From chemistry-request@ccl.net Fri Aug 6 09:28:45 2004 Received: from smtpout.mac.com (smtpout.mac.com [17.250.248.45]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i76EShFE008041 for ; Fri, 6 Aug 2004 09:28:44 -0500 Received: from mac.com (smtpin01-en2 [10.13.10.146]) by smtpout.mac.com (Xserve/MantshX 2.0) with ESMTP id i76EaGH3009583 for ; Fri, 6 Aug 2004 07:36:18 -0700 (PDT) Received: from [192.168.169.238] (momentum.chem.duke.edu [152.3.169.5]) (authenticated bits=0) by mac.com (Xserve/smtpin01/MantshX 4.0) with ESMTP id i76EaCfs001215 for ; Fri, 6 Aug 2004 07:36:13 -0700 (PDT) Mime-Version: 1.0 (Apple Message framework v618) Content-Transfer-Encoding: 7bit Message-Id: Content-Type: text/plain; charset=ISO-2022-JP; format=flowed To: chemistry*at*ccl.net From: Takumi Hori Subject: pKa prediction with QM/MM Date: Fri, 6 Aug 2004 10:36:18 -0400 X-Mailer: Apple Mail (2.618) X-Spam-Status: No, hits=0.3 required=7.5 tests=FVGT_s_OBFU_Q1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL members, I am looking for the informations about pKa calculations with QM/MM method in solution or proteins. Does anyone know good references? Thanks in advance. Sincerely yours, Takumi Hori -- Takumi Hori ---------------------------------------------------- Department of Chemistry Duke University Durham, NC 27708-0346 USA $B!! (B Tel : 1-919-660-1658 E-mail : thori*at*duke.edu thori3jp*at*mac.com -------------------------------------------------------------------- From chemistry-request@ccl.net Fri Aug 6 09:59:30 2004 Received: from mhub-m3.tc.umn.edu (mhub-m3.tc.umn.edu [160.94.23.33]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i76ExTFE010380 for ; Fri, 6 Aug 2004 09:59:29 -0500 Received: from pobox.com (abacavir.pharmacy.umn.edu [160.94.172.208] (may be forged)) by mhub-m3.tc.umn.edu with ESMTP for chemistry!at!ccl.net; Fri, 6 Aug 2004 10:06:59 -0500 (CDT) X-Umn-Remote-Mta: [N] abacavir.pharmacy.umn.edu [160.94.172.208] #+HF+LO Message-ID: <41139F8C.3040405!at!pobox.com> Date: Fri, 06 Aug 2004 10:11:08 -0500 From: Eric Bennett User-Agent: Mozilla/5.0 (X11; U; IRIX64 IP30; en-US; rv:1.4.1) Gecko/20040326 X-Accept-Language: en-us, en MIME-Version: 1.0 To: "'chemistry!at!ccl.net'" Subject: Parallel Jaguar on x86-64 / MPI question Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.3 required=7.5 tests=FCS_URI_NODOTS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello, I have seen people report running Jaguar succesfully on x86_64 systems, but I have not seen any reports as to whether these were parallel or serial jobs. I am having trouble running parallel jobs on an SMP Intel x86_64 system. I assume that because I'm an MPI novice, my problem is a configuration error, but Schrodinger's first response was to say that they do not compile for 64-bit systems. So, has anyone run parallel Jaguar on x86_64 succesfully? My serial jobs work fine. Alternatively, can someone who knows more about MPI than I do suggest where I might have gone wrong to obtain the following error, assuming that it is not an incompatibility with x86_64? The mpich test suite appears to run fine and uses all the CPUs. FATAL: FATAL: MPI_Comm_size (2) does not equal nprocs (1)MPI_Comm_size (2) does not equal nprocs (1)[0] MPI Abort by user Aborting program ! [1] MPI Abort by user Aborting program ! [0] Aborting program! [1] Aborting program! p0_27431: p4_error: : 1 p1_27432: p4_error: : 1 More info: Jaguar version 5.5, release 16 [bennette@localhost bms]$ uname -a Linux localhost.localdomain 2.4.21-15.EL #1 SMP Thu Apr 22 00:09:47 EDT 2004 x86_64 x86_64 x86_64 GNU/Linux TIA, Eric -- Dr. Eric Bennett, Center for Drug Design, U of Minnesota Our enemies are innovative and resourceful, and so are we. They never stop thinking about new ways to harm our country and our people, and neither do we. -George W. Bush http://www.whitehouse.gov/news/releases/2004/08/20040805-3.html From chemistry-request@ccl.net Fri Aug 6 11:35:29 2004 Received: from ntmms01.chla.usc.edu ([128.125.179.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i76GZSFE018047 for ; Fri, 6 Aug 2004 11:35:29 -0500 Received: from 10.3.1.165 by ntmms01.chla.usc.edu with ESMTP (CHLA SMTP Relay (MMS v5.6.0)); Fri, 06 Aug 2004 09:42:38 -0700 X-Server-Uuid: 3F66CE27-8E7A-45D4-9872-50BC1A7F95DE Received: by ntsmtp01.chla.usc.edu with Internet Mail Service ( 5.5.2653.19) id ; Fri, 6 Aug 2004 09:42:38 -0700 Message-ID: <73564B8DE398D61180500008C75D7E49033E6091@NTMAIL03> From: "Pandey, Jaya" To: "'chemistry)at(ccl.net'" Subject: Binding energy Date: Fri, 6 Aug 2004 09:42:32 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) X-WSS-ID: 6D0D6B741VS77775-01-01 Content-Type: text/plain Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear All, I screened about 1900 small ligands using AutoDock and the lowest energy of binding I could get was -10.00. Is it worth trying this ligand in the lab? Another query is that how to improve the binding energy. The grid was calculated centered on the target for all the atom types in the ligands. Please advice and help, what kind of energy one should look for to get a lead? Jaya From chemistry-request@ccl.net Fri Aug 6 08:47:13 2004 Received: from web52005.mail.yahoo.com (web52005.mail.yahoo.com [206.190.39.61]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i76DlC7g004968 for ; Fri, 6 Aug 2004 08:47:12 -0500 Message-ID: <20040806135443.6383.qmail..at..web52005.mail.yahoo.com> Received: from [128.112.141.35] by web52005.mail.yahoo.com via HTTP; Fri, 06 Aug 2004 06:54:43 PDT Date: Fri, 6 Aug 2004 06:54:43 -0700 (PDT) From: Konstantin Kudin Subject: Re: CCL:SCF Convergence problem in G03 To: chemistry..at..ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net > First, look at the initial gues around the homo-lumo gap.. Are there > unfilled orbitals that are essentially degenerate with orbitals to be > filled? If so a single determinate solution may not work.... and bad > convergence would not be a surprise Actually, does anyone know examples where B3LYP only leads to solutions where LUMO is below HOMO in energy, i.e. with holes below the Fermi level? My impression was that 20% of the HF exchange pretty much always stabilized the occupied orbitals, in the same way as the HF method does. Kostya __________________________________ Do you Yahoo!? New and Improved Yahoo! Mail - 100MB free storage! http://promotions.yahoo.com/new_mail From chemistry-request@ccl.net Fri Aug 6 15:51:54 2004 Received: from caladan.vcu.edu (caladan.vcu.edu [128.172.1.138]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i76KppFE008778 for ; Fri, 6 Aug 2004 15:51:54 -0500 Received: from mail1.vcu.edu (localhost.localdomain [127.0.0.1]) by caladan.vcu.edu (8.11.6/8.11.6) with ESMTP id i76KxR314655; Fri, 6 Aug 2004 16:59:27 -0400 Message-Id: <200408062059.i76KxR314655.-at-.caladan.vcu.edu> Date: Fri, 06 Aug 2004 16:59:27 -0300 From: Paul Momoh MIME-Version: 1.0 Subject: CASSCF KEYWORD Content-Type: text/plain; charset=iso-8859-1 User-Agent: IMHO/0.98.3 (Webmail for Roxen) To: chemistry.-at-.ccl.net, help.-at-.gaussian.com Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=0.6 required=7.5 tests=SUBJ_ALL_CAPS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi, Is the number of electrons and orbitals in a CASSCF job used arbitrarily or is there some kind of governing rule? Also, are there any special considerations for application to molecular clusters (ie. C2H2 clusters)? Paul Momoh. Virginia Commonwealth University P.O. BOX 842006 804 827 1222 From chemistry-request@ccl.net Fri Aug 6 19:05:17 2004 Received: from be-research.ucsd.edu (be-research.ucsd.edu [132.239.236.13]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i7705EFE028598 for ; Fri, 6 Aug 2004 19:05:14 -0500 Received: from localhost (dsteiger@localhost) by be-research.ucsd.edu (8.11.1/8.11.1) with ESMTP id i770Cma1331785 for ; Fri, 6 Aug 2004 17:12:50 -0700 (PDT) Date: Fri, 6 Aug 2004 17:12:48 -0700 From: Don Steiger To: chemistry!at!ccl.net Subject: Solution of the multi-ion specie Poisson Boltzmann equation. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I think that I can derive the Boundary integral equations for the nonlinear Poisson Boltzmann equation for proteins contained in a multi-ion specie solvent. The Integral equations should then be numerically solvable. The current state of the art is to solve the linearized equation. However, the linearized equation is only practical for 1:1 electrolytes. The nonlinear equation can be solved with a finite element approach; however this approach can only be used for relatively small systems. My question is whether there really is a need for being able to solve the multi-ion specie nonlinear Poisson Boltzmann equation. Or is this simply a solution in search of a problem. Thanks, Don