -0400 Content-return: allowed Date: Thu, 07 Jun 2001 10:20:59 -0400 From: "Shobe, Dave" Subject: RE: nth-order saddle point, n>1 To: "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629DDAAF66@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f57EKp511160 A question about "higher-order" saddle points: What happens for functions of the form: E(r,.theta.) = r**n * sin(k*.theta.) for various n and k? These should have k ridges and k valleys converging on r=0. (I should say at some point that r and .theta. are polar coordinates not cartesian). Anyway, how does the usual vibrational analysis treat such points? --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: Robinson, James [mailto:james.robinson@evotecoai.com] Sent: Thursday, June 07, 2001 4:14 AM To: 'Sofia Godinho' Cc: 'CCL' Subject: CCL:nth-order saddle point, n>1 A transition state should have only ONE imaginary frequency. It would be odd if a single TS could lead to different products. How would the TS distinguish between paths to follow. I suspect that attempting to rationalise some mathematical result will be academic. I doubt if it has any physio/chemical meaning and is probably just the result of computation. Simple finding some computational result does not mean anything. Results should be reconciled with real-world problems. James -----Original Message----- From: Sofia Godinho [mailto:sgodinho@itqb.unl.pt] Sent: Wednesday, June 06, 2001 6:43 PM To: CCL Subject: CCL:nth-order saddle point, n>1 Dear CCLers, I wonder what is the chemical/physical meaning of a nth-order saddle point (n>1)? That is...for instance, when I get four immaginary frequencies does it mean that I have to "pass through" four vibrational modes to arrive to a minimum? (Or to three to get to a transition state?) Or it simply has nothing to do with it and it is only a mathematical definition of a saddle point? Or...? May I thank you in advance for any help, Sofia Sofia Godinho Ph-D student ITQB-UNL-Portugal email: sgodinho@itqb.unl.pt -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Thu Jun 7 10:26:52 2001 Received: from gq3.fcen.uba.ar ([157.92.18.19]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f57EQk511376 for ; Thu, 7 Jun 2001 10:26:49 -0400 Received: from RUPERTO([157.92.19.40]) (668 bytes) by gq3.fcen.uba.ar via sendmail with P:smtp/R:inet_hosts/T:smtp (sender: ) id for ; Thu, 7 Jun 2001 11:23:41 -0300 (ARST) (Smail-3.2.0.101 1997-Dec-17 #6 built 1998-Jul-13) Message-Id: Date: Thu, 7 Jun 2001 11:23:41 -0300 (ARST) X-Sender: albores@cuca.q1.fcen.uba.ar X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: Pablo Albores Subject: convergence failure Hello, i am running a geometry optimization of an open-shell system with an unpair electron, that is in principle spin multipliciy = 2. I try with HF and DFT but the system doesn't converge (I try with 100 cycles). My starting geometry is experimental (X-ray data). Any sugerence?. From chemistry-request@server.ccl.net Thu Jun 7 10:37:10 2001 Received: from gate.syntem-sa.fr ([146.19.248.65]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f57Eb9511553 for ; Thu, 7 Jun 2001 10:37:09 -0400 Received: (from uucp@localhost) by gate.syntem-sa.fr (980427.SGI.8.8.8/980728.SGI.AUTOCF) id QAA80362 for <@firewall.syntem-sa.fr:chemistry@ccl.net>; Thu, 7 Jun 2001 16:36:06 +0200 (MDT) Received: from syntem-sa.fr(10.0.0.2) by gate.syntem-sa.fr via smap (4.1) id xma484277; Thu, 7 Jun 01 16:35:35 +0200 Received: from victoria.syntem-sa.fr (victoria.syntem-sa.fr [10.0.0.44]) by laetitia.syntem-sa.fr (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id QAA12025 for <@laetitia.syntem-sa.fr:chemistry@ccl.net>; Thu, 7 Jun 2001 16:32:40 +0200 (MDT) Received: from syntem-sa.fr (localhost [127.0.0.1]) by victoria.syntem-sa.fr (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id QAA04707 for ; Thu, 7 Jun 2001 16:38:59 +0200 (MDT) Sender: dturner@syntem-sa.fr Message-ID: <3B1F9203.34DBA5DB@syntem-sa.fr> Date: Thu, 07 Jun 2001 16:38:59 +0200 From: David Turner Reply-To: dturner@syntem.com Organization: Computational Drug Design, Syntem 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: Docking of Covalently Bound ligands References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all Can anybody point me to some overviews/discussions of the docking of ligands that are (or are potentially) covalently bound to the receptor site. I am looking at this mainly but not solely from the view-point of high throughput virtual screening. David -- ________________________________________________________________ David Turner Synt:em Senior Modeling Scientist Parc Scientifique G.Besse Computational Drug Discovery 30000 Nimes email: dturner@syntem.com France Tel: Switchboard: +33 (0)4 66 04 86 66 Fax: +33 (0)4 66 04 86 67 Direct Line: +33 (0)4 66 04 22 85 ________________________________________________________________ Discover New Drugs, Discover Synt:em http://www.syntem.com ________________________________________________________________ From chemistry-request@server.ccl.net Thu Jun 7 14:52:26 2001 Received: from ultra.chem.ucsb.edu ([128.111.114.119]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f57IqQ515784 for ; Thu, 7 Jun 2001 14:52:26 -0400 Received: from localhost (bushnell@localhost) by ultra.chem.ucsb.edu (8.9.3+Sun/8.9.1) with ESMTP id LAA15378; Thu, 7 Jun 2001 11:51:58 -0700 (PDT) Date: Thu, 7 Jun 2001 11:51:58 -0700 (PDT) From: John Bushnell To: Victor Anisimov cc: chemistry@ccl.net Subject: Re: CCL:Summary: Protein structures In-Reply-To: <00e301c0ef40$0ff65080$320a0a0a@fqspl.com.pl> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 7 Jun 2001, Victor Anisimov wrote: > I may guess that the best program for adding hydrogen atoms to relatively > small proteins is AMPAC graphical interface. The situation with large > proteins is less favourive. It means, if one decide running QM calculation > on 100 000 atoms protein the guy should be ready to spend few months > on atom by atom manual check. Hope the situation will change in future > but now we can rely on our selves only. Wow, are people really doing quantum mechanics on proteins with 100,000 atoms these days?! How many cpu hours (months) does that involve? - John bushnell@chem.ucsb.edu