From chemistry-request@server.ccl.net Tue Apr 22 01:13:19 2003 Received: from mail.staff.site.ntu.edu.au ([138.80.69.54]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3M5DIa09248 for ; Tue, 22 Apr 2003 01:13:18 -0400 Received: from mail.staff.site.ntu.edu.au ([138.80.49.23]) by mail.staff.site.ntu.edu.au with Microsoft SMTPSVC(5.0.2195.5329); Tue, 22 Apr 2003 14:43:08 +0930 Received: by mail.staff.site.ntu.edu.au (sSMTP sendmail emulation); Tue, 22 Apr 2003 14:41:28 +0930 Date: Tue, 22 Apr 2003 14:41:28 +0930 From: Brian Salter-Duke To: Comp Chem List Subject: G98 MP2 Frequency error Message-ID: <20030422051128.GC2533@monster.ntu.edu.au> Reply-To: Brian Salter-Duke Mail-Followup-To: Comp Chem List Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.5.3i X-OriginalArrivalTime: 22 Apr 2003 05:13:09.0424 (UTC) FILETIME=[DD641300:01C3088D] Can anyone help in getting around this G98 MP22 Frequency error. It is before the MP2 energy is evaluated yet the MP2 optimisation went fine. I have tried raising the memory but it just keeps giving the error. SCF Done: E(RHF) = -1369.92661795 A.U. after 1 cycles Convg = 0.1521D-08 -V/T = 2.0015 S**2 = 0.0000 KE= 1.367893146828D+03 PE=-7.187312373164D+03 EE= 2.464054415544D+03 Leave Link 502 at Tue Apr 22 14:32:57 2003, MaxMem= 8000000 cpu: 227.9 (Enter /home/qchem/g98/l801.exe) Range of M.O.s used for correlation: 28 387 NBasis= 387 NAE= 86 NBE= 86 NFC= 27 NFV= 0 NROrb= 360 NOA= 59 NOB= 59 NVA= 301 NVB= 301 Leave Link 801 at Tue Apr 22 14:32:57 2003, MaxMem= 8000000 cpu: 0.0 (Enter /home/qchem/g98/l906.exe) Frozen-core derivative calculation, NFC= 27 NFV= 0. DE2Beg-1 allocation failure: iend,mxcore= 19301005 8000000 Error termination via Lnk1e in /home/qchem/g98/l906.exe. Job cpu time: 0 days 0 hours 3 minutes 55.1 seconds. File lengths (MBytes): RWF= 3938 Int= 0 D2E= 0 Chk= 14 Scr= 1 Thanks, Brian. -- "Faith is the great cop-out, the great excuse to evade the need to think and evaluate evidence. Faith is belief inspite of, even perhaps because of, the lack of evidence." -- Richard Dawkins Brian Salter-Duke (Brian Duke) Email: b_duke@octa4.net.au From chemistry-request@server.ccl.net Tue Apr 22 12:08:54 2003 Received: from hellmouth4.gatech.edu ([130.207.165.164]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3MG8sa23380 for ; Tue, 22 Apr 2003 12:08:54 -0400 Received: from hellmouth4.gatech.edu (localhost [127.0.0.1]) by hellmouth4.gatech.edu (Postfix) with SMTP id 93376A538 for ; Tue, 22 Apr 2003 12:08:54 -0400 (EDT) (envelope-from scott.stagg@biology.gatech.edu) Received: from mailprx1.gatech.edu (mailprx1.prism.gatech.edu [130.207.171.15]) (using TLSv1 with cipher EDH-RSA-DES-CBC3-SHA (168/168 bits)) (Client CN "smtp.mail.gatech.edu", Issuer "RSA Data Security? Inc." (verified OK)) by hellmouth4.gatech.edu (Postfix) with ESMTP id 7AFBCA487 for ; Tue, 22 Apr 2003 12:08:54 -0400 (EDT) (envelope-from scott.stagg@biology.gatech.edu) Received: from biology.gatech.edu (DHCP-90.biology.gatech.edu [130.207.66.90]) (using TLSv1 with cipher DES-CBC3-SHA (168/168 bits)) (No client certificate requested) (sasl: method=PLAIN, username=ss396, sender=n/a) by mailprx1.gatech.edu (Postfix) with ESMTP id 101B53A601 for ; Tue, 22 Apr 2003 12:08:54 -0400 (EDT) (envelope-from scott.stagg@biology.gatech.edu) Date: Tue, 22 Apr 2003 12:08:53 -0400 Mime-Version: 1.0 (Apple Message framework v552) Content-Type: text/plain; charset=US-ASCII; format=flowed Subject: top and par for a small molecule From: Scott Stagg To: chemistry@ccl.net Content-Transfer-Encoding: 7bit Message-Id: X-Mailer: Apple Mail (2.552) Hi, I am trying to do molecular dynamics on a small molecule. I have been all over the web trying to find the CHARMM-style topology and parameter files for decyloxy methanol (DEM). I was able to find it on the hic-up website (http://xray.bmc.uu.se/hicup/), but the files it generates are without hydrogens. Does anyone know where I might be able to find the topology and parameter files or how I can generate them myself? Thanks, Scott Stagg From chemistry-request@server.ccl.net Tue Apr 22 14:52:11 2003 Received: from schrodinger.com ([192.156.98.99]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3MIqAa27480 for ; Tue, 22 Apr 2003 14:52:10 -0400 Received: from tandoori (root@tandoori.schrodinger.com [216.216.237.99]) by schrodinger.com (8.8.5/8.8.5) with ESMTP id LAA06496; Tue, 22 Apr 2003 11:52:09 -0700 Received: from sally.schrodinger.com (banks@sally.schrodinger.com [216.216.237.92]) by tandoori (8.8.5/8.8.5) with ESMTP id OAA18224; Tue, 22 Apr 2003 14:52:04 -0400 Received: (from banks@localhost) by sally.schrodinger.com (8.8.8/8.8.5) id OAA26087; Tue, 22 Apr 2003 14:52:08 -0400 Date: Tue, 22 Apr 2003 14:52:08 -0400 Message-Id: <200304221852.OAA26087@sally.schrodinger.com> From: Jay Banks To: chemistry@ccl.net Subject: Grid energy minimization Hi -- Does anyone have experience with minimizing potential energy functions defined at (or interpolated between) points on a 3-dimensional grid? The minimizer I've been using has occasional problems, which I think are associated with discontinuities at the edges of grid boxes, etc. I know that the "downhill simplex" algorithm (Nelder & Mead, Computer J. 7: 308 (1965)) can be useful for discontinuous functions (and/or discontinuous derivatives), but I doubt that it is practical for my purposes given the high dimensionality of my problem. So I'd be interested in hearing about modifications of other "standard" methods, as well as anything "new" that anyone has come up with. Sincerely, Jay Banks (banks "at" schrodinger "dot" com) From chemistry-request@server.ccl.net Tue Apr 22 12:35:26 2003 Received: from web21207.mail.yahoo.com ([216.136.175.165]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h3MGZPa24407 for ; Tue, 22 Apr 2003 12:35:25 -0400 Message-ID: <20030422163524.86601.qmail@web21207.mail.yahoo.com> Received: from [129.109.73.75] by web21207.mail.yahoo.com via HTTP; Tue, 22 Apr 2003 09:35:24 PDT Date: Tue, 22 Apr 2003 09:35:24 -0700 (PDT) From: IEJMD Subject: Internet Electronic Journal of Molecular Design To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Internet Electronic Journal of Molecular Design, http://www.biochempress.com Email: iejmd@yahoo.com Part 7 of the IEJMD special issue dedicated to Professor Haruo Hosoya on the occasion of the 65th birtday is available for download from the IEJMD Web site: http://www.biochempress.com Contents: 1. QSAR Study on Some Dihydrofolate Reductase Inhibitors 2. Compound Similarity Used in Solvent-Solute Interaction Modeling 3. On the Hosoya Z Index of General Graphs 4. The Solvent Boundary Potential: A New Approach for Computer Simulation of Large Systems 5. Aquatic Toxicity Prediction for Polar and Nonpolar Narcotic Pollutants with Support Vector Machines __________________________________________________ Do you Yahoo!? The New Yahoo! Search - Faster. Easier. Bingo http://search.yahoo.com From chemistry-request@server.ccl.net Tue Apr 22 20:31:18 2003 Received: from ns.ciac.jl.cn ([202.98.16.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3N0VAa03038 for ; Tue, 22 Apr 2003 20:31:15 -0400 Received: from zhang1 (localhost [127.0.0.1]) by ns.ciac.jl.cn (8.9.1/8.9.1) with SMTP id IAA19631 for ; Wed, 23 Apr 2003 08:34:41 +0800 (CST) Message-Id: <200304230034.IAA19631@ns.ciac.jl.cn> From: "zjwu" To: "chemistry@ccl.net" Subject: CPCM TS location X-mailer: Foxmail 4.2 [cn] Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====002_Dragon016740886545_=====" Date: Wed, 23 Apr 2003 8:29:53 +0800 This is a multi-part message in MIME format. --=====002_Dragon016740886545_===== Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Dear members, I am trying to locate the transition state using cpcm model. The initial structure is from gas phase optimized transition structure (with correct vibrational mode). The optimization at cpcm level fails by the following keywords #b3lyp/6-31g(d,p) opt=(ts, readfc, noeigen) scrf=(cpcm,solvent=water) Do anybody has experience in cpcm transition structure calculation? Thanks a lot. Best regards, Zhijian Wu --=====002_Dragon016740886545_===== Content-Type: text/html; charset="GB2312" Content-Transfer-Encoding: 7bit

Dear members,

 

I am trying to locate the transition state using cpcm model. The initial structure is from gas phase optimized transition structure (with correct vibrational mode). The optimization at cpcm level fails by the following keywords

 

#b3lyp/6-31g(d,p) opt=(ts, readfc, noeigen) scrf=(cpcm,solvent=water)

 

Do anybody has experience in cpcm transition structure calculation?

 

Thanks a lot.

 

Best regards,

 

Zhijian Wu

--=====002_Dragon016740886545_=====--