From chemistry-request@server.ccl.net Mon May 28 04:44:00 2001 Received: from melia.qut.edu.au ([131.181.127.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4S8hwS11806 for ; Mon, 28 May 2001 04:43:59 -0400 Received: from tu02m2.qut.edu.au ([131.181.127.148]) by melia.qut.edu.au (PMDF V5.2-33 #40788) with ESMTP id <0GE10491LEX415@melia.qut.edu.au> for chemistry@ccl.net; Mon, 28 May 2001 18:43:52 +1000 (EST) Received: by tu02m2.qut.edu.au id SAA1317615; Mon, 28 May 2001 18:43:41 +1000 (EST) Date: Mon, 28 May 2001 18:43:41 +1000 (EST) From: Sergio Manzetti Subject: AUTODOCK To: chemistry@ccl.net Message-id: <991039421.3b120fbd1607b@email.qut.edu.au> MIME-version: 1.0 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.3 X-IMP-User: n2618117 X-Originating-IP: 131.181.120.220 Hello, I am attemptin to use freely available software to prepare the files in AUTODOCK. I have come quite a long way, however, I get a misterious behaviour when I run autodock3. The output *.dlg shows that there are conflicts the *.gpf filenames. As seen below: DPF> map macro.C.map # C-atomic affinity map file Opened Grid Map 1 (C): macro.C.map Checking header information. autodock3: Filename mismatch: "macro.gpf" :: "1m.macro.gpf" Looking for 226981 energies from Grid Map 1... Closing file. 226981 energies found for map 1 Minimum energy = 0.00, maximum energy = 0.00 Time taken (s): Real= 1.28, CPU= 1.00, System= 0.27 DPF> map macro.N.map # N-atomic affinity map file Opened Grid Map 2 (N): macro.N.map Checking header information. autodock3: Filename mismatch: "macro.gpf" :: "1m.macro.gpf" Looking for 226981 energies from Grid Map 2... Closing file. 226981 energies found for map 2 Minimum energy = 0.00, maximum energy = 0.00 Time taken (s): Real= 1.09, CPU= 1.06, System= 0.03 DPF> map macro.O.map # O-atomic affinity map file Opened Grid Map 3 (O): macro.O.map Checking header information. autodock3: Filename mismatch: "macro.gpf" :: "1m.macro.gpf" Looking for 226981 energies from Grid Map 3... Closing file. 226981 energies found for map 3 Minimum energy = 0.24, maximum energy = 0.24 Time taken (s): Real= 1.42, CPU= 1.39, System= 0.03 DPF> map macro.S.map # S-atomic affinity map file Opened Grid Map 4 (S): macro.S.map Checking header information. autodock3: Filename mismatch: "macro.gpf" :: "1m.macro.gpf" Looking for 226981 energies from Grid Map 4... Closing file. 226981 energies found for map 4 Minimum energy = 0.00, maximum energy = 0.00 Time taken (s): Real= 1.09, CPU= 1.05, System= 0.02 DPF> map macro.H.map # H-atomic affinity map file Opened Grid Map 5 (H): macro.H.map Checking header information. autodock3: Filename mismatch: "macro.gpf" :: "1m.macro.gpf" Looking for 226981 energies from Grid Map 5... Closing file. 226981 energies found for map 5 Minimum energy = 0.12, maximum energy = 0.12 Time taken (s): Real= 1.43, CPU= 1.38, System= 0.02 DPF> map macro.e.map # electrostatics map file Opened Grid Map 6 (e): macro.e.map Checking header information. autodock3: Filename mismatch: "macro.gpf" :: "1m.macro.gpf" Looking for 226981 energies from Grid Map 6... Closing file. 226981 energies found for map 6 Minimum energy = 0.02, maximum energy = 0.13 Time taken (s): Real= 1.39, CPU= 1.36, System= 0.03 DPF> DPF> move 1m.pdbq # small molecule file Atomic coordinate, partial charge, PDBQ file = "1m.pdbq" The only abnormal thing I have found about this procedure is a charge error, in the *.err file generate when checking the macromolecule for charges using the check-qs script. Could this have impact on the grid map, and yield this problem? Best Regards Sergio Sergio Manzetti Research Scholar Centre of Molecular Biotechnology/ Supercomputer Facility Queensland University of Tehnology 2 George St, BRISBANE 4000 QLD AUSTRALIA Tlf: +61 7 3864 1434 email: s.manzetti@student.qut.edu.au WWW: http://www.its.qut.edu.au/hpc From chemistry-request@server.ccl.net Mon May 28 06:24:04 2001 Received: from oc30.uni-paderborn.de ([131.234.240.90]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4SAO2S21453 for ; Mon, 28 May 2001 06:24:03 -0400 Received: from localhost (cpilger@localhost) by oc30.uni-paderborn.de (SGI-8.9.3/8.9.3) with ESMTP id NAA30283; Mon, 28 May 2001 13:49:36 +0200 (CEST) Date: Mon, 28 May 2001 13:49:36 +0200 From: Christian Pilger To: amber@heimdal.compchem.ucsf.edu cc: chemistry@ccl.net Subject: titratable amino acids and counter ions In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear protein modelers, while preparing a protein structure as input for MD simulations, I encountered the following points, which I would like to ask your advice: - How do you usually deal with titratable residues (GLU, ASP, LYS, ARG) ? Are all of them simply taken in their ionized forms ? Would it be good to try to rationalize the ionization states of these residues by manually inspecting their environment ? Which methods/rules of thumb are available for the estimation of these ionization states ? - In my case the protein has an experimentally determined isoelectric point of roughly pH=4.7. Does this mean, that the protein will have a negative net charge at pH=7 ? Then, is there a method to correlate the isoelectric point with this net charge ? And, are MD calculations reasonable, when the net charge of the system differs from zero ? - In case the net charge is neutralized by counter ions: how and where should these be positioned ? Should one counter ion be placed directly at each titratable residue (i.e. number of counter ions = number of ioniziable residues) or should counter ions be placed (arbitrarily ?) around the protein structure (i.e. number counter ions = net charge of the whole system) ? Any comments are highly appreciated. Cheers, Christian ---------------------------------------------------------------- Dr. Christian Pilger Uni-GH Paderborn FB 13 - Organische Chemie Warburger Str. 100 D-33098 Paderborn/Germany Tel.: 05251-602498 Fax : 05251-603245 email: cpilger@oc30.uni-paderborn.de ---------------------------------------------------------------- From chemistry-request@server.ccl.net Mon May 28 02:01:53 2001 Received: from hotmail.com ([64.4.15.141]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4S61rS05332 for ; Mon, 28 May 2001 02:01:53 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Sun, 27 May 2001 23:01:48 -0700 Received: from 196.1.114.240 by lw10fd.law10.hotmail.msn.com with HTTP; Mon, 28 May 2001 06:01:47 GMT X-Originating-IP: [196.1.114.240] From: "vishwanatha sastry" To: chemistry@ccl.net Subject: References on Hydration patterns of ethylene and propylene glycols Date: Mon, 28 May 2001 11:31:47 +0530 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 28 May 2001 06:01:48.0125 (UTC) FILETIME=[AE6400D0:01C0E73B] Hello fellow research colleques and friends, I am looking for references both latest and past on the experimental and spectroscopic studies on hydration patterns or liquid mixtures of ethylene and propylene glycols + water. I request all those netters who are working in these particular systems or alcohol - water systems in general to respond with the literature references they may have in their files as well as with the addresses of research groups they know. We have started some work on these sytems in bulk solution as well as in gas phase using ab initio MESP calculations. Our aim is to understand explicitly the molecular interactions between the glycols and water and also ascertain the role played by the hydrophobic groups such as methyl groups on the cooperative interactions among wate - water contacts etc.. The past and contemporary references on such work are highly useful in planning our work properly. Thanking in advance. With best regards yours sincerely (Dr. N. V. Sastry) C/O Prof. S. R. Gadre Department of Chemistry University of Pune Pune - 411 007, India email: nvs_4@hotmail.com _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. From chemistry-request@server.ccl.net Mon May 28 02:03:49 2001 Received: from matavnet.hu ([195.228.240.10]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f4S63mS05384 for ; Mon, 28 May 2001 02:03:48 -0400 Received: (qmail 1756 invoked from network); 28 May 2001 08:03:45 +0200 Received: from adsl158.225.matavnet.hu (HELO chemaxon.com) (195.228.225.158) by mail.matavnet.hu with SMTP; 28 May 2001 08:03:46 +0200 Message-ID: <3B11EB4B.2B653F0E@chemaxon.com> Date: Mon, 28 May 2001 08:08:11 +0200 From: Ferenc Csizmadia Organization: ChemAxon X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: Artem Masunov CC: chemistry@ccl.net Subject: Re: CCL:Databases to support Comb.Chem.? References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Artem, JChem is a software for handling chemical databases and structure files. http://www.jchem.com It runs under both Unix and Windows (even Mac) since it is written in Java. (At our web site you can try examples running on a Sun machine.) We are walking into the area of combinatorial chemistry with a new module, JKlustor, that can perform diversity calculations and clustering. http://www.jchem.com/doc/admin/JKlustor.html The software is developed continuously, we are open to suggestions on future directions. Please let me know if you have any question or if there are features that you miss. Best regards, Ferenc -- Dr. Ferenc Csizmadia ChemAxon Ltd. http://www.chemaxon.com T:+3620 9570988 mailto:fcsiz@chemaxon.com Artem Masunov wrote: > Dear CCLers, > What software do you use nowadays to support combinatorial chemistry/high > throughput screening? Comprehensive solutions from MSI seem to be too > expensive for Academia (especially maintenance), and Windows based > products (like Chem Finder from CambridgeSoft) do not seem to be able to > handle large (hundreds of thousands) libraries.. > > Artem > > -= 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 May 28 07:22:33 2001 Received: from mail.fqspl.com.pl ([212.244.147.7]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f4SBMQS23332 for ; Mon, 28 May 2001 07:22:32 -0400 Received: (qmail 30251 invoked from network); 28 May 2001 13:22:48 -0000 Received: from test.fqspl.com.pl (HELO test) (10.10.10.50) by fqspl.com.pl with SMTP; 28 May 2001 13:22:48 -0000 Message-ID: <00c301c0e768$a3d56460$320a0a0a@fqspl.com.pl> From: "Victor Anisimov" To: Subject: Protein structures Date: Mon, 28 May 2001 13:23:37 +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, Can someone advise me on the following topic: Applying quantum chemical calculations to proteins I always spend a lot of my time on mechanical preliminary purification of the protein structures setting hydrogen atoms in proper positions and checking the structure errors. The software that can automate this process is usually not enough reliable and requires a posteriori expert's check. The manual correction is tremendously impractical for hundreds of proteins with thousands of residues that I need to submit for QM calculation. Could you please share with me your experience what software you consider as the most trustworthy or may be there is some free or commercially available database of proteins with correct hydrogen atoms already assigned. What would be your normal procedure if you would need to submit 50000 atoms' protein for QM calculation taking the structure from the PDB database? My second question is related to protein structure correction feature of graphical applications that goes beyond adding hydrogen atoms. There are many graphical applications that can advise a user to correct some part of the molecule. To best of my knowledge all of them are based on the Lewis structure rules. As PDB structures not always obeying Lewis principles and valence rules the result of the automatic correction is not reliable enough. Could you please recommend me a software free or commercial if it exists that can safely repair protein structure or can check it and graphically select those parts of the protein that require human expertise for correction. Once the user qualified the fragment as valid the next time check should not suggest this fragment for correction. Thanks for your help, 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 chemistry-request@server.ccl.net Mon May 28 09:35:58 2001 Received: from web13908.mail.yahoo.com ([216.136.175.71]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f4SDZwS26820 for ; Mon, 28 May 2001 09:35:58 -0400 Message-ID: <20010528133557.12607.qmail@web13908.mail.yahoo.com> Received: from [216.104.228.150] by web13908.mail.yahoo.com; Mon, 28 May 2001 06:35:57 PDT Date: Mon, 28 May 2001 06:35:57 -0700 (PDT) From: Dimitri Bondarev Reply-To: bondarev@videotron.ca Subject: Re: CCL:Databases to support Comb.Chem.? To: chemistry@ccl.net In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Artem, You may want to try out the Molecular Operating Environment from http://www.chemcomp.com. We do have HTS and virtual combinatorial chemistry tools, and provide a 30-day evaluation (customer support included!). We also have an academic discount policy. Regards, Dimitri Bondarev support@chemcomp.com Scientific Support, Chemical Computing Group --- Artem Masunov wrote: > Dear CCLers, > What software do you use nowadays to support > combinatorial chemistry/high > throughput screening? Comprehensive solutions from > MSI seem to be too > expensive for Academia (especially maintenance), and > Windows based > products (like Chem Finder from CambridgeSoft) do > not seem to be able to > handle large (hundreds of thousands) libraries.. > > Artem > > > -= 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 > > > > > __________________________________________________ Do You Yahoo!? Yahoo! Auctions - buy the things you want at great prices http://auctions.yahoo.com/ From chemistry-request@server.ccl.net Sun May 27 03:22:49 2001 Received: from mdl.ipc.pku.edu.cn (IDENT:postfix@[162.105.177.40]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4R7MmS02314 for ; Sun, 27 May 2001 03:22:48 -0400 Received: by mdl.ipc.pku.edu.cn (Postfix, from userid 3200) id DFE0A2A1F0; Sun, 27 May 2001 23:23:15 +0800 (CST) Received: from localhost (localhost [127.0.0.1]) by mdl.ipc.pku.edu.cn (Postfix) with ESMTP id C99AB2A1EB for ; Sun, 27 May 2001 23:23:15 +0800 (CST) Date: Sun, 27 May 2001 23:23:15 +0800 (CST) From: Fenglou Mao To: "CHEMISTRY@www.ccl.net" Subject: rasmol bug? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII when loading the second molecule, it can not color the molecule via structure. Did anyone others meet this problem? -- Sincerely Yours, FengLou Mao ******************************* ADD:Mr. FengLou Mao Institute of Physical Chemistry Peking University BeiJing P.R.China Tel:86-10-62756833 Fax:86-10-62751725 E-mail:mao@mdl.ipc.pku.edu.cn Homepage:http://mdl.ipc.pku.edu.cn/~mao From chemistry-request@server.ccl.net Mon May 28 11:12:27 2001 Received: from admin.cnrs-orleans.fr ([163.9.1.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4SFCQS29680 for ; Mon, 28 May 2001 11:12:26 -0400 Received: from chinon.cnrs-orleans.fr (chinon.cnrs-orleans.fr [163.9.6.107]) by admin.cnrs-orleans.fr (8.9.1a/jtpda-5.3.2) with ESMTP id RAA08427 ; Mon, 28 May 2001 17:12:14 +0200 (MET DST) Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.9.3/8.9.3) id RAA13769; Mon, 28 May 2001 17:11:35 +0200 Date: Mon, 28 May 2001 17:11:35 +0200 Message-Id: <200105281511.RAA13769@chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: Konrad Hinsen To: mike_smith07@yahoo.com CC: chemistry@ccl.net In-reply-to: <20010525180954.81149.qmail@web13205.mail.yahoo.com> (message from mike smith on Fri, 25 May 2001 11:09:54 -0700 (PDT)) Subject: Re: CCL:Temperature fluctuation during a const T simulation References: <20010525180954.81149.qmail@web13205.mail.yahoo.com> > In molecular dynamics, there are a lot of techniques to keep the > Temperature(T) constant, such as velocity scaling, NOSE heat bath, > Langevin dynamics, and so on. However, these techniques do not give equivalent results. Some guarantee the correct thermodynamic averages in the NpT ensemble, others only the correct averages for quantities that do not depend on the momenta, and yet others not even that. No technique can generate "correct" dynamics at constant temperature, it is not even clear what exactly that means. > However, as you know that the T can't always be a constant, but > fluctuating around the input value. It depends on what you call T. I suppose you mean the instantaneous kinetic energy, which is indeed not constant. The quantity that you should identify with the thermodynamic temperature is some long-time average of the kinetic energy. > about 50K). I think this will weaken any of my conclusions based on > the simulation, especially for those temperature senstive > quantuties. Not necessarily. The kinetic energy is a fluctuating energy in the NpT ensemble, and its fluctuations can even be calculated. If your simulation uses the correct physical parameters (an ideal that is never achieved, of course), then the fluctuations you get out must be the correct ones. Anyway, you cannot reduce the fluctuations without changing physical parameters, and that is not necessarily a good idea. Regards, Konrad Hinsen. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Mon May 28 11:48:32 2001 Received: from wally.uh.cu ([216.72.24.101]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4SFmSS30529 for ; Mon, 28 May 2001 11:48:29 -0400 Received: from alma.uh.cu (alma.uh.cu [192.168.100.67]) by wally.uh.cu (8.11.0/8.11.0/MZ) with ESMTP id f4SFsMN21701; Mon, 28 May 2001 11:54:22 -0400 Received: from ffserver.ff.oc.uh.cu (ff.oc.uh.cu [192.168.100.83]) by alma.uh.cu (Postfix) with ESMTP id 9F4BCA564A; Mon, 28 May 2001 11:52:37 -0400 (CDT) Received: from ffuh.ff.oc.uh.cu (IDENT:root@ffuh.ff.oc.uh.cu [192.168.11.1] (may be forged)) by ffserver.ff.oc.uh.cu (8.9.3/8.9.3/JP) with ESMTP id LAA23473; Mon, 28 May 2001 11:48:09 -0400 Received: from raman.ff.oc.uh.cu (IDENT:root@raman.ff.oc.uh.cu [192.168.11.201]) by ffuh.ff.oc.uh.cu (8.9.3/8.9.3/JP) with ESMTP id LAA01422; Mon, 28 May 2001 11:47:18 -0400 Received: from localhost (eariel@localhost) by raman.ff.oc.uh.cu (8.8.7/8.8.7/JP) with SMTP id KAA07501; Mon, 28 May 2001 10:32:49 -0400 Date: Mon, 28 May 2001 10:32:49 -0400 (EDT) From: "Eduardo A. Menendez Proupin" Reply-To: "Eduardo A. Menendez Proupin" To: mike smith Cc: chemistry@ccl.net Subject: Re: CCL:Temperature fluctuation during a const T simulation In-Reply-To: <20010525180954.81149.qmail@web13205.mail.yahoo.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Mike and CCLers, The temperature fluctuaction in the NVE ensemble is /T^2=2/3N, where N is the number of atoms in your simulation. Check if your variance sqrt()=50 K is in agreement with this formula. If it is, you should increase N, or increase the simulation time, or run several paralell simulations with independent initial configurations and average them. If you receive other answers, please, let know them. Regards, Eduardo On Fri, 25 May 2001, mike smith wrote: > Dear listers, > > In molecular dynamics, there are a lot of techniques > to keep the Temperature(T) constant, such as velocity > scaling, NOSE heat bath, Langevin dynamics, and so on. > > However, as you know that the T can't always be a > constant, but fluctuating around the input value. > > I am doing a simulation by Langevin dynamics, and my > trouble is that the T fluctuation of my results is > very big (The variance of T is about 50K). I think > this will weaken any of my conclusions based on the > simulation, especially for those temperature senstive > quantuties. > > Since I don't have much experience on Langevin > dynamics, I am wondering if anyone could give me some > help on how to MINIMIZE the temperature fluctuation > for Langevin dynamics. Thanks a lot in advance. > > Sincerely, > > Mike Smith > > __________________________________________________ > Do You Yahoo!? > Yahoo! Auctions - buy the things you want at great prices > http://auctions.yahoo.com/ > > > -= 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 > > > > > Eduardo Ariel Menendez Proupin, Ph.D. ------------------------------------- Laboratorio de Ingenieria de Zeolitas Instituto de Materiales y Reactivos Universidad de La Habana San Lazaro y L. Vedado 10400 La Habana, Cuba E-mail:eariel@raman.ff.oc.uh.cu Fax : (53+7)+320018/794651 Phone: (53+7)+788950/788956/788957 ext 553 (53+7)+707666/705707 From chemistry-request@server.ccl.net Mon May 28 14:26:38 2001 Received: from mail.chem.tamu.edu ([165.91.176.8]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4SIQcS01307 for ; Mon, 28 May 2001 14:26:38 -0400 Received: from mail.chem.tamu.edu ([165.91.179.32]) by mail.chem.tamu.edu (Post.Office MTA v3.5.3 release 223 ID# 0-64333U1000L100S0V35) with ESMTP id edu for ; Mon, 28 May 2001 13:27:48 -0500 Message-ID: <3B129832.2C692514@mail.chem.tamu.edu> Date: Mon, 28 May 2001 13:25:54 -0500 From: lakshmi@mail.chem.tamu.edu (Sahasranaman Mahalakshmi) X-Mailer: Mozilla 4.05 [en] (WinNT; I) MIME-Version: 1.0 To: chemistry@ccl.net Subject: SUmmary : for eigenvalue problems Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I thank all those who have responded to my question. I am summarizing their replies in this mail. The various sites suggested are listed below 1) try ARPACK from netlib 2) www.netlib.org 3) >I am not exactly sure what your are attempting to solve, but there is a >highly advanced mathematics program that may solve your problem. You can > check out their website: www.maplesoft.com 4) Try this one: ! 5) http://www.netlib.org Thanking You, Mahalakshmi From chemistry-request@server.ccl.net Mon May 28 11:51:58 2001 Received: from toronto.acdlabs.com ([207.176.233.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4SFpwS30631 for ; Mon, 28 May 2001 11:51:58 -0400 Received: from NOTEBIBM1 (noteb-ibm1.acdlabs.com [207.176.233.10]) by toronto.acdlabs.com (8.9.0/8.9.0) with SMTP id LAA15942; Mon, 28 May 2001 11:46:46 -0400 (EDT) From: "Gavin Shear" To: "Artem Masunov" , Subject: RE: Databases to support Comb.Chem.? Date: Mon, 28 May 2001 11:48:18 -0400 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" 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) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 In-Reply-To: <3B11EB4B.2B653F0E@chemaxon.com> Dear Artem, Advanced Chemistry Development (ACD) offers various tools for combinatorial/high throughput applications. For example, ACD clients are using our physicochemical (pKa, LogP, LogD, solubility) prediction software in high throughput drug discovery environments. These products also allow the user to create and utilize large training databases to improve predictions based on experimental data. Please see: http://www.acdlabs.com/clients/pr_pfizer0201.html Integration with third party applications such as ISIS/HOST, SpotFire, and more, is also available, as are tools such as ActiveX controls, and Java applets for integration to existing solutions. For Spectroscopy, and Chromatography, ACD offers SpecManager SQL, and enterprise solution for processing, databasing and analyzing experimental data. http://www.acdlabs.com/products/glob_sol_lab/spec_manager_sql/ For analysis of high throughput HNMR spectral plates, ACD/Combi NMR uses the ACD HNMR prediction engine, along with user trainable databases. Please see: http://www.acdlabs.com/products/spec_lab/complex_tasks/combinmr/ Please contact info@acdlabs.com, or sales@acdlabs.com for more information or visit our website: www.acdlabs.com Many thanks, Gavin Shear Advanced Chemistry Development -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On Behalf Of Ferenc Csizmadia Sent: Monday, May 28, 2001 2:08 AM To: Artem Masunov Cc: chemistry@ccl.net Subject: CCL:Databases to support Comb.Chem.? Dear Artem, JChem is a software for handling chemical databases and structure files. http://www.jchem.com It runs under both Unix and Windows (even Mac) since it is written in Java. (At our web site you can try examples running on a Sun machine.) We are walking into the area of combinatorial chemistry with a new module, JKlustor, that can perform diversity calculations and clustering. http://www.jchem.com/doc/admin/JKlustor.html The software is developed continuously, we are open to suggestions on future directions. Please let me know if you have any question or if there are features that you miss. Best regards, Ferenc -- Dr. Ferenc Csizmadia ChemAxon Ltd. http://www.chemaxon.com T:+3620 9570988 mailto:fcsiz@chemaxon.com Artem Masunov wrote: > Dear CCLers, > What software do you use nowadays to support combinatorial chemistry/high > throughput screening? Comprehensive solutions from MSI seem to be too > expensive for Academia (especially maintenance), and Windows based > products (like Chem Finder from CambridgeSoft) do not seem to be able to > handle large (hundreds of thousands) libraries.. > > Artem > -= 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 May 28 15:43:43 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4SJhhS02994 for ; Mon, 28 May 2001 15:43:43 -0400 Received: from gap.cco.caltech.edu (gap.cco.caltech.edu [131.215.139.43]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id PAA08004 for ; Mon, 28 May 2001 15:43:42 -0400 (EDT) Received: (from news@localhost) by gap.cco.caltech.edu (8.9.3/8.9.3) id MAA12724; Mon, 28 May 2001 12:02:11 -0700 (PDT) To: mlist-chemistry@nntp-server.caltech.edu Path: news From: "Richard P. Muller" Newsgroups: mlist.chemistry Subject: Re: CCL:Summary: Integrals over Gaussian Functions Date: Mon, 28 May 2001 13:01:14 -0700 Organization: California Institute of Technology, Pasadena Lines: 20 Message-ID: <3B12AE8A.3B46933A@wag.caltech.edu> References: NNTP-Posting-Host: dhcp-26-202.wag.caltech.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.76 [en] (Win98; U) X-Accept-Language: en One addition and one correction to my earlier post on this topic. First the correction. I said: "Richard P. Muller" wrote: > I haven't (yet) gotten Boys RMP article, It actually isn't the RMP article, but the Proc Royal Soc (A200, 542, 1950), that contains Boys' original work on Gaussian Orbitals. I would also like to point out an excellent review by Saunders: V. R. Saunders. "Molecular Integrals for Gaussian Type Functions." in _Methods in Computational Molecular Physics_, Giercksen and Wilson, eds. Reidel, 1983. -- Richard P. Muller, Ph.D. rpm@wag.caltech.edu http://www.wag.caltech.edu/home/rpm From chemistry-request@server.ccl.net Mon May 28 16:29:48 2001 Received: from france.chem.duke.edu ([152.3.169.99]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4SKTlS03730 for ; Mon, 28 May 2001 16:29:47 -0400 Received: from mole.chem.duke.edu (mole.chem.duke.edu [152.3.169.102]) by france.chem.duke.edu (8.9.3/8.9.3) with ESMTP id QAA11464; Mon, 28 May 2001 16:29:47 -0400 (EDT) Received: from localhost (andres@localhost) by mole.chem.duke.edu (8.9.3+Sun/8.9.1) with ESMTP id QAA11435; Mon, 28 May 2001 16:29:46 -0400 (EDT) X-Authentication-Warning: mole.chem.duke.edu: andres owned process doing -bs Date: Mon, 28 May 2001 16:29:46 -0400 (EDT) From: Gerardo Andres Cisneros To: help@gaussian.com cc: chemistry@server.ccl.net Subject: URGENT: compiling on Linux alpha Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello I'm trying to compile g98 (i'm not sure if A7 or A9) on a dual processor alpha running RH7, i've installed the compaq fortran and math libraries but I still can't get it to compile. Every time I run bldg98 it stops because it tries to ling bsd/g98.make to generic.make which doesn't exist!!. I've tried modifying bldg98 so when it reaches the generic machine if it links g98.make to alpha-osf.make which is the only Makefile for alpha as far as I can tell but no go. The weird thing is that gau-machine does know what machine it is: [root@master bsd]# ../gau-machine alpha-openvms Here's a little piece of bldg98.log: ... unset x gau-unlimit rehash set x = `gau-machine` gau-machine echo machine type is alpha-openvms machine type is alpha-openvms gau-unlimit set ARFLAGS = `gau-arflags` gau-arflags rm -f bsd/g98.make @ generic = 0 @ sun = 0 ... if ( alpha-openvms == alpha-osf1 ) then @ generic = 1 cd bsd ln -s generic.make g98.make endif ... cp ../bsd/mdutil.c bsd make -f ../bsd/g98.make JUNK1=JUNK mdutil.o make: ../bsd/g98.make: No such file or directory make: *** No rule to make target `../bsd/g98.make'. Stop. ar rlv ../util.a mdutil.o ar: mdutil.o: No such file or directory else if ( 0 ) then rm mdutil.o rm: cannot remove `mdutil.o': No such file or directory endif That's when it tries to use generic.make. If I modify bldg98 I get: ... gau-machine echo machine type is alpha-openvms machine type is alpha-openvms ... if ( alpha-openvms == alpha-osf1 ) then @ generic = 1 cd bsd ln -s alpha-osf1.make g98.make endif ... make -f bsd/g98.make gau-fsplit gau-cpp cc -DALPHA_OSF1 -DI64 -DUSE_SYSV -I/usr/local/g98 -DDEFMAXSHL=20000 -DDEFMAXATM=20000 -DDEFMAXNZ=20000 -DDEFMAXINFO=200 -DDEFNVDIM=257 -DDEFARCREC=1024 -DDEFLMAX=13 -DDEFCACHE=128 -DDEFN3MIN=10 -DDEFMAXOP=120 -DDEFMAXTIT=100 -DDEFMAXRTE=4000 -DDEFMAXOV=500 -DDEFMAXIOP=100 -DDEFMAXCHR=1024 -DDEFMAXHEV=2000 -DDEFMAXLECP=10 -DDEFMAXFUNIT=5 -DDEFMAXFFILE=10000 -DDEFMAXFPS=1300 -DDEFMXTS=1500 -DDEFMXBAS=500 -DDEFMXOPT=50 -DDEFMXBOND=12 -DDEFMXSPH=250 -DDEFMXINV=1500 -DMERGE_LOOPS -DGAUSS_PAR -DGAUSS_THPAR -DUSE_PMM -DLITTLE_END -O -tune host -trapuv -o gau-fsplit bsd/fsplit.c cc: host: No such file or directory cc: unrecognized option `-tune' cc: unrecognized option `-trapuv' bsd/fsplit.c: In function `getline': bsd/fsplit.c:236: warning: assignment makes integer from pointer without a cast make: *** [gau-fsplit] Error 1 And it cascades from there, could anyone help me please?. Thanks in advance Andres -- G. Andres Cisneros Department of Chemistry Duke University andres@chem.duke.edu From chemistry-request@server.ccl.net Mon May 28 22:05:48 2001 Received: from marie.chem.purdue.edu ([128.210.142.219]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4T25mS17133 for ; Mon, 28 May 2001 22:05:48 -0400 Received: from localhost (lev@localhost) by marie.chem.purdue.edu (SGI-SGI-8.9.3/8.9.3) with ESMTP id VAA14829 for ; Mon, 28 May 2001 21:05:43 -0500 (EST) X-Authentication-Warning: marie.chem.purdue.edu: lev owned process doing -bs Date: Mon, 28 May 2001 21:05:41 -0500 From: Lev Gorenstein X-X-Sender: cc: Subject: CCL:Protein structures - what are the limits? In-Reply-To: <00c301c0e768$a3d56460$320a0a0a@fqspl.com.pl> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, On Mon, 28 May 2001, Victor Anisimov wrote: VA> What would be your normal procedure if you would need to VA> submit 50000 atoms' protein for QM calculation Which made me think of a question: what are current "limits" (due to RAM/performance/time requirements/cost/etc.) for QM calculations of large molecules? What's the largest peptide that can be dealt with on an ab initio level (insert your favorite basis set here) in a reasonable time? What's the similar state of the art protein for semiempirical methods? And, for comparison sake, what's the state of the art for molecular mechanics? Can anyone suggest any references or data for such comparison? Regards, Lev -- Daddy, why doesn't this magnet pick up this floppy disk? From chemistry-request@server.ccl.net Mon May 28 22:09:13 2001 Received: from ivory.trentu.ca ([192.75.12.103]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4T29CS17324 for ; Mon, 28 May 2001 22:09:12 -0400 Received: from trentu.ca ([204.225.13.50]) by trentu.ca (PMDF V5.2-32 #37862) with ESMTP id <01K442S86NMO0005D9@trentu.ca> for chemistry@ccl.net; Mon, 28 May 2001 22:08:25 EDT Date: Mon, 28 May 2001 22:14:23 -0400 From: elewars Subject: IR INTENSITIES BY MM, SUMMARY To: chemistry@ccl.net Message-id: <3B1305FE.2DE8CD67@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en 2001 May 28 Here is the summary of answers to my question whether molecular mechanics can calculate IR intensities. I thank all who showed an interest; they are acknowledged (#1- - #6) below--I hope I haven't missed anyone. Briefly, MM can. One such commercially-available program is a version of MM3, developed by the Allinger group. Dr J-H Lii of the University of Georgia (USA) was kind enough to calculate some IRs for me. E. Lewars ===== The Question: 2001 May 22 Hello, Molecular mechanics programs can now calculate the positions (cm**-1) of normal-mode vibrations. However, MM by itself cannot calculate the _intensities_ of these vibrations, since this depends on the change in dipole moment, which in turn depends on electron distribution, a concept outside MM theory. It seems, however, that in principle MM could calculate intensities using assigned bond moments or atom charges, which would provide a rapid way of calculating IR spectra. Has this been implemented in any program? Thanks E. Lewars ======== The Answers: #1 Hi, For periodic systems, try GULP (General Utility Lattice Program, by Dr. Julian Gale ) I've never done it, but this is from the help file: ------------------------------------------------------------------------- @@intensity Topic : intensity Type : Information Info : Infra-red phonon intensities are output when the eigenvectors : have been calculated using "eigen". Intensities are in nominal : units of charge**2. Raman intensities are also now output. : However, it should be noted that they are approximate and only : valid for systems with a single type of bond in (such as a : silicate). ------------------------------------------------------------------------- Hope this helps. Ricardo Ricardo Grau-Crespo rgrau@ceinpet.inf.cu Centro de Investigaciones del Petroleo CUBA ================ #2 Hi, you can calculate the intensities from the dipole moment change as a function of the Cartesian coordinates. In principle the charges can be whatever, but the intensities will be extremely dependent on them. A way to obtain good and cheap charges is to use QCFF/PI (see, for example Warshel, Computers&Chemistry, 1,195-202,1977), but if you are not so worried about the charges quality even with regular CFF (see Warshel-Levitt-Lifson, J. Mol. Spectr. 33,84-99(1970)) you can do the above job. Apart from QCFF/PI I don't know which other programs have this implemented. Sorry about that. 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 ================ #3 Greetings, Allinger has published a paper on IR intensities... I might guess in J Comp Chem.. Regards, John McKelvey jmmckel@attglobal.net =================== #4 You should check the book by K. Machida "Principles of molecular mechanics". I believe that the RISE program by the same author is able to calculate IR intensities. Rehards -- Dr. Rafael R. Pappalardo Dept. Quimica Fisica, Fac. de Quimica, Univ. de Sevilla. 41012-Sevilla (Spain) e-mail: rafapa@simulux.us.es =========== #5 could you summarize the answers you will get. Thanks regards Francois -- F.-Y. Dupradeau http://www.u-picardie.fr/UPIC/UPJV/recherche/labos/bpd/fyd.htm ============== #6 Dear Lewars, The MM3 program uses bond dipole moments and bond charge flux to calculate the IR intensity. Here is the reference you might want to look at.... Lii, J.-H. and Allinger, N.L. "Intensities of Infrared Bands in Molecular Mechanics (MM3)", J. Comput. Chemistry, 13, 1138-1141 (1992) Best regards, -Robert +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dr. Jenn-Huei Lii Computational Center for Molecular Structure and Design Department of Chemistry, University of Georgia, Athens, USA Tel: (706)542-2044 Fax: (404)542-2673 CCMSD Home Page: http://europa.chem.uga.edu +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dear Professor Lewars, Let me answer your questions in turns... (1) Yes, MM3 is available from Tripos, Inc. It also available from QCPE for academic users. (2) MM3 uses bond moments instead. It converts bond moment to atomic charge then calculate IR intensity. (3) We found Bond Charge Flux (even Angle Charge Flux) parameters play important role in IR intensity calculation in MM. Therefore, I am not sure if the error were small in Benzene or not. It needs to be investigated. -Robert ----- Original Message ----- From: "elewars" To: "Jenn-Huei Lii" Sent: Sunday, May 27, 2001 5:46 PM Subject: Re: QUICK QUESTIONS > Hello, > > May I ask just three short questions? > > (1) Is the version of MM3 you used to calculate intensities commercially > available, and if so who sells it? > (2) Does MM3 use atom charges to calculate dipole moments and thus intensities > (e.g. C and H for benzene)? > (3) I think for benzene you mean that you are still working on parameterizing > charges (?); can I assume any error for that calculation was fairly small? > > Thank you very much. > > E. Lewars > =========== ==============