From chemistry-request@server.ccl.net Mon May 12 08:00:37 2003 Received: from hkusua.hku.hk ([147.8.2.91]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4CC0at07458 for ; Mon, 12 May 2003 08:00:36 -0400 Received: from hkusua.hku.hk (localhost [127.0.0.1]) by hkusua.hku.hk (8.12.8p1/8.12.8/check_local5.4) with ESMTP id h4CC21sr027103 for ; Mon, 12 May 2003 20:02:02 +0800 (HKT) X-Spam-Filter: check_local@hkusua.hku.hk by digitalanswers.org Received: from localhost (h9807907@localhost) by hkusua.hku.hk (8.12.8p1/8.12.8/Submit) with ESMTP id h4CC21JO027075 for ; Mon, 12 May 2003 20:02:01 +0800 (HKT) Date: Mon, 12 May 2003 20:02:00 +0800 (HKT) From: Wong Lai Ho X-Sender: h9807907@hkusua To: CHEMISTRY@ccl.net Subject: Error estimation of gibbs free energy Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-MailScanner: 0 Dear CCLers, I have a question regarding error estimation of the experimental values of gibbs free energy. As we knows that: delta G(formation) = delta H(formation) - Temp * [entropy(molecule)-sum(entropy(atoms to form the molecules))] Can I claim that the experimental error bar of the gibbs free energy(delta G) is equal to the error bar of the enthalpy change of formation(delta H)? (since the error introduced by the entropy is usually very small) Is there any papers or books talking about this error? I would be grateful if you can give some comments on this claim. Larry From chemistry-request@server.ccl.net Mon May 12 09:58:10 2003 Received: from gwia.kvl.dk ([130.225.43.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4CDw9t10494 for ; Mon, 12 May 2003 09:58:09 -0400 Received: from kvl.dk (pwt.kemi.kvl.dk [130.225.43.124]) by gwia.kvl.dk; Mon, 12 May 2003 15:57:46 +0200 Sender: pwt@ccl.net Message-ID: <3EBFA918.6921F28@kvl.dk> Date: Mon, 12 May 2003 16:00:56 +0200 From: Peter Waaben Thulstrup Organization: Royal Veterinary and Agricultural University X-Mailer: Mozilla 4.79 [en] (X11; U; Linux 2.4.18-4GB i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Database on kinetic data for beta-lactamase - substrate/inhibitor binding ? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL, I could use some help in getting experimental data for a new modeling project. Is anyone aware of database resources with kinetic data for beta-lactamase - inhibitor/substrate binding? A list of references on the subject would also be very interesting. Thanks in advance for any help that you can offer, Peter -- Peter W. Thulstrup Chemistry Department / Royal Veterinary and Agricultural University Thorvaldsensvej 40 / DK-1871 Frederiksberg C / Denmark Phone (Chemistry Dep't): +45 35282400 / Fax: +45 35282398 Phone (Office - direct): +45 35282464 / E-mail: pwt@kvl.dk From chemistry-request@server.ccl.net Mon May 12 02:10:46 2003 Received: from dux.ru ([193.125.210.65]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4C6Ajt19860 for ; Mon, 12 May 2003 02:10:46 -0400 Received: from dux.ru (localhost [127.0.0.1]) by dux.ru (8.12.6/8.12.6) with ESMTP id h4C6GqXN097154 for ; Mon, 12 May 2003 10:16:53 +0400 (MSD) (envelope-from dima@xenon.spb.ru) Received: (from uucp@localhost) by dux.ru (8.12.6/8.12.1/Submit) with UUCP id h4C6GqNg097152 for chemistry@ccl.net; Mon, 12 May 2003 10:16:52 +0400 (MSD) (envelope-from dima@xenon.spb.ru) Received: from goblin ([192.168.3.2]) by shadow with smtp (Exim 3.35 #1 (Debian)) id 19F6Po-00037b-00 for ; Mon, 12 May 2003 10:04:00 +0400 Message-ID: <008c01c3184c$56f56610$0203a8c0@goblin> From: "Dmitry Rozmanov" To: "CCL" Subject: ab initio with periodic conditions Date: Mon, 12 May 2003 10:04:25 +0400 MIME-Version: 1.0 Content-Type: text/plain; charset="koi8-r" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4910.0300 Dear Colleagues. Could you give me a hit about free software for ab initio computations with periodic boundary conditions? I need it for condensed phase modelling, for water solutions to be precise. As I understand such programs are more sutable for solid phase, but I guess that modelling water solution as an ice-like structure may be interesting as well, wont't it? GAMESS (US) can use effective fragments for cheaper solvent modelling. Is there any periodic software that is capable of doing such thing? Thank you in advance. Regards. ---Dmitry. From chemistry-request@server.ccl.net Mon May 12 09:59:27 2003 Received: from simon.cs.cornell.edu ([128.84.154.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4CDxRt10549 for ; Mon, 12 May 2003 09:59:27 -0400 Received: from sundial.cs.cornell.edu (sundial.cs.cornell.edu [128.84.96.115]) by simon.cs.cornell.edu (8.11.7/8.11.7/R-3.8) with ESMTP id h4CDxR512640 for ; Mon, 12 May 2003 09:59:27 -0400 (EDT) Received: from ringding.cs.cornell.edu (ringding.cs.cornell.edu [128.84.96.109]) by sundial.cs.cornell.edu (8.11.7/8.11.7/M-3.12) with ESMTP id h4CDxQt01365 for ; Mon, 12 May 2003 09:59:26 -0400 (EDT) Received: from localhost (alfredo@localhost) by ringding.cs.cornell.edu (8.11.7/8.11.7/C-3.3) with SMTP id h4CDxQ022957 for ; Mon, 12 May 2003 09:59:26 -0400 (EDT) Date: Mon, 12 May 2003 09:59:26 -0400 (EDT) From: Alfredo Cardenas To: chemistry@ccl.net Subject: Re:Exposed surface area routine In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I want to thank the people that reply to my inquiry. Their suggestions are quite helpful. Here are their responses. Alfredo Cardenas alfredo@cs.cornell.edu ************************************************* Date: Wed, 7 May 2003 15:08:55 -0500 (CDT) From: Abhishek Jha To: Alfredo Cardenas Subject: Re: CCL:Exposed surface area routine Try TINKER. It has a subroutine that does it. -Abhishek ************************************************* Swiss PDB Viewer / Deep View does this: http://us.expasy.org/spdbv/ Dr. N. Sukumar http://www.drugmining.com/ Visiting Scientist Rensselaer Department of Chemistry and Wadsworth Center, New York State Dept.of Health ************************************************ Date: Wed, 7 May 2003 17:05:45 -0400 (EDT) From: Avijit Ghosh To: Alfredo Cardenas Subject: Re: CCL:Exposed surface area routine On Wed, 7 May 2003, Alfredo Cardenas wrote: Hey Alfredo, I seem to recall GEPOL93 did this reasonably well. http://server.ccl.net/cca/software/SOURCES/FORTRAN/molecular_surface/gepol93/ind ex.shtml *************************************************** Date: Wed, 7 May 2003 17:37:15 -0400 (EDT) From: Manoj Pal To: Alfredo Cardenas Subject: Re: CCL:Exposed surface area routine Hi Alfredo, You can use naccess.f available at http://wolf.bms.umist.ac.uk/naccess/ for your work. ****************************************************** Date: Fri, 9 May 2003 14:20:00 +0200 From: Andrea Carotti To: Alfredo Cardenas Subject: Re: CCL:Exposed surface area routine You can try this link: http://molvis.sdsc.edu/protexpl/frntdoor.htm ****************************************************** Look to the ASV freeware on the following site: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ASV There are both the analytical calculation and the Monte-Carlo computation. If you have hundreds of intersecting spheres, the Monte-Carlo is faster (try, say, N=10^5 ou 10^6) Michel Petitjean, Email: petitjean@itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean@ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html From chemistry-request@server.ccl.net Mon May 12 09:58:00 2003 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4CDw0t10473 for ; Mon, 12 May 2003 09:58:00 -0400 Received: from cornell.edu (cs666981-224.satx.rr.com [66.69.81.224]) by postoffice.mail.cornell.edu (8.9.3p2/8.9.3) with ESMTP id JAA23484; Mon, 12 May 2003 09:57:45 -0400 (EDT) Message-ID: <3EBFA850.C68E108E@cornell.edu> Date: Mon, 12 May 2003 08:57:37 -0500 From: "Dr. Richard L. Wood" Organization: Cornell University X-Mailer: Mozilla 4.5 [en]C-CCK-MCD {TLC;RETAIL} (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: Wong Lai Ho CC: CHEMISTRY@ccl.net Subject: Re: CCL:Error estimation of gibbs free energy References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Wouldn't the following be true d(dG) = square root([d(dH)]^2 + [d(dS)]^2)? dG is delta G, d(dG) is the error in delta G, dH is delta H, d(dH) is the error in delta H, dS is delta S and d(dS) is the error in delta S. This is taken from a simple error propagation analysis as taught in some physical/analytical chemistry laboratories. Richard Wong Lai Ho wrote: > Dear CCLers, > > I have a question regarding error estimation of the experimental values of > gibbs free energy. > As we knows that: > delta G(formation) > = delta H(formation) > - Temp * [entropy(molecule)-sum(entropy(atoms to form the molecules))] > > Can I claim that the experimental error bar of the gibbs free energy(delta > G) is equal to the error bar of the enthalpy change of formation(delta H)? > (since the error introduced by the entropy is usually very small) > Is there any papers or books talking about this error? > > I would be grateful if you can give some comments on this claim. > > Larry > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Department of Chemistry Trinity University, San Antonio, TX 78212 From chemistry-request@server.ccl.net Mon May 12 04:26:11 2003 Received: from web15211.mail.bjs.yahoo.com ([202.3.77.141]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h4C8Q9t03387 for ; Mon, 12 May 2003 04:26:10 -0400 Message-ID: <20030512082608.9428.qmail@web15211.mail.bjs.yahoo.com> Received: from [218.30.18.116] by web15211.mail.bjs.yahoo.com via HTTP; Mon, 12 May 2003 16:26:08 CST Date: Mon, 12 May 2003 16:26:08 +0800 (CST) From: =?gb2312?q?Jinsong=20Zhao?= Subject: How to calculate molecular volume To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Dear all, I hope to know if there is any program or routine could calculate the molecular volume with high precision and reliability, moreover, to figure out the length, width and high of the grid that contain the molecule. Any comments, suggestion are welcome! Thanks for essential responses! Best regards, Jinsong _________________________________________________________ Do You Yahoo!? 相见不如聊天!不出门一样面对面！网络摄像头对对派送中~赶快用你的雅虎电邮帐号参与吧…… http://cn.rd.yahoo.com/mail_cn/tag/?http://cn.messenger.yahoo.com/ From chemistry-request@server.ccl.net Sun May 11 15:29:07 2003 Received: from richardson.uni2.net ([130.227.52.104]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4BJT6t12243 for ; Sun, 11 May 2003 15:29:06 -0400 Received: from HLUSF26A.lundbeck.com (mail.lundbeck.com [130.227.160.31]) by richardson.uni2.net (8.11.6/8.11.6) with SMTP id h4BJT6H25771 for ; Sun, 11 May 2003 21:29:06 +0200 Received: from ([172.16.0.163]) by HLUSF26A.lundbeck.com; Sun, 11 May 2003 21:30:38 +0200 (CEST) Received: FROM ludk0006.lundbeck.com BY ludk0163.lundbeck.com ; Sun May 11 21:29:02 2003 +0200 Received: from [10.201.1.114] (10.201.1.114 [10.201.1.114]) by ludk0006.lundbeck.com with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id JRRSPL89; Sun, 11 May 2003 21:29:03 +0200 Subject: Protein folding and simulation problem finally solved ? From: Jan Torleif Pedersen To: chemistry@ccl.net Content-Type: text/plain Content-Transfer-Encoding: 7bit X-Mailer: Ximian Evolution 1.0.8 (1.0.8-10) Date: 11 May 2003 22:27:54 +0200 Message-Id: <1052684880.1016.18.camel@localhost.localdomain> Mime-Version: 1.0 Greetings, Apparently, the protein folding and simulation problem has been solved by a small Cambridge, UK based company called Cambridge Proteomics Ltd.(http://www.camprot.com). Is anybody familiar with this new and revolutionary technology? - I would be quite interested in hearing from anybody that has more information. Many Regards -- Jan Dr. Jan T. Pedersen Section Head, Bioinformatics H. Lundbeck A/S Ottiliavej 9 2500 Valby Denmark phone: 36 43 28 87 email: jatp@lundbeck.com From chemistry-request@server.ccl.net Sun May 11 18:41:02 2003 Received: from mx3.trentu.ca ([192.75.12.4]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h4BMf2t14858 for ; Sun, 11 May 2003 18:41:02 -0400 Received: (qmail 5723 invoked by uid 504); 11 May 2003 22:41:02 -0000 Received: from elewars@trentu.ca by mx3.trentu.ca by uid 501 with qmail-scanner-1.14 (fsecure: 4.15/4370/2003-05-09/2003-05-08. 2003-05-07/ Clear:. Processed in 16.289036 secs); 11 May 2003 22:41:02 -0000 X-Qmail-Scanner-Mail-From: elewars@trentu.ca via mx3.trentu.ca X-Qmail-Scanner: 1.14 (Clear:. Processed in 16.289036 secs) Received: from unknown (HELO trentu.ca) (209.42.101.30) by mx3.trentu.ca with SMTP; 11 May 2003 22:40:45 -0000 Message-ID: <3EBED228.3A272946@trentu.ca> Date: Sun, 11 May 2003 18:43:52 -0400 From: elewars X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: Jan Labanowski , chemistry@ccl.net Subject: Re: CCL:cartesians to z-mat and back References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit 2003 May 11 I might just add that As Jan Labanowski implies, writing an algorithm to convert a general set of molecular Cartesians to a good Z-matrix is a problem in artificial intelligence (the converse is trivial). The dying (?) art of writing a Z-matrix is treated nicely and compactly, with useful caveats, in _A Handbook of Computational Chemistry_, Tim Clark, Wiley, New York, 1985; pp 102-119. E. Lewars ====== Jan Labanowski wrote: > I love MOLDEN and use it often for my geometry conversions. It comes > with the Z-matrix editor: > > http://www.cmbi.kun.nl/~schaft/molden/molden.html > > It should be stressed that conversion of cartesians to Z-matrix can only > be a trivial task for molecules that are trees (i.e., do not contain cycles). > When rings (or more complicated arrangements, like cages, say, cubane) are > present, the well behaved Z-matrix should contain dummy atoms. You can try > to understand the problem by build the Z-matrix in such a way > that changing one parameter does not affect any other parameters. > > For example, the z-matrix for benzene ring has to involve a centroid (a dummy > atom in the center of the ring) or otherwise, changing one torsion angles > within the ring will change other torsion angles. With the centroid, and > the rays going from it to the real atoms, you can build a Z-matrix which > does not involve dependencies between parameters. > > Now... Can the software detect such situations automatically and deal with > them. Sure... However, quite frankly, I did not see much of such > packages around. It is not a trivial problem, and even for simple molecules > with cycles, there are many ways to represent their geometry as a Z-matrix. > And deciding which Z-matrix is better, is again not a trivial thing. While > there are obviously objective measures, this is still an art, and the > beauty of the Z-matrix is in the eye of the beholder. And while there are > methods which make Z-matrix less important for unconstrained optimization > of the whole molecule (e.g., redundant internal coordinates in Gaussian), > there is nothing better than a well behaved Z-matrix when doing partial > optimizations of chosen geometrical features of the molecule(s), e.g., > when studying transition states and reaction paths. > > Jan > > Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 > Ohio Supercomputer Center | E-mail: jkl@ccl.net > 1224 Kinnear Rd, | http://www.ccl.net/~jkl > Columbus, OH 43212-1163 | http://www.ccl.net/ http://asdn.net/ > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Mon May 12 16:41:32 2003 Received: from is.dal.ca ([129.173.1.52]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4CKfVt24961 for ; Mon, 12 May 2003 16:41:32 -0400 Received: from localhost (fban@localhost) by is.dal.ca (AIX4.3/8.9.3p2/8.9.3) with SMTP id RAA70062 for ; Mon, 12 May 2003 17:41:13 -0300 X-Authentication-Warning: is.dal.ca: fban owned process doing -bs Date: Mon, 12 May 2003 17:41:13 -0300 (ADT) From: Fuqiang Ban To: chemistry@ccl.net Subject: Compilation NBO 5.0 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I cannot compile the modified l607.F (for unix) of NBO 5.0 successfuly using the G98 utility libraries by issuing the command "bsd/bldg98 linkrest l607.exe". The problem is that the "GauNBO" subroutine taken from l607.F.old does not seem to work with the NBO 5.0. Could anybody tell me what need to be done (besides commenting out the five lines as suggested by NBO 5.0 manual) for the GauNBO subroutine to be workable with NBO 5.0. Your help is highly appreciated. Thanks, Fuqiang Ban From chemistry-request@server.ccl.net Mon May 12 17:26:34 2003 Received: from julesburg.uits.indiana.edu ([129.79.1.75]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4CLQXt26677 for ; Mon, 12 May 2003 17:26:33 -0400 Received: from yogibear.uits.iupui.edu (yogibear.uits.iupui.edu [134.68.220.201]) by julesburg.uits.indiana.edu (8.12.9/8.12.9/IUPO) with ESMTP id h4CLQWAE001852 for ; Mon, 12 May 2003 16:26:32 -0500 (EST) Received: from iupui.edu ([134.68.57.154]) by yogibear.uits.iupui.edu (8.12.9/8.12.9/IUPUIPO.20030331) with ESMTP id h4CLQUkK019779 for ; Mon, 12 May 2003 16:26:33 -0500 (EST) Sender: qin@yogibear.uits.iupui.edu Message-ID: <3EC0119A.579C3CEC@iupui.edu> Date: Mon, 12 May 2003 16:26:50 -0500 From: qin@iupui.edu X-Mailer: Mozilla 4.78 [en] (X11; U; Linux 2.4.7-10 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: false positive in autodock Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear All, I am new to Autodock. I just finishd running autodock using adt interface on a known protein-ligand complex. Apparently, I have one false hit in which the rmsd of the ligand from the crystallograpic position is way high (14 A) while there is a second rank culster (three conformations) has rmsd of 0.88A. The false hit is located on the protein surface. When I prepared my protein and added Kollman charge, the net charge was -9. Wonder if that is not reasonable for the sake of docking? I would like to know anything in general how to correct these problems. Thanks in advance. Q. From chemistry-request@server.ccl.net Mon May 12 20:17:43 2003 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4D0Hht31784 for ; Mon, 12 May 2003 20:17:43 -0400 Received: from cornell.edu (cs666981-224.satx.rr.com [66.69.81.224]) by postoffice.mail.cornell.edu (8.9.3p2/8.9.3) with ESMTP id UAA11784; Mon, 12 May 2003 20:17:22 -0400 (EDT) Message-ID: <3EC03989.B947CCE2@cornell.edu> Date: Mon, 12 May 2003 19:17:13 -0500 From: "Dr. Richard L. Wood" Organization: Cornell University X-Mailer: Mozilla 4.5 [en]C-CCK-MCD {TLC;RETAIL} (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: Wong Lai Ho , CHEMISTRY@ccl.net Subject: Re: CCL:Error estimation of gibbs free energy References: <3EBFA850.C68E108E@cornell.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Opps, it should be d(dG) = square root([d(dH)]^2 + [T d(dS)]^2) so the units come out in kcal/mol (or kJ/mol). Richard "Dr. Richard L. Wood" wrote: > Wouldn't the following be true > > d(dG) = square root([d(dH)]^2 + [d(dS)]^2)? > > dG is delta G, d(dG) is the error in delta G, dH is delta H, d(dH) is the error > in delta H, dS is delta S and d(dS) is the error in delta S. > > This is taken from a simple error propagation analysis as taught in some > physical/analytical chemistry laboratories. > > Richard > > Wong Lai Ho wrote: > > > Dear CCLers, > > > > I have a question regarding error estimation of the experimental values of > > gibbs free energy. > > As we knows that: > > delta G(formation) > > = delta H(formation) > > - Temp * [entropy(molecule)-sum(entropy(atoms to form the molecules))] > > > > Can I claim that the experimental error bar of the gibbs free energy(delta > > G) is equal to the error bar of the enthalpy change of formation(delta H)? > > (since the error introduced by the entropy is usually very small) > > Is there any papers or books talking about this error? > > > > I would be grateful if you can give some comments on this claim. > > > > Larry > > > > -- > Richard L. Wood, Ph. D. > Physical/Computational Chemist > Post-doctoral Associate > Department of Chemistry > Trinity University, San Antonio, TX 78212 > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Department of Chemistry Trinity University, San Antonio, TX 78212 From chemistry-request@server.ccl.net Mon May 12 13:26:30 2003 Received: from h28n2fls34o1123.telia.com ([81.224.175.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4CHQTt18949 for ; Mon, 12 May 2003 13:26:29 -0400 Received: from h28n2fls34o1123.telia.com (localhost.localdomain [127.0.0.1]) by h28n2fls34o1123.telia.com (8.12.8/8.12.8) with ESMTP id h4CJR3s6002014; Mon, 12 May 2003 21:27:03 +0200 Received: (from spoel@localhost) by h28n2fls34o1123.telia.com (8.12.8/8.12.8/Submit) id h4CJR2Sw002012; Mon, 12 May 2003 21:27:02 +0200 X-Authentication-Warning: h28n2fls34o1123.telia.com: spoel set sender to spoel@xray.bmc.uu.se using -f Subject: Re: CCL:Protein folding and simulation problem finally solved ? From: David To: Jan Torleif Pedersen Cc: chemistry@ccl.net In-Reply-To: <1052684880.1016.18.camel@localhost.localdomain> References: <1052684880.1016.18.camel@localhost.localdomain> Content-Type: text/plain Content-Transfer-Encoding: 7bit Organization: Message-Id: <1052767622.1785.13.camel@h28n2fls34o1123.telia.com> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.2.2 (1.2.2-5) Date: 12 May 2003 21:27:02 +0200 On Sun, 2003-05-11 at 22:27, Jan Torleif Pedersen wrote: > Greetings, > > Apparently, the protein folding and simulation problem has been solved > by a small Cambridge, UK based company called Cambridge Proteomics > Ltd.(http://www.camprot.com). Is anybody familiar with this new and > revolutionary technology? - I would be quite interested in hearing from > anybody that has more information. I suggest you contact them directly. There is no information on their website, and I haven't seen any publications from them. Until it is published and proven for many different proteins, it is just advertising. -- Groeten, David. ________________________________________________________________________ Dr. David van der Spoel, Dept. of Cell and Molecular Biology Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel@xray.bmc.uu.se spoel@gromacs.org http://xray.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Mon May 12 14:52:23 2003 Received: from dux.ru ([193.125.210.65]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4CIqMt21559 for ; Mon, 12 May 2003 14:52:22 -0400 Received: from dux.ru (localhost [127.0.0.1]) by dux.ru (8.12.6/8.12.6) with ESMTP id h4CIwYwu055719 for ; Mon, 12 May 2003 22:58:34 +0400 (MSD) (envelope-from dima@xenon.spb.ru) Received: (from uucp@localhost) by dux.ru (8.12.6/8.12.1/Submit) with UUCP id h4CIwXhY055717 for chemistry@ccl.net; Mon, 12 May 2003 22:58:33 +0400 (MSD) (envelope-from dima@xenon.spb.ru) Received: from goblin ([192.168.3.2]) by shadow with smtp (Exim 3.35 #1 (Debian)) id 19FHtw-0004Si-00 for ; Mon, 12 May 2003 22:19:52 +0400 Message-ID: <00be01c318b3$2591f180$0203a8c0@goblin> From: "Dmitry Rozmanov" To: "CCL" References: <008c01c3184c$56f56610$0203a8c0@goblin> <004701c318a7$c6e83e60$3e505882@pirx> Subject: Re: CCL:ab initio with periodic conditions Date: Mon, 12 May 2003 22:20:20 +0400 MIME-Version: 1.0 Content-Type: text/plain; charset="koi8-r" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4910.0300 Thank you for the suggestion. Actually I know about CPMD, but still have not tried it. I have no access to unix computer, only to windows ones. And could not compile CPMD under windows. Though, I ran into AbInit code. Have you know anything about it? Is it better or worse than CPMD? Is it the same thing as CPMD? Regards. ---Dmitry. ----- Original Message ----- From: "Matthias Mohr" To: "Dmitry Rozmanov" Sent: Monday, May 12, 2003 8:58 PM Subject: Re: CCL:ab initio with periodic conditions > Hi, > > I think the best choice for liquid water is the CPMD code of Parrinellos > group (www.cpmd.org) > Can be used for ab initio dynamics, but for stationary points as well. > It does quite well for several "liquid-water-problems". See > Laasonen, K.; Sprik, M.; Parrinello, M.; Car. R. J. Chem. Phys. 1993, 99, > 9080. > > Tuckerman, M.; Laasonen, K.; Sprik, M.; Parrinello, M. J. Chem. Phys. 1995, > 103, 150 > > > Regards, Matthias > > > > ---- > Dr Matthias Mohr > Dept. of Chemistry > University of Manchester > Oxford Road > M13 9PL Manchester, UK > Matthias.Mohr@man.ac.uk > http://www.ch.man.ac.uk/theory/mohr > >