From chemistry-request@server.ccl.net Tue Jan 15 10:08:07 2002 Received: from mail-nord.nord.univ-mrs.fr ([194.214.97.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0FF86I18989 for ; Tue, 15 Jan 2002 10:08:06 -0500 Received: from [194.214.91.105] ([194.214.91.105]) by mail-nord.nord.univ-mrs.fr (8.9.3/8.9.3) with ESMTP id QAA05714 for ; Tue, 15 Jan 2002 16:30:33 +0100 X-Sender: sampieri@mail-nord.nord.univ-mrs.fr Message-Id: In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 15 Jan 2002 16:02:25 +0200 To: CHEMISTRY@ccl.net From: Francois Sampieri Subject: Re: CCL: Not really a summary "Free softw. for pot. energy calc." Dear all, Almost one week ago, I sent a message to the list for getting help in a batch calculation of potential energy of many protein structures. I'm wondering if my question was well formulated since I obtained only one response (Thanks again Marc!) as a proposal for compiling for me the (few) softwares I had yet got as source code only. Unfortunately, I soon realized that the executables that Marc sent to me will not solve my present problem, though these softwares could be very useful in other respects. I would like to understand such a poor response, and I wonder if I under-estimated the complexity of the process of potential energy calculations. These must be performed with sophisticated force field algorithms and generally, such FF are part of packages which are rarely free. So, I resign myself to cope with what I'm equipped with: INSIGHT II or MODELLER, even if they are not the best solution for the type of calculation I want to perform. I will inform the list if I eventually succeed. Best regards Francois Sampieri ___________________ My previous message: > >I have to sort a huge number (more than 3000 pdb files) of conformations of >the same protein, according to their potential energies (bonded + >non-bonded). >The first step could be to automatically launch a software capable of >achieving energy calculation from each pdb file, then to extract the energy >values from the ca. 3000 created files, and sort them into a single file, >the all processes being driven by a Perl script running on O2 SGI under >Irix 6.5. >I got references for some such free softwares, but I found them as source >files only and this is a problem for us since we don't have (and don't have >skills for coping with) Fortran or C compilers. > >After unsuccessfully searching on the Web, I'm asking to the CCL community >if anyone could point me to such executable programs. >All responses will be summarized. > ____________________________________________ UMR 6560 CNRS-Universite de la Mediterranee Laboratoire de Biochimie - IFR Jean Roche Faculte de Medecine Nord Bd Pierre Dramard 13916 Marseille Cedex 20 E-mail: sampieri.f@jean-roche.univ-mrs.fr Fax: (33) 4 91 65 75 95 Tel: (33) 4 91 69 88 44 From chemistry-request@server.ccl.net Tue Jan 15 11:24:18 2002 Received: from chilaca ([129.49.94.210]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0FGOII21141 for ; Tue, 15 Jan 2002 11:24:18 -0500 Received: from localhost (cuigl@localhost) by chilaca (8.11.6/8.11.6) with ESMTP id g0FGKEl31381; Tue, 15 Jan 2002 11:20:14 -0500 X-Authentication-Warning: chilaca: cuigl owned process doing -bs Date: Tue, 15 Jan 2002 11:20:14 -0500 (EST) From: "CUI, Guanglei" X-X-Sender: To: Francois Sampieri cc: Subject: Re: CCL:Not really a summary "Free softw. for pot. energy calc." In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, You happen to have AMBER6. The sander module can post-process a trajectory file and calculate the potential energy of each structure it has with imin = 5. It might not be the best solution for you but at least it could be a try. Good luck. Guangelei Cui On Tue, 15 Jan 2002, Francois Sampieri wrote: > Dear all, > > Almost one week ago, I sent a message to the list for getting help in a > batch calculation of potential energy of many protein structures. I'm > wondering if my question was well formulated since I obtained only one > response (Thanks again Marc!) as a proposal for compiling for me the (few) > softwares I had yet got as source code only. > Unfortunately, I soon realized that the executables that Marc sent to me > will not solve my present problem, though these softwares could be very > useful in other respects. > I would like to understand such a poor response, and I wonder if I > under-estimated the complexity of the process of potential energy > calculations. These must be performed with sophisticated force field > algorithms and generally, such FF are part of packages which are rarely > free. > So, I resign myself to cope with what I'm equipped with: INSIGHT II or > MODELLER, even if they are not the best solution for the type of > calculation I want to perform. > I will inform the list if I eventually succeed. > Best regards > > Francois Sampieri > > ___________________ > My previous message: > > > > >I have to sort a huge number (more than 3000 pdb files) of conformations of > >the same protein, according to their potential energies (bonded + > >non-bonded). > >The first step could be to automatically launch a software capable of > >achieving energy calculation from each pdb file, then to extract the energy > >values from the ca. 3000 created files, and sort them into a single file, > >the all processes being driven by a Perl script running on O2 SGI under > >Irix 6.5. > >I got references for some such free softwares, but I found them as source > >files only and this is a problem for us since we don't have (and don't have > >skills for coping with) Fortran or C compilers. > > > >After unsuccessfully searching on the Web, I'm asking to the CCL community > >if anyone could point me to such executable programs. > >All responses will be summarized. > > > > ____________________________________________ > UMR 6560 CNRS-Universite de la Mediterranee > Laboratoire de Biochimie - IFR Jean Roche > Faculte de Medecine Nord > Bd Pierre Dramard > 13916 Marseille Cedex 20 > E-mail: sampieri.f@jean-roche.univ-mrs.fr > Fax: (33) 4 91 65 75 95 > Tel: (33) 4 91 69 88 44 > > > > > -= 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 > > > > > > -- Guanglei Cui Dept. of Chemistry SUNY at Stony Brook Stony Brook, NY 11790 From chemistry-request@server.ccl.net Tue Jan 15 09:01:02 2002 Received: from kodakr.kodak.com ([192.232.119.69]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0FE11I17347 for ; Tue, 15 Jan 2002 09:01:02 -0500 Received: from acadia.image.kodak.com (acadia.image.kodak.com [150.220.67.56]) by kodakr.kodak.com (8.11.1/8.11.1) with ESMTP id g0FE0pp26453 for ; Tue, 15 Jan 2002 09:00:51 -0500 (EST) Received: from kodak.com (berlioz.rl.kodak.com [150.220.89.22]) by acadia.image.kodak.com (8.10.2+Sun/8.10.2) with ESMTP id g0FE0o023900 for ; Tue, 15 Jan 2002 09:00:51 -0500 (EST) Sender: david.giesen@kodak.com Message-ID: <3C443339.2E38BA6C@kodak.com> Date: Tue, 15 Jan 2002 08:48:41 -0500 From: David J Giesen Organization: Eastman-Kodak X-Mailer: Mozilla 4.05C-SGI [en] (X11; I; IRIX64 6.5 IP25) MIME-Version: 1.0 To: CHEMISTRY@server.ccl.net Subject: Program to calculate con vs time Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Is anyone aware of a non-commercial computer program available to calculate concentration versus time for a series of reactions with known rates and known initial conditions? I am aware of Kintecus in the CCL archives and http://www.kintecus.com (very nice, but too expensive), Kinsim from http://www.biochem.wustl.edu/cflab/message.html (works just fine, but I was hoping for a bit better interface), and MSIMPC from QCPE http://qcpe.chem.indiana.edu (which I haven't tried as it costs too much just to get access). That's all I was able to find with all my web and ccl archive searching tricks. Any other suggestions? Dave -- Dr. David J. Giesen Eastman Kodak Company david.giesen@kodak.com 2/83/RL MC 02216 (ph) 1-716-58(8-0480) Rochester, NY 14650 (fax)1-716-588-1839 From chemistry-request@server.ccl.net Tue Jan 15 09:26:29 2002 Received: from mail2.zrz.tu-berlin.de ([130.149.4.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0FEQTI17955 for ; Tue, 15 Jan 2002 09:26:29 -0500 Received: from mailszrz.zrz.tu-berlin.de ([130.149.4.11]) by mail2.zrz.tu-berlin.de with esmtp (exim-3.34) for id 16QUXU-0005hY-00; Tue, 15 Jan 2002 15:26:12 +0100 Received: from natrium.chem.tu-berlin.de ([130.149.169.143]) by mailszrz.zrz.tu-berlin.de with esmtp (exim-3.34) for id 16QUXA-0003gG-00; Tue, 15 Jan 2002 15:25:53 +0100 Mime-Version: 1.0 X-Sender: chwu0531@mailszrz.zrz.tu-berlin.de (Unverified) Message-Id: Date: Tue, 15 Jan 2002 15:25:53 +0100 To: chemistry@ccl.net From: Christoph van =?iso-8859-1?Q?W=FCllen?= Subject: Any comparisons of LAM-MPI vs. MPI-CH on LINUX/86? Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g0FEQTI17956 Are there any performance comparisons of the two free MPI-implementations in the subject line on PC/Linux computers? I tried both with a simple program sending and receiving blocks of different size, and LAM-MPI was slightly ahead. This is however only a first hit, so I wonder if there have been thorough comparisons. Moreover, although MPI-CH is better supported on a broad range of platforms, since MPI is assumed to be standard, is this a reason to prefer MPI-CH? Yours, +---------------------------------+----------------------------------+ | Prof. Christoph van Wüllen | Tele-Phone (+49) (0)30 314 27870 | | Technische Universität Sekr. C3 | Tele-Fax (+49) (0)30 314 23727 | | Straße des 17. Juni 135 | eMail | | D-10623 Berlin, Germany | Christoph.vanWullen@TU-Berlin.De | +---------------------------------+----------------------------------+ From chemistry-request@server.ccl.net Tue Jan 15 11:29:44 2002 Received: from sd.accelrys.com ([146.202.0.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0FGThI21304 for ; Tue, 15 Jan 2002 11:29:43 -0500 Received: (from johnw@localhost) by sd.accelrys.com (8.11.0/8.11.0) id g0FGUlt16164 for chemistry@ccl.net; Tue, 15 Jan 2002 08:30:47 -0800 Received: from JOHNWLAP (dhcp528.sd.accelrys.com [172.30.202.20]) by sd.accelrys.com (8.11.0/8.11.0) with SMTP id g0FGUlK16147 for ; Tue, 15 Jan 2002 08:30:47 -0800 From: "John Wintersteen" To: Subject: ViewerPro 4.2 available from Accelrys Date: Tue, 15 Jan 2002 08:28:13 -0800 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Hello, Accelrys Inc. is pleased to announce the availability of the ViewerPro 4.2. The ViewerPro is a PC based 3D molecular visualization and chemical communication application. Version 4.2 is available as an upgrade, free of charge, to all licensed WebLab ViewerPro 4.0 users. Users of any 3.X version of the WebLab ViewerPro can purchase a version 4.2 upgrade. For more information please visit the ViewerPro 4.2 upgrade home page at: http://www.accelrys.com/viewer/viewerpro/viewerpro_upgrade.php Enhancements in this new version include an mmCIF file importer; improved PDB and MSV file reading speed; improved VRML, QUANTA, and SMILES file handling; support for PNG file export. For more information about the 4.2 upgrade and Accelrys’ Viewer products, please visit Accelrys' Viewer web site here: http://www.accelrys.com/viewer/ Sincerely, John Wintersteen Sr. Product Manager, Experimental Chemistry Accelrys Inc. johnw@accelrys.com From chemistry-request@server.ccl.net Tue Jan 15 13:22:53 2002 Received: from chilaca ([129.49.94.210]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0FIMrI23864 for ; Tue, 15 Jan 2002 13:22:53 -0500 Received: from localhost (cuigl@localhost) by chilaca (8.11.6/8.11.6) with ESMTP id g0FIIiP31419; Tue, 15 Jan 2002 13:18:44 -0500 X-Authentication-Warning: chilaca: cuigl owned process doing -bs Date: Tue, 15 Jan 2002 13:18:44 -0500 (EST) From: "CUI, Guanglei" X-X-Sender: To: Francois Sampieri cc: Subject: Re: CCL:Not really a summary "Free softw. for pot. energy calc." In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII It's going to be in AMBER7. Sorry about the confusion. Regards, On Tue, 15 Jan 2002, CUI, Guanglei wrote: > Hi, > You happen to have AMBER6. The sander module can post-process a trajectory > file and calculate the potential energy of each structure it has with imin = 5. > It might not be the best solution for you but at least it could be a try. Good > luck. > > Guangelei Cui > > On Tue, 15 Jan 2002, Francois Sampieri wrote: > > > Dear all, > > > > Almost one week ago, I sent a message to the list for getting help in a > > batch calculation of potential energy of many protein structures. I'm > > wondering if my question was well formulated since I obtained only one > > response (Thanks again Marc!) as a proposal for compiling for me the (few) > > softwares I had yet got as source code only. > > Unfortunately, I soon realized that the executables that Marc sent to me > > will not solve my present problem, though these softwares could be very > > useful in other respects. > > I would like to understand such a poor response, and I wonder if I > > under-estimated the complexity of the process of potential energy > > calculations. These must be performed with sophisticated force field > > algorithms and generally, such FF are part of packages which are rarely > > free. > > So, I resign myself to cope with what I'm equipped with: INSIGHT II or > > MODELLER, even if they are not the best solution for the type of > > calculation I want to perform. > > I will inform the list if I eventually succeed. > > Best regards > > > > Francois Sampieri > > > > ___________________ > > My previous message: > > > > > > > >I have to sort a huge number (more than 3000 pdb files) of conformations of > > >the same protein, according to their potential energies (bonded + > > >non-bonded). > > >The first step could be to automatically launch a software capable of > > >achieving energy calculation from each pdb file, then to extract the energy > > >values from the ca. 3000 created files, and sort them into a single file, > > >the all processes being driven by a Perl script running on O2 SGI under > > >Irix 6.5. > > >I got references for some such free softwares, but I found them as source > > >files only and this is a problem for us since we don't have (and don't have > > >skills for coping with) Fortran or C compilers. > > > > > >After unsuccessfully searching on the Web, I'm asking to the CCL community > > >if anyone could point me to such executable programs. > > >All responses will be summarized. > > > > > > > ____________________________________________ > > UMR 6560 CNRS-Universite de la Mediterranee > > Laboratoire de Biochimie - IFR Jean Roche > > Faculte de Medecine Nord > > Bd Pierre Dramard > > 13916 Marseille Cedex 20 > > E-mail: sampieri.f@jean-roche.univ-mrs.fr > > Fax: (33) 4 91 65 75 95 > > Tel: (33) 4 91 69 88 44 > > > > > > > > > > > > > > > > > > > > > > -- Guanglei Cui Dept. of Chemistry SUNY at Stony Brook Stony Brook, NY 11790 From chemistry-request@server.ccl.net Tue Jan 15 13:32:25 2002 Received: from chilaca ([129.49.94.210]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0FIWOI24113 for ; Tue, 15 Jan 2002 13:32:25 -0500 Received: from localhost (cuigl@localhost) by chilaca (8.11.6/8.11.6) with ESMTP id g0FISMG31457 for ; Tue, 15 Jan 2002 13:28:22 -0500 X-Authentication-Warning: chilaca: cuigl owned process doing -bs Date: Tue, 15 Jan 2002 13:28:22 -0500 (EST) From: "CUI, Guanglei" X-X-Sender: To: Subject: replica exchange method Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I have a question about replica exchange method (REM). I wonder how the pair of replicas are chosen when it is possible for one replica to exchange temperature with both of its neightbors. If such situation happens, what would be the best way to pick one out of two exchanges? Thanks. Regards, -- Guanglei Cui Dept. of Chemistry SUNY at Stony Brook Stony Brook, NY 11790 From chemistry-request@server.ccl.net Tue Jan 15 12:51:03 2002 Received: from mh1-cam.cam.accelrys.com ([192.190.183.253]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0FHp3I23342 for ; Tue, 15 Jan 2002 12:51:03 -0500 Received: from dhcp81.scipark.cam.accelrys.com ([192.168.122.81] helo=water) by mh1-cam.cam.accelrys.com with smtp (Exim 3.12 #1 (Debian)) id 16QXjT-0003GM-00 for ; Tue, 15 Jan 2002 17:50:47 +0000 Message-ID: <02a001c19ded$29a4f110$517aa8c0@water> From: "Tien Luu" To: Subject: Accelrys Life Science Training in Munich, Germany Date: Tue, 15 Jan 2002 17:43:54 -0000 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit 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 Accelrys will be holding a pair of 2-day workshops at our office in Munich, Germany, in March, 2002. On March 19-20, the "Introduction to Cerius2 for Life Sciences Workshop" will be offered. This course provides an overview of molecular modelling techniques for life sciences applications using Cerius2. The workshop will focus on basic skills for use of the interface and will explore various modules in the areas of rational-drug design, structure-based drug design, and combinatorial chemistry. Prior modelling experience is not assumed making this course a great place to learn molecular modelling with Cerius2. On March 21-22, the "Pharmacophore Generation with Catalyst" workshop will be presented. This workshop is intended to introduce customers to pharmacophore generation and to the Catalyst user interface. The workshop begins with the basics of the Catalyst interface and builds to simple pharmacophore generation, selection of training sets, and three-dimensional database searching. Methods used within Catalyst for automatic hypothesis generation and manual hypothesis construction will be discussed. Some optimisation of training sets and database searching will be covered as well. Attendees should possess knowledge of basic UNIX commands and have a basic understanding of QSAR theory. Fees for each 2-day course are EUR1120 commercial, EUR560 government, and EUR450 academic. However, register for both courses and receive a 25% discount for the second course. Registration is on-line at URL http://www.accelrys.com/training/lifesci/registration.php. Further detailed information about this and other Accelrys training workshops can be found at the Accelrys website (http://www.accelrys.com/training/lifesci/schedule.html). Please do not hesitate to contact us should you have any questions. Please note that on 1 June 2001, MSI, Synopsys, Oxford Molecular, and GCG became Accelrys. Thank you very much. Tien Luu +44 1223 402 895 Chris Arzt +1 858-799-5340 From chemistry-request@server.ccl.net Tue Jan 15 15:30:21 2002 Received: from deimos.email.Arizona.EDU ([128.196.133.166]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0FKULI25924 for ; Tue, 15 Jan 2002 15:30:21 -0500 Received: from u.arizona.edu (128.196.184.158) by deimos.email.Arizona.EDU (6.0.036) (authenticated as mcafiero@email.arizona.edu) id 3C438597000181D7; Tue, 15 Jan 2002 13:30:09 -0700 Sender: mcafiero@ccl.net Message-ID: <3C449151.27913BE@u.arizona.edu> Date: Tue, 15 Jan 2002 20:30:09 +0000 From: Maurice Cafiero X-Mailer: Mozilla 4.61 [en] (X11; I; Linux 2.2.13-7mdk i686) X-Accept-Language: en MIME-Version: 1.0 To: Christoph van =?iso-8859-1?Q?W=FCllen?= , chemistry@ccl.net Subject: Re: CCL:Any comparisons of LAM-MPI vs. MPI-CH on LINUX/86? References: Content-Type: multipart/alternative; boundary="------------D67D8214A35B2C02057F2063" --------------D67D8214A35B2C02057F2063 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I really do not know too many of the technical aspects, but we had LAM and MPICH on two different clusters. The one with LAM has run smoothly for almost 3 years, while we had to replace MPICH after 6 months due to instability. If you want, I can ask our main sys admin to email you details... -- Mauricio Cafiero Doctoral Candidate : Theoretical and Computational Quantum Chemistry Department of Chemistry University of Arizona --------------D67D8214A35B2C02057F2063 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit I really do not know too many of the technical aspects, but we had LAM and MPICH on two different clusters.
The one with LAM has run smoothly for almost 3 years, while we had to replace MPICH after 6 months due to instability.
If you want, I can ask our main sys admin to email you details... 
-- 
Mauricio Cafiero
Doctoral Candidate : Theoretical
                     and Computational
                     Quantum Chemistry
Department of Chemistry
University of Arizona
  --------------D67D8214A35B2C02057F2063-- From chemistry-request@server.ccl.net Tue Jan 15 12:10:57 2002 Received: from lauca.usach.cl ([158.170.64.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0FHAuI22501 for ; Tue, 15 Jan 2002 12:10:56 -0500 Received: from danilo ([158.170.51.186]) by lauca.usach.cl (8.10.2+Sun/8.10.2) with ESMTP id g0FH8kw26566 for ; Tue, 15 Jan 2002 14:08:46 -0300 (CLST) From: "Danilo Gonzalez" To: Subject: SASA program Date: Tue, 15 Jan 2002 14:07:55 -0300 Message-ID: <000001c19de7$2d547340$ba33aa9e@usach.cl> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0001_01C19DCE.08073B40" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 This is a multi-part message in MIME format. ------=_NextPart_000_0001_01C19DCE.08073B40 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit Hi all! Somebody know a free program (with sources, if is possible) to calculate the Surface Area Solvent Accessibility (SASA)? Thanks a lot for any help!, Danilo Gonzalez-Nilo University of Santiago of Chile Faculty of Chemistry and Biology Casilla 40, Correo 33, Santiago - Chile. ------=_NextPart_000_0001_01C19DCE.08073B40 Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable

Hi all!

 

        = ;    Somebody know a free program (with sources, if is possible) to calculate the = Surface Area Solvent Accessibility (SASA)?

 

Thanks a lot for any help!,

 

Danilo = Gonzalez-Nilo

 

University of Santiago of Chile<= span style=3D'mso-no-proof:yes'>

Faculty of Chemistry and = Biology

Casilla 40, Correo = 33,

Santiago - = Chile<= span style=3D'mso-no-proof:yes'>.

 

------=_NextPart_000_0001_01C19DCE.08073B40-- From chemistry-request@server.ccl.net Tue Jan 15 15:44:23 2002 Received: from web14906.mail.yahoo.com ([216.136.225.58]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g0FKiMI26090 for ; Tue, 15 Jan 2002 15:44:22 -0500 Message-ID: <20020115204412.25976.qmail@web14906.mail.yahoo.com> Received: from [195.87.115.144] by web14906.mail.yahoo.com via HTTP; Tue, 15 Jan 2002 12:44:12 PST Date: Tue, 15 Jan 2002 12:44:12 -0800 (PST) From: Alimet Ozen Subject: PCM and transition states... To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCL members, I am trying to model some radical reactions in DFT using Gaussian98 - both in the gas phase and in water as solvent. I have run solvent calculations with scrf=PCM...etc.. and they seem fine so far in terms of energy and molecular geometry for the ground and transition states. Also the results are somewhat "expected" when compared to the gas phase calculations. But as far as I know, 2nd derivatives are not available for PCM in g98. So, my question is: how am I going to confirm my transition state structures in PCM in the absence of frequency calculations? is there a way of getting that legendary 1 imaginary frequency? Any kind of help is appreciated... Thanks in advance... Sincerely yours, Alimet S. Ozen Chemistry Dept. Bogazici University Istanbul ps.I have the papers about procedures for the analytical second derivatives by Prof Tomasi's and Prof.Barone's groups and I think these are implemented in the development version of Gaussian program. But not in g98, are they? ===== "The major difference between a thing that might go wrong and a thing that cannot possibly go wrong is that when a thing that cannot possibly go wrong goes wrong it usually turns out to be impossible to get at or repair." -- One of the laws of computers and programming revealed ozensem@boun.edu.tr http://www.geocities.com/alchemistrial http://www.geocities.com/alimet __________________________________________________ Do You Yahoo!? Send FREE video emails in Yahoo! Mail! http://promo.yahoo.com/videomail/ From chemistry-request@server.ccl.net Tue Jan 15 12:39:02 2002 Received: from websmtp01.sohu.com ([61.135.132.105]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0FHd0I23078 for ; Tue, 15 Jan 2002 12:39:01 -0500 Received: from mail.sohu.com (unknown [192.168.41.40]) by websmtp01.sohu.com (Postfix) with ESMTP id 236FF9C186 for ; Tue, 15 Jan 2002 15:38:47 +0800 (CST) Message-ID: <3870732.1011080294692.JavaMail.postfix@mailsrv0.mail.sohu.com> Date: Tue, 15 Jan 2002 15:37:32 +0800 (CST) From: To: Subject: monte carlo Mime-Version: 1.0 Content-Type: multipart/related; boundary="----=_Part_294_3162544.1011080252064" X-Mailer: Sohu Web MailComposer 2.0.12 ------=_Part_294_3162544.1011080252064 Content-Type: multipart/alternative; boundary="----=_Part_293_2307092.1011080252063" ------=_Part_293_2307092.1011080252063 Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: 8bit Dear CCLer, I want to do simulation on a system of two kinds organic solutes in aqueous solution. Is there any FREE Monte Carlo software available in web? Any respondence would be highly appreciated. thank you. Chen ------=_Part_293_2307092.1011080252063 Content-Type: text/html Content-Transfer-Encoding: 8bit

Dear CCLer,

I want to do simulation on a system of two kinds organic solutes in aqueous solution. Is there any FREE Monte Carlo software available in web? Any respondence would be highly appreciated.

thank you.

Chen

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