From chemistry-request@ccl.net Tue Aug 19 04:07:21 2003 Received: from soul.helsinki.fi (soul.helsinki.fi [128.214.3.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7J87K98010172 for ; Tue, 19 Aug 2003 04:07:21 -0400 Received: (from llaakkon@localhost) by soul.helsinki.fi (8.9.3p2/8.9.3) id LAA47737; Tue, 19 Aug 2003 11:07:41 +0300 (EEST) Message-ID: <20030819110740.42691-.at.-soul.helsinki.fi> Date: Tue, 19 Aug 2003 11:07:40 +0300 From: Liisa laakkonen To: CHEMISTRY-.at.-ccl.net Subject: CCL: charmm/PBEQ Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 0.68e Reply-to: liisa.laakkonen-.at.-helsinki.fi Dear CCL, Does anyone know, and succesfully use the membrane headgroup definitions HTMEMB and EPSH in the PBEQ module in charmm? I've tried definign the headgroup area in two versions of the program (see below), on different platforms. The command is ignored: **** Warning **** The following extraneous characters were found while command processing in PBEQ HTMEMB 10.0 Otherwise PBEQ seems to be functioning ok. Thank you in advance, Liisa Laakkonen Institute of Biotechnology University of Helsinki Finland ---------------------------------------------------------- (CHARMm) - Version 29.1 Revision: 2002.1029 Current operating system: IRIX64-6.5(IP27) (CHARMM) - Developmental Version 27b4 February 15, 2001 Current operating system: IBM RS/6000 AIX From chemistry-request@ccl.net Tue Aug 19 10:52:49 2003 Received: from ccl.net (email.ccl.net [192.148.249.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7JEqn98020666 for ; Tue, 19 Aug 2003 10:52:49 -0400 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h7JEqnA15551; Tue, 19 Aug 2003 10:52:49 -0400 (EDT) Date: Tue, 19 Aug 2003 10:53:24 -0400 (EDT) From: "Dr. Jan K Labanowski" To: chemistry:at:ccl.net, microelectronics:at:AtomicScaleDesign.net cc: "Dr. Jan K Labanowski" Subject: 03.11.13 US-Russian Workshop on Software Development, Tempe, AZ, US Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII US-Russian Workshop on Software Development Bridging atomic and macroscopic scales for materials, process, and device design (SWN2003). November 13-15, 2003 Arizona State University, Tempe, AZ, USA. http://www.asdn.net/swn2003/ Computer modeling and simulation continues to have increasing impact on process, material, and device design, eliminating a significant amount of experimental work based on a trail-and-error approaches and reducing the costs of the products and technologies. However, incorporation of atomic and molecular scale information into simulations of macroscopic systems remains a challenge. Opportunities exist for the development of integrated software tools that bridge the atomic and macroscopic scales, to enable solutions to complex scientific and technological problems. This workshop will bring together scientists and software designers who are working in the area of process, material and device design on the atomic scale with a particular focus on computation and predicting measurable macroscopic characteristics. One goal of the workshop is to stimulate an active collaboration and partnership between scientists and software designer in developing the integrated tools and interfaces between computer programs, which will allow the incorporation of atomic-scale information in macroscopic simulations in an efficient and reliable manner. Another aim of the workshop is to explore opportunities for developing the expertise of scientists and engineers in the US and Russia, former nuclear rivals, in the area of theoretical material science to promote science, education and cooperation in non-military technological areas. Organizers (Co-chairmen: B. Garrett & A. Korkin): ================================================ James Adams - Arizona State University, Tempe, AZ, USA Bruce Garrett - Pacific Northwest National Laboratory, Richland, WA, USA Bill Johnson - RJ Consulting, Scotsdale, AZ, USA Anatoli Korkin - Nano & Giga Solutions, Gilbert, AZ, USA Jan Labanowski - Ohio Supercomputer Center, OH, USA Maria Oseeva - SarovLabs, Sarov, Russia Boris Potapkin - Kinetic Technologies, Moscow, Russia Matt Stoker - DigitalDNA Lab Motorola, Tempe, AZ, USA Sponsors: ========= Arizona State University Initiative for Proliferation Prevention Kinetic Technologies Nuclear Cities Initiative Ohio Supercomputer Center Pacific Northwest National Laboratory SarovLabs Contact Info: ============= Maria Oseeva SarovLabs,23/16 Varlamovskaya Road Sarov, Nizhni Novgorod Region, 607188, Russia Phone: +7 83130 40201; Fax: +7 83130 44854/43871 e.mail: Maria.Oseeva[at]sarovlabs.com Registration deadline - October 15th, 2003 For further details and registration visit the web site: http://www.asdn.net/swn2003/ From chemistry-request@ccl.net Mon Aug 18 18:29:12 2003 Received: from julesburg.uits.indiana.edu (julesburg.uits.indiana.edu [129.79.1.75]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7IMTC98000761 for >ccl.net>; Mon, 18 Aug 2003 18:29:12 -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 h7IMTTLx005838 for >ccl.net>; Mon, 18 Aug 2003 17:29:33 -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 h7IMTVum023561 for >ccl.net>; Mon, 18 Aug 2003 17:29:31 -0500 (EST) Sender: qin<>yogibear.uits.iupui.edu Message-ID: <3F41534C.26CA70E5<>iupui.edu> Date: Mon, 18 Aug 2003 17:29:32 -0500 From: "Q." >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: CCL:add hydrogen to a sepecific atom Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, everyone, I am trying to use autodock to dock a small ligand to a protein. The complex should involve a H-bond between the side chain oxygen of a glutamate and the ligand. The glutamate residue is assumed to be protanated (i.e. neutral). However, i am having a hard time to add a proton to the glutamate. Autodock ( using ADT interface) adds H to many atoms but the glutamate. I also tried to use Whatif web server. Same thing happened. I wonder if anyone out there would have any suggestion on any programs ( free ones will be great) that can add H to specific atoms. Thanks a bunch. Q. Zou, Ph D. Indiana Univ. Medical Center From chemistry-request@ccl.net Tue Aug 19 06:44:23 2003 Received: from smtp.hotbox.ru (smtp.hotbox.ru [80.68.244.50]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7JAiM98014435 for >ccl.net>; Tue, 19 Aug 2003 06:44:23 -0400 Received: from verena.ineos.ac.ru (verena.ineos.ac.ru [193.233.4.18]) (authenticated bits=0) by smtp.hotbox.ru (8.12.9/8.12.9) with ESMTP id h7JAVbCe060531 for >ccl.net>; Tue, 19 Aug 2003 14:31:39 +0400 (MSD) (envelope-from dengolovanov<>pisem.net) Date: Tue, 19 Aug 2003 14:51:58 +0400 From: dengolovanov >pisem.net> X-Mailer: The Bat! (v1.61) Reply-To: dengolovanov >pisem.net> X-Priority: 3 (Normal) Message-ID: <65494931.20030819145158<>pisem.net> To: chemistry<>ccl.net Subject: NMR calculations MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL's Presently I'm trying to calculate NICS value for my molecules. 1. Which parameter should I use: Isotropic or Anisotropic magnetic shielding at point? 2. I should use magnetic shielding for dummy atom with respect to H1 TMS chemical shifts or ...? Thank's in advance -- Best regards, Denis G. Golovanov mailto:dengolovanov<>pisem.net From chemistry-request@ccl.net Tue Aug 19 12:11:18 2003 Received: from osgood.cc.nd.edu (osgood.cc.nd.edu [129.74.250.227]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7JGBI98022952 for ; Tue, 19 Aug 2003 12:11:18 -0400 Received: from nd.edu (frenchy.chem.nd.edu [129.74.74.11]) by osgood.cc.nd.edu (Switch-3.1.0/Switch-3.1.0) with ESMTP id h7JGBeqm002896 for ; Tue, 19 Aug 2003 11:11:41 -0500 (EST) Message-ID: <3F424BD0.5060706~at~nd.edu> Date: Tue, 19 Aug 2003 11:09:52 -0500 From: Jean-Christophe Ducom User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20021003 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry~at~ccl.net Subject: g03 error Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-ND-MTA-Date: Tue, 19 Aug 2003 11:11:42 -0500 (EST) X-ND-Virus-Scan: engine v4.2.40; dat v4287 Dear CCL'ers: We are running gaussian 03 on a four-processor Xeon-MP based workstation (4 GB of memory) using the ONIOM option. The machines runs Redhat7.3 with the stock kernel. The calculations run fine when nproc=2. However, when nproc=4, we get the error below. I wonder if anyone has encountered this issue and was able to resolve it. The stacksize on the system is already set to unlimited (from shell and > from the Portland environment variable MPSTKZ). The error persists whether g03 is compiled with version 4 or version 5 of the Portland Group compiler. Is it a problem with G03 and pthread? Any other sggestion? Thanks JC -------------------------------- Leave Link 716 at Tue Aug 19 05:21:35 2003, MaxMem= 104857600 cpu: 0.0 (Enter /usr/g03/l120.exe) ONIOM: saving gridpoint 3 ONIOM: restoring gridpoint 17 ONIOM: generating point 2 -- high level on model system. ChrgS2: IScale= 0 0 5 5 5 5 Leave Link 120 at Tue Aug 19 05:21:38 2003, MaxMem= 104857600 cpu: 0.5 (Enter /usr/g03/l301.exe) Standard basis: 6-31++G(d,p) (6D, 7F) Integral buffers will be 262144 words long. Raffenetti 2 integral format. Two-electron integral symmetry is turned off. 597 basis functions, 1013 primitive gaussians, 600 cartesian basis functions 101 alpha electrons 101 beta electrons nuclear repulsion energy 2370.7211695892 Hartrees. IExCor= 205 DFT=T Ex=S Corr=VWN ExCW=0 ScaHFX= 0.000000 ScaDFX= 1.000000 1.000000 1.000000 1.000000 IRadAn= 0 IRanWt= -1 IRanGd= 0 ICorTp=0 NAtoms= 8467 NActive= 44 NUniq= 44 SFac= 1.00D+00 NAtFMM= 60 Big=F Leave Link 301 at Tue Aug 19 05:21:41 2003, MaxMem= 104857600 cpu: 1.3 (Enter /usr/g03/l302.exe) NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1 NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0. One-electron integrals computed using PRISM. **ERROR: in a parallel region there is a stack overflow: thread 0, max 262128KB, used 0KB, request 48B **ERROR: in a parallel region there is a stack overflow: thread 0, max 262128KB, used 0KB, request 48B ------------------------------ From chemistry-request@ccl.net Tue Aug 19 14:25:37 2003 Received: from mercure.neokimia.com (mercure.med.usherbrooke.ca [132.210.158.207]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7JIPa98025981 for ; Tue, 19 Aug 2003 14:25:37 -0400 content-class: urn:content-classes:message Subject: CCL: GB/SA for different solvents MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C3667F.10D2A1A8" Date: Tue, 19 Aug 2003 14:24:02 -0400 X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: CCL: GB/SA for different solvents Thread-Index: AcNmfEXER9+Gc58LSViUuWBPisfzmQAAsC7w From: "Axel Mathieu" To: "CCL" This is a multi-part message in MIME format. ------_=_NextPart_001_01C3667F.10D2A1A8 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable =20 -----Original Message----- From: Axel Mathieu=20 Sent: 19 ao=FBt, 2003 14:04 To: CCL (chemistry:at:ccl.net) Subject: GB/SA for different solvents Hello everybody, =20 I was wondering if someone would have optimized GB/SA parameters for a = variety of solvents including methanol, chloroform, DMSO, etc ... If = not, can anyone point me to where I may find them if they exist. Your = comments and suggestions are greatly appreciated. I know MacroModel has = parameter files for water and chloroform (water.svl and chcl3.svl) but I = unfortunately do not have access to MacroModel. =20 APM =20 =20 ------_=_NextPart_001_01C3667F.10D2A1A8 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Message
 
-----Original Message-----
From: Axel Mathieu =
Sent:=20 19 ao=FBt, 2003 14:04
To: CCL = (chemistry:at:ccl.net)
Subject:=20 GB/SA for different solvents

Hello = everybody,
 
I was wondering if = someone would=20 have optimized GB/SA parameters for a variety of solvents including = methanol,=20 chloroform, DMSO, etc ... If not, can anyone point me to where I may = find them=20 if they exist. Your comments and suggestions are greatly appreciated. I = know=20 MacroModel has parameter files for water and chloroform (water.svl and=20 chcl3.svl) but I unfortunately do not have access to = MacroModel.
 
APM
 
 
= =00 ------_=_NextPart_001_01C3667F.10D2A1A8--