From chemistry-request@server.ccl.net Mon Jan 7 10:30:59 2002 Received: from hschipaa.hsc.usf.edu ([131.247.16.97]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g07FUxI26027 for ; Mon, 7 Jan 2002 10:30:59 -0500 Received: from hschipaa.hsc.usf.edu ([131.247.16.105]) by hsc.usf.edu (8.9.3+Sun/8.9.3) with SMTP id KAA02504; Mon, 7 Jan 2002 10:30:53 -0500 (EST) Message-ID: <3C39BF32.34E0A775@mindless.com> Date: Mon, 07 Jan 2002 10:30:58 -0500 From: David Smith X-Mailer: Mozilla 4.78 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: amor san juan CC: Chemistry@ccl.net Subject: Re: CCL:Freeware for ligand & protein preparation References: <20020105093143.90807.qmail@web12806.mail.yahoo.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Try ADT (Autodocktools) http://www.scripps.edu/pub/olson-web/doc/autodock/tools.html#ADT good luck. amor san juan wrote: > > To All Autodockers, > > Is there anyone who use a shareware in preparation of > ligand & protein prior to using AutoDock program. Im > looking for alternative for the commercial softwares > such as Sybyl & Amber. > > Thanks for all suggestions to be given. > > Amor San Juan > University of the Philippines > 1101 Diliman, Quezon City > Philippines > > __________________________________________________ > Do You Yahoo!? > Send FREE video emails in Yahoo! Mail! > http://promo.yahoo.com/videomail/ > > -= 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 Mon Jan 7 08:27:36 2002 Received: from Salicet.ucd.ie ([137.43.1.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g07DRaI24330 for ; Mon, 7 Jan 2002 08:27:36 -0500 X-Confirm-reading-to: Laurence.Cuffe@ucd.ie X-PMrqc: 1 Received: from CONVERSION-DAEMON.Salicet.ucd.ie by Salicet.ucd.ie (PMDF V6.1 #40617) id <0GPK00D01KTGLA@Salicet.ucd.ie> for CHEMISTRY@ccl.net; Mon, 07 Jan 2002 13:27:26 +0000 (GMT) Received: from elvira.ucd.ie ([137.43.24.26]) by Salicet.ucd.ie (PMDF V6.1 #40617) with ESMTP id <0GPK006B1JE0PG@Salicet.ucd.ie>; Mon, 07 Jan 2002 12:44:24 +0000 (GMT) Date: Mon, 07 Jan 2002 12:44:40 +0000 From: Laurence Cuffe Subject: Re: CCL:Zn ion coordination In-reply-to: To: Sergio Manzetti , CHEMISTRY@ccl.net Message-id: <3C399838.5200.86B851@localhost> Organization: University College Dublin X-Mailer: Pegasus Mail for Win32 (v3.12c) Content-type: TEXT/PLAIN Priority: normal Date sent: Sun, 06 Jan 2002 18:06:20 +0100 From: Sergio Manzetti Subject: CCL:Zn ion coordination To: Chemistry Discussion G >Dear CCLers, a Zn ion gives me headaches since it occurs hexa-coordinated in >a molecular simulations, is tricoordinated in the crystal structures, but is >cited to be tetra- and penta-coordinated at transition states in >metalloenzymes. The neighbours chelating this Zn-ion are: Imidazole ring, >Glutamate and a backbone carbonyl oxygen. > >Can anybody recommend a good review or publication of Zn in metalloenzymes? >I have Parkin (2001), but my questions still remains after reading it. > Have you seen Nadassy's web site? www.ebi.ac.uk/~nadassy/analysis.htm also Alberts I.L. Nadassy K. Wodak, S. J. Protein science 1998 7:1700-1716 Analysis of zinc binding sites in protein crystal structures is worth looking at All the best Laurence Cuffe >Best regards and Happy New year > >Sergio > > > >-= 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 Mon Jan 7 15:45:40 2002 Received: from fort-point-station.mit.edu ([18.7.7.76]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g07KjeI30804 for ; Mon, 7 Jan 2002 15:45:40 -0500 Received: from grand-central-station.mit.edu (GRAND-CENTRAL-STATION.MIT.EDU [18.7.21.82]) by fort-point-station.mit.edu (8.9.2/8.9.2) with ESMTP id PAA04477 for ; Mon, 7 Jan 2002 15:45:36 -0500 (EST) Received: from melbourne-city-street.mit.edu (MELBOURNE-CITY-STREET.MIT.EDU [18.7.21.86]) by grand-central-station.mit.edu (8.9.2/8.9.2) with ESMTP id PAA15183 for ; Mon, 7 Jan 2002 15:41:47 -0500 (EST) Received: from jwolfskill.mit.edu (ERRATA.MIT.EDU [18.36.0.129]) by melbourne-city-street.mit.edu (8.9.2/8.9.2) with ESMTP id PAA28148 for ; Mon, 7 Jan 2002 15:41:41 -0500 (EST) Message-Id: <5.0.2.1.2.20020107152906.00b07140@po14.mit.edu> X-Sender: wolfskil@po14.mit.edu (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Mon, 07 Jan 2002 15:41:38 -0500 To: chemistry@server.ccl.net From: Jud Wolfskill Subject: New Book on Systems Biology available Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed I thought readers of the Computational Chemistry List might be interested in this book. For more information please visit http://mitpress.mit.edu/0262112663 Foundations of Systems Biology edited by Hiroaki Kitano 7 x 9, 320 pp., 100 illus., cloth, ISBN 0262112663 This book covers the central topics of systems biology: comprehensive and automated measurements, reverse engineering of genes and metabolic networks > from experimental data, software issues, modeling and simulation, and system-level analysis. Best, Jud Jud Wolfskill Associate Publicist MIT Press 5 Cambridge Center, 4th Floor Cambridge, MA 02142 617.253.2079 617.253.1709 fax wolfskil@mit.edu From chemistry-request@server.ccl.net Tue Jan 8 07:45:11 2002 Received: from nikias.cc.uoa.gr ([195.134.68.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g08CjAI22716 for ; Tue, 8 Jan 2002 07:45:11 -0500 Received: from localhost (jkerkin@localhost) by nikias.cc.uoa.gr (8.9.3/8.9.3) with SMTP id OAA08426 for ; Tue, 8 Jan 2002 14:45:05 +0200 (EET) Date: Tue, 8 Jan 2002 14:45:05 +0200 (EET) From: Ioannis Kerkines To: chemistry@ccl.net Subject: Re: CCL:Frozen core definition in Gaussian In-Reply-To: <200201080024.QAA07700@talisker.emsl.pnl.gov> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I agree, I've had once the same problem doing the same calculation on a Kr containing molecule with Molpro and Gaussian. Molpro's frozen core contains the 3d electrons, but Gaussian's does not, so one has to be very careful to what is the "default" in each program. I'd just like to point out that a similar situation exists also with Zn: Although no low-lying states exist with excitations from the 3d orbitals (see the Moore's atomic data tables), it is not easy to estimate the actual effect of this "semi-core" 3d shell. As Prof. Peterson pointed out, one would need basis sets specifically developed for this situation, and I am not aware of any (of course, I am not talking about pseudopotentials). I myself have seen "strange" results when correlating the 3d shell in Zn or Kr (e.g. lowering of the binding energy), which I am not sure of their validity. I have, too, seen papers about Zn compounds and there is no mention about whether the 3d orbitals are included or not. I only figured it out after noticing the code with which the calculation was done, and comparing the total energy with my results. Best regards, Ioannis On Mon, 7 Jan 2002, Kirk Peterson wrote: > > All: > > after stumbling across something today, I thought that it would > be of enough interest to bring it to people's attention. Perhaps > this is common knowledge, but I'm guessing it's not. When > carrying out ab initio calculations on molecules containing 3rd row > main group elements, i.e., Ga - Kr, the natural definition of the > core electrons for these 3rd row elements (at least in my opinion) > includes the following electrons: 1s, 2s, 2p, 3s, 3p, and 3d. (Of course, > when doing calculations on Ga- or Ge-containing species, one should at > some point be interested in 3d correlation.) Much to my surprise, > it appears that the default frozen core in Gaussian does NOT > include the 3d electrons (i.e., the 3d electrons are included in > the valence shell with the 4s and 4p electrons). Perhaps this was > to make the definition consistent with the 3d transition metals where > they are obviously valence, but I would be willing to guess that not > too many people would guess this choice for an element such as Br. > > Besides probably doing much more work than desired (correlating 10's > of extra electrons usually adds nontrivial amounts of computational > expense), most basis sets for these elements do not describe 3d correlation. > In particular, the cc-pVnZ basis sets for these elements were developed for > valence correlation only, the definition of which did NOT include the 3d > electrons of these elements. So in addition to the added computational expense, > you might actually do some harm since one may be introducing extra BSSE > > from correlating core-like electrons with a valence basis set (never a good idea). > > Of course, one can change the definition of the frozen core in Gaussian > by using the old ReadWindow (RW) option, but the quick FC (i.e., > MP2=FC or just MP2) will result in the situation described above. I guess > one should note that just mentioning in a publication that the frozen core > approximation was used is surprisingly ambiguous... > > best wishes, > > Kirk Peterson > Washington State University > EMSL/Pacific Northwest Nat'l Laboratory > > -= 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 Tue Jan 8 08:07:28 2002 Received: from mailhub.health.nb.ca ([207.179.181.34]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g08D7SI23262 for ; Tue, 8 Jan 2002 08:07:28 -0500 Received: from oncoirmb ([10.10.100.12]) by mailhub.health.nb.ca (Post.Office MTA v3.5.3 release 223 ID# 607-57574U3000L300S0V35) with SMTP id ca for ; Tue, 8 Jan 2002 09:07:18 -0400 Message-ID: <003d01c19845$9cda4480$0c640a0a@oncoirmb> From: miroslavac@health.nb.ca (Miroslava Cuperlovic-Culf) To: Subject: RNA/DNA modelling Date: Tue, 8 Jan 2002 09:08:48 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_003A_01C19824.156B9060" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 This is a multi-part message in MIME format. ------=_NextPart_000_003A_01C19824.156B9060 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear All, I would like to find out what are the most popular (best) programs for = modelling of DNA/protein interactions and RNA/RNA antisense bonding. Off = course shareware programs are the most interesting but we wouldn't mind = even paying for the good one(s).=20 Thanks for your help, Mira Miroslava Cuperlovic-Culf Ph.D. Institute for Biomedical Research, 37 Providence Street Moncton, NB E1C 8X3 Canada fax: 506-862-4222 tel: 506-862-4848 ------=_NextPart_000_003A_01C19824.156B9060 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear All,
I would like to find out what are the = most popular=20 (best) programs for modelling of DNA/protein interactions and RNA/RNA = antisense=20 bonding. Off course shareware programs are the most interesting but we = wouldn't=20 mind even paying for the good one(s).
Thanks for your help,
Mira
 
Miroslava Cuperlovic-Culf = Ph.D.
Institute for=20 Biomedical Research,
37 Providence Street
Moncton, NB E1C=20 8X3
Canada
fax: 506-862-4222
tel: =20 506-862-4848
------=_NextPart_000_003A_01C19824.156B9060--