From chemistry-request@ccl.net Wed Jun 2 02:32:44 2004 Received: from idmailgate1.unizh.ch (idmailgate1.unizh.ch [130.60.68.105]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i527WgmH003026 for ; Wed, 2 Jun 2004 02:32:43 -0500 Received: from zimail2.unizh.ch (zimail2.unizh.ch [130.60.128.12]) by idmailgate1.unizh.ch (8.12.10/8.12.10/Debian-2) with ESMTP id i527aCKv003451 for ; Wed, 2 Jun 2004 09:36:12 +0200 Received: from zisgi.unizh.ch (zisgi.unizh.ch [130.60.68.15]) by zimail2.unizh.ch (8.12.10/8.12.10/smMTA-17) with ESMTP id i527aBQZ008082 for ; Wed, 2 Jun 2004 09:36:12 +0200 (MEST) Date: Wed, 2 Jun 2004 09:36:11 +0200 From: "Dr. Peter Burger" To: CHEMISTRY)at(ccl.net Subject: CCL:Unichem Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by amavisd-milter (http://www.amavis.org/) X-Spam-Status: No, hits=2.0 required=7.5 tests=COMBINED_FROM 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 CCLers someone knows the fate of Unichem? Is it still available after Accelrys took over Oxmol? Regards Peter From chemistry-request@ccl.net Wed Jun 2 08:11:32 2004 Received: from anubis.medic.chalmers.se (anubis.medic.chalmers.se [129.16.30.218]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i52DBVja017804 for ; Wed, 2 Jun 2004 08:11:31 -0500 Received: from fy.chalmers.se (f2-pc31.fy.chalmers.se [129.16.110.231]) by anubis.medic.chalmers.se (Postfix) with ESMTP id 2FE171BB0; Wed, 2 Jun 2004 15:15:02 +0200 (MEST) Message-ID: <40BDD39B.6020403-.at.-fy.chalmers.se> Date: Wed, 02 Jun 2004 15:18:19 +0200 From: Patrik Johansson User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry Subject: CCL:ADMP in G03 - temeperature? Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit 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 Dear CCLers, Has anyone tried the ADMP part included in the G03 package and tried to control the temperature? I would basically like to run two simulations at two different temperatures - but I do not know how to control this - by initial velocities of the centra applies only to NVE? If anyone from Gaussian is listening I would be happy for some response. sincerely /Patrik From chemistry-request@ccl.net Tue Jun 1 12:07:03 2004 Received: from mailer.gwdg.de (mailer.gwdg.de [134.76.10.26]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i51H72Te001459 for ; Tue, 1 Jun 2004 12:07:02 -0500 Message-Id: <200406011707.i51H72Te001459=at=server.ccl.net> Received: from mailbox.gwdg.de ([134.76.10.21] helo=gwdg.de) by mailer.gwdg.de with esmtp (Exim 4.34) id 1BVCmT-0003Dq-49 for chemistry=at=ccl.net; Tue, 01 Jun 2004 19:10:30 +0200 Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 01 Jun 2004 19:10:25 +0200 MIME-Version: 1.0 Subject: X3LYP Content-Transfer-Encoding: 8bit User-Agent: IMHO/0.98.3+G (Webmail for Roxen) X-Originating-IP: crice[134.76.68.227] From: To: chemistry=at=ccl.net X-Virus-Scanned: (clean) by exiscan+sophie X-Spam-Status: No, hits=2.9 required=7.5 tests=IMPRONONCABLE_1,MY_BAD_DOT, NO_REAL_NAME 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 everyone, I was wondering if anyone had any information on how to run X3LYP calculations described by Xin Xu and William Goddard III in any other program besides JAGUAR. This extended density functional seems very interesting to me, and if it describes hydrogen bonding much better than B3LYP, it would be a much faster and better DFT method. Thanks, Corey Rice Institut fuer Physikalische Chemie Georg-August-Universitaet Tammannstrasse 6 D-37077 Goettingen Tel: (49)-551-3914322 Fax: (49)-551-39 3117 Email: crice=at=gwdg.de From chemistry-request@ccl.net Tue Jun 1 13:48:24 2004 Received: from mailserv.unb.ca (mailserv.unb.ca [131.202.3.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i51ImKTe004883 for ; Tue, 1 Jun 2004 13:48:23 -0500 Received: from gollum.unb.ca (gollum.unb.ca [131.202.3.51]) by mailserv.unb.ca (8.12.10/8.12.10) with ESMTP id i51InmDU015095 for ; Tue, 1 Jun 2004 15:49:52 -0300 Received: from gollum.unb.ca (localhost.localdomain [127.0.0.1]) by gollum.unb.ca (8.12.8/8.12.8) with ESMTP id i51IphAD021615 for ; Tue, 1 Jun 2004 15:51:43 -0300 Received: (from apache@localhost) by gollum.unb.ca (8.12.8/8.12.8/Submit) id i51Ipdup021600 for chemistry=at=ccl.net; Tue, 1 Jun 2004 15:51:39 -0300 Received: from imac1.chem.unb.ca (imac1.chem.unb.ca [131.202.174.199]) by webmail.unb.ca (IMP) with HTTP for ; Tue, 1 Jun 2004 15:51:39 -0300 Message-ID: <1086115899.40bcd03b1fbfc=at=webmail.unb.ca> Date: Tue, 1 Jun 2004 15:51:39 -0300 From: Joey Harriman To: CCL posting Subject: freezing atoms in g03 optimizations MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 X-Originating-IP: 131.202.174.199 X-UNB-MailScanner-Information: Please contact the ISP for more information X-UNB-VirusScanner: Found to be clean X-UNB-SpamDetails: X-MailScanner-From: s808o=at=unb.ca 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 Hi, I am trying to do a geometry optimization on a large system which contains some atoms that are involved in a transition-state structure. I would like to fix the portion of the molecule with the TS geometry and do an optimization on the rest of the atoms. What is the best method to freeze the TS atoms? I have been looking at the ModRedundant function, but am unaware of how to create the secondary input after the zmatrix for this. Any help would be greatly appreciated. Thanks in advance, Joe Harriman ---------------------------------- Joe Harriman Computational Chemistry University of New Brunswick Room 228 Toole Hall s808o=at=unb.ca ---------------------------------- From chemistry-request@ccl.net Wed Jun 2 08:46:01 2004 Return-Path: From: Pinchas Aped Message-Id: <200406021303.i52D3mD418002$at$gefen.os.biu.ac.il> Subject: CCL: Running Gaussian 03 on Linux (RedHat) system To: "Dr. Jan K. Labanowski" Date: Wed, 2 Jun 2004 16:03:48 +0300 (IDT) Dear All: I have installed Gaussian 03 on a RedHat 9.0 Linux system. The hardware configuration I am using is - IBM xSeries 225, model 8647 2 Intel Xeon processors (2.4 GHz) 512 Kb Second Level Cache on each processor 2 Gb DDR RAM SCSI Ultra320 2 removable disks of 73.4 Gb each I have started to run some simple jobs as benchmarks, and found the following results (2 other unix systems were added for comparison) - [1] Gaussian Benchmark (HF/3-21G Opt=Z-matrix, 18 heavy atoms) [2] [3] [4] WS1 WS2 WS3 ============================================= 1-Processor 2049 3759 3793 2-Processors 1330 2038 2064 Scalability 1.54 1.84 1.84 speed ratio (for 1-Proc) 2.54 1.38 1.37 2 1-Proc jobs simultaneously 2570 % reduction 25 ============================================= [1] Clock time in seconds. [2] WS1: IBM X-225; Intel Xeon 2.4 GHZ; Linux RedHat 9.0; Gaussian 03 Rev B.04 [3] WS2: IBM-RS6000 7026-B80; PowerPC_POWER3 375 MHZ; AIX 5.2; Gaussian 03 Rev B.04 [4] WS3: SGI-Origin 300; R14000 600 MHZ; IRIX64 6.5.19; Gaussian 03 Rev B.04 It seems that the scalability on the Linux system is very low, even for 2 processors. Moreover, running 2 separate jobs simultaneously (each using one processor) seems to reduce heavily the performance of both processors. Does anyone has experience with Gaussian 03 (or other heavy chemistry applications) on Linux system? Did you get better results? Thanks in advance for your help Regards Pinchas Aped ------------------------------------------------------------------------ Dr. Pinchas Aped Tel.: (+972-3) 531-7683 Department of Chemistry FAX : (+972-3) 535-1250 Bar-Ilan University E-Mail: aped$at$mail.biu.ac.il 52900 Ramat-Gan, ISRAEL WWW: http://www.biu.ac.il/~aped ------------------------------------------------------------------------ From David.Clark@ArgentaDiscovery.com Wed Jun 2 08:42:35 2004 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.5.1 Date: Thu, 27 May 2004 14:45:08 +0100 From: "David Clark" To: Cc: Subject: Software for distance geometry calculations Hi Does anyone know of any freely available/open source software for distance geometry calculations for small molecules? I'm particularly interested in the initial set up of distance bounds and then the smoothing of them using the triangle (and possibly tetrangle) inequalities. Many thanks David Clark From chemistry-request@ccl.net Wed Jun 2 09:18:25 2004 Received: from host20.lctn.uhp-nancy.fr (host20.lctn.uhp-nancy.fr [193.50.239.24]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i52EINja026012 for ; Wed, 2 Jun 2004 09:18:24 -0500 Received: from lctn.uhp-nancy.fr (host5.lctn.uhp-nancy.fr [193.50.239.5]) by host20.lctn.uhp-nancy.fr (AIX4.3/8.9.3/8.9.3) with ESMTP id QAA35570; Wed, 2 Jun 2004 16:22:58 +0200 Sender: moreau[at]host20.lctn.uhp-nancy.fr Message-ID: <40BDE268.36C8AC29[at]lctn.uhp-nancy.fr> Date: Wed, 02 Jun 2004 16:21:28 +0200 From: Yohann Moreau Organization: Equipe de Chimie et Biochimie =?iso-8859-1?Q?Th=E9oriques?= X-Mailer: Mozilla 4.7iC-CCK-MCD [en_US] (X11; I; AIX 4.3) X-Accept-Language: fr, en MIME-Version: 1.0 To: Joey Harriman CC: CCL posting Subject: Re: CCL:freezing atoms in g03 optimizations References: <1086115899.40bcd03b1fbfc[at]webmail.unb.ca> Content-Type: multipart/alternative; boundary="------------17F4B741BA57B02995A4BF5F" X-Spam-Status: No, hits=1.0 required=7.5 tests=HTML_MESSAGE,LINES_OF_YELLING autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --------------17F4B741BA57B02995A4BF5F Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hello Joey, If I understand, you just want to make a partial geometry optimization, i.e. without moving some atoms of the molecule. To do so, there are two ways in Gaussian : it depends if you use cartesian coordinates or a z-matrix In the first case, just put the flag "-1" between the atom type and its coordinates (see my answer to Kadri a few days ago) (just be careful not to put a non frozen atom in first which is atomatically frozen) In the second, you'll freeze internal coordinates : use the keyword "opt=z-mat" write your Z matrix not with numerical values but with variables after your Z matrix, you must give values to the variables : name of the variable follewd by the value (this is in fact the general way to write a Z-matrix, nothing new) To freeze some values, juste put in first the set of variables, a blank line and second, the set of constants. I'm not sure to be clear enough, so here is an example : # RHF/STO-3G opt=z-mat title : methanol 0 1 C H 1 R1 H 1 R1 2 A1 H 1 R1 2 A1 3 D1 O 1 R2 2 A1 3 -D1 H 5 R3 1 A2 2 D2 R1 1.083 R2 1.44 A1 109.47122 D1 120.0 R3 0.96 A2 104.48 D2 180.0 R1, R2, A1 and D1 will be allowed to vary whereas R3, A2 and D2 won't be. I hope this will help you, Yohann Joey Harriman wrote: > Hi, > > I am trying to do a geometry optimization on a large system which contains some atoms > that are involved in a transition-state structure. I would like to fix the portion of > the molecule with the TS geometry and do an optimization on the rest of the atoms. > What is the best method to freeze the TS atoms? I have been looking at the > ModRedundant function, but am unaware of how to create the secondary input after the > zmatrix for this. Any help would be greatly appreciated. > > Thanks in advance, > > Joe Harriman > > ---------------------------------- > Joe Harriman > Computational Chemistry > University of New Brunswick > Room 228 > Toole Hall > s808o[at]unb.ca > ---------------------------------- > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY[at]ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST[at]ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow[at]nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -- Yohann MOREAU, Doctorant Equipe de Chimie et Biochimie Thioriques UMR CNRS-UHP 7565 "SRMSC" BP 239, F-54506 Vandoeuvre-lhs-Nancy http://www.lctn.uhp-nancy.fr/Etudiants/Yohann.Moreau.html --------------17F4B741BA57B02995A4BF5F Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hello Joey,

If I understand, you just want to make a partial geometry optimization, i.e. without moving some atoms of the molecule.
To do so, there are two ways in Gaussian : it depends if you use cartesian coordinates or a z-matrix

In the first case, just put the flag "-1" between the atom type and its coordinates (see my answer to Kadri a few days ago)
(just be careful not to put a non frozen atom in first which is atomatically frozen)

In the second, you'll freeze internal coordinates :
use the keyword "opt=z-mat"
write your Z matrix not with numerical values but with variables

after your Z matrix, you must give values to the variables : name of the variable follewd by the value
(this is in fact the general way to write a Z-matrix, nothing new)
To freeze some values, juste put in first the set of variables, a blank line and second, the set of constants.
I'm not sure to be clear enough, so here is an example :
 
 

# RHF/STO-3G opt=z-mat

title : methanol

0 1
C
H   1   R1
H   1   R1   2   A1
H   1   R1   2   A1   3 D1
O   1   R2   2   A1   3 -D1
H   5   R3   1   A2   2 D2

R1 1.083
R2 1.44
A1 109.47122
D1 120.0

R3 0.96
A2 104.48
D2 180.0
 
 

R1, R2, A1 and D1 will be allowed to vary whereas R3, A2 and D2 won't be.
 
 

I hope this will help you,

Yohann
 
 
 

Joey Harriman wrote:

Hi,

I am trying to do a geometry optimization on a large system which contains some atoms
that are involved in a transition-state structure.  I would like to fix the portion of
the molecule with the TS geometry and do an optimization on the rest of the atoms.
What is the best method to freeze the TS atoms?  I have been looking at the
ModRedundant function, but am unaware of how to create the secondary input after the
zmatrix for this.  Any help would be greatly appreciated.

Thanks in advance,

Joe Harriman

----------------------------------
Joe Harriman
Computational Chemistry
University of New Brunswick
Room 228
Toole Hall
s808o[at]unb.ca
----------------------------------

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-- 

               Yohann MOREAU, Doctorant                 
       Equipe de Chimie et Biochimie Théoriques   
               UMR CNRS-UHP 7565 "SRMSC"        
          BP 239, F-54506 Vandoeuvre-lès-Nancy  
http://www.lctn.uhp-nancy.fr/Etudiants/Yohann.Moreau.html
  --------------17F4B741BA57B02995A4BF5F-- From chemistry-request@ccl.net Wed Jun 2 09:50:40 2004 Received: from www4.ctimail.com (www4.ctimail.com [203.186.94.49]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i52Eocja028675 for ; Wed, 2 Jun 2004 09:50:39 -0500 Received: (from cgiuser@localhost) by www4.ctimail.com (8.10.1/8.10.1) id i52Es7W19149; Wed, 2 Jun 2004 22:54:07 +0800 (HKT) Date: Wed, 2 Jun 2004 22:54:07 +0800 (HKT) Message-Id: <200406021454.i52Es7W19149~at~www4.ctimail.com> X-Authentication-Warning: www4.ctimail.com: cgiuser set sender to skpang~at~ctimail.com using -f From: skpang~at~ctimail.com To: chemistry~at~ccl.net Subject: derivation of results calculated from different kinds of computer Cc: X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_REAL_NAME 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, Is there any information for evaluation of results such as electronic energy from different kinds of computer? I want to know the derivation of results from different kinds of computer. For example, when Gaussian software is used, the same molecule's electronic energies calculated from different kinds of computer are: Intel Pentium III PC vs. Intel Pentium III PC cluster vs. Alphaworkstation vs. IBM RS/6000 SP Supercomputer vs. ... etc. Thank you for your attention. Best regards, Patrick My-email address is skpang~at~ctimail.com From chemistry-request@ccl.net Wed Jun 2 09:40:46 2004 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i52Eejja027779 for ; Wed, 2 Jun 2004 09:40:45 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailserver.unimi.it (iPlanet Messaging Server 5.2 Patch 1 (built Aug 19 2002)) with ESMTP id <0HYO00KQJRLURJ|at|mailserver.unimi.it> for chemistry|at|ccl.net; Wed, 02 Jun 2004 16:44:18 +0200 (MEST) Received: from heisenberg.chimica.unimi.it (heisenberg.chimica.unimi.it [159.149.240.30]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0HYO00H88RLQL5|at|smtp.unimi.it> for chemistry|at|ccl.net; Wed, 02 Jun 2004 16:44:14 +0200 (MEST) Date: Wed, 02 Jun 2004 16:49:01 +0200 From: Alessandro Contini Subject: Re: CCL:freezing atoms in g03 optimizations In-reply-to: <1086115899.40bcd03b1fbfc|at|webmail.unb.ca> To: Joey Harriman Cc: CCL posting Reply-to: alessandro.contini|at|unimi.it Message-id: <200406021649.02004.alessandro.contini|at|unimi.it> Organization: =?iso-8859-1?q?Universit=E0=20di?= Milano MIME-version: 1.0 Content-type: text/plain; charset=iso-8859-1 Content-disposition: inline User-Agent: KMail/1.5.4 References: <1086115899.40bcd03b1fbfc|at|webmail.unb.ca> 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 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i52Eekja027783 Hi Joey, yes, the modredundant optimization is a good choice. If you have gaussview the procedure is pretty symple trhough the reduntant coordinate editor. If you are not using gaussview it could be pretty challanging if your sistem is rather big. However you have to put your redundant specifications after a blank line at the end of the g03 input. If you need to freeze an atom coordinate (cartesian) you'll write X N0 F where N0 is the atom number you want to freeze if you want to freeze a bond lenght the syntax will be B N1 N2 F for an angle A N1 N2 N3 F and for a dihedral D N1 N2 N3 N4 F where Nn are the respective atom numbers Hope this help Alessandro Alle 20:51, martedl 1 giugno 2004, Joey Harriman ha scritto: > Hi, > > I am trying to do a geometry optimization on a large system which contains > some atoms that are involved in a transition-state structure. I would like > to fix the portion of the molecule with the TS geometry and do an > optimization on the rest of the atoms. What is the best method to freeze > the TS atoms? I have been looking at the ModRedundant function, but am > unaware of how to create the secondary input after the zmatrix for this. > Any help would be greatly appreciated. > > Thanks in advance, > > Joe Harriman > > ---------------------------------- > Joe Harriman > Computational Chemistry > University of New Brunswick > Room 228 > Toole Hall > s808o|at|unb.ca > ---------------------------------- > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: > line and send your message to: CHEMISTRY|at|ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST|at|ccl.net HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow|at|nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -- Alessandro Contini, Ph.D. Istituto di Chimica Organica "Alessandro Marchesini" Universit` degli Studi di Milano, Facolt` di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini|at|unimi.it From chemistry-request@ccl.net Wed Jun 2 10:19:18 2004 Received: from e500-gw1.utmb.edu (mx1.utmb.edu [129.109.195.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i52FJHja032219 for ; Wed, 2 Jun 2004 10:19:17 -0500 Received: from mx1.utmb.edu(129.109.195.3) by e500-gw1.utmb.edu via csmap id 0c23a82c_b4a9_11d8_9e1e_00304823f3bd_12210; Wed, 02 Jun 2004 10:25:15 -0500 (CDT) Received: from e500-gw1.utmb.edu (histidine.utmb.edu [129.109.65.24]) by utmb.edu (PMDF V6.1 #38124) with ESMTP id <0HYO0068XTE5BM~at~utmb.edu> for chemistry~at~ccl.net; Wed, 02 Jun 2004 10:22:53 -0500 (CDT) Received: from histidine.utmb.edu(129.109.65.24) by e500-gw1.utmb.edu via csmap id 0bc4b506_b4a9_11d8_8156_00304823f3bd_12204; Wed, 02 Jun 2004 10:25:14 -0500 (CDT) Received: from localhost (localhost [[UNIX: localhost]]) by histidine.utmb.edu (8.12.11/8.12.11/Submit) id i52FMnRu046444 for chemistry~at~ccl.net; Wed, 02 Jun 2004 10:22:49 -0500 (CDT envelope-from bdodson) Date: Wed, 02 Jun 2004 10:22:49 -0500 From: "M. L. Dodson" Subject: Re: CCL:Software for distance geometry calculations In-reply-to: <200406021007.27189.bdodson~at~scms.utmb.edu> To: chemistry~at~ccl.net Reply-to: bdodson~at~scms.utmb.EDU Message-id: <200406021022.49117.bdodson~at~scms.utmb.edu> Organization: University of Texas Medical Branch MIME-version: 1.0 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7bit Content-disposition: inline User-Agent: KMail/1.6.2 References: <200406021007.27189.bdodson~at~scms.utmb.edu> 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 Sorry. Forgot to copy the list. On Wednesday 02 June 2004 10:07 am, M. L. Dodson wrote: > On Thursday 27 May 2004 08:45 am, you wrote: > > Hi > > > > Does anyone know of any freely available/open source software for > > distance geometry calculations for small molecules? > > > > I'm particularly interested in the initial set up of distance > > bounds and then the smoothing of them using the triangle (and > > possibly tetrangle) inequalities. > > > > Many thanks > > David Clark > > Check out nab: http://www.scripps.edu/case/ > > This is a "molecular manipulation language" loosely associated, via > the Dave Case connection, with AMBER, but it can work with anything > that can be described by a PDB file. AMBER is not required. > Extensive distance geometry capabilities are built in. You might > have to write a short program in nab to achieve your goals. Nab is > quite similar to c, but with "molecular objects" as primitive data > types. > > Good luck, > Bud Dodson -- M. L. Dodson bdodson~at~scms.utmb.edu 409-772-2178 FAX: 409-747-8608 From chemistry-request@ccl.net Wed Jun 2 10:33:19 2004 Received: from up.univ-mrs.fr (mailup.univ-mrs.fr [147.94.113.16]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i52FXIja001715 for ; Wed, 2 Jun 2004 10:33:18 -0500 Received: from localhost (localhost [127.0.0.1]) by up.univ-mrs.fr (Postfix) with ESMTP id BAC4119C6F6 for ; Wed, 2 Jun 2004 17:33:58 +0200 (CEST) Received: from up.univ-mrs.fr ([127.0.0.1]) by localhost (mailup.univ-mrs.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 512307-04 for ; Wed, 2 Jun 2004 17:33:57 +0200 (CEST) Received: from up.univ-mrs.fr (unknown [147.94.185.160]) by up.univ-mrs.fr (Postfix) with ESMTP id DCDC21E1513 for ; Wed, 2 Jun 2004 17:33:57 +0200 (CEST) Message-ID: <40BDF41F.8030100:at:up.univ-mrs.fr> Date: Wed, 02 Jun 2004 17:37:03 +0200 From: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= Organization: LCTMM User-Agent: Mozilla/5.0 (X11; U; Linux i686; fr-FR; rv:1.6) Gecko/20040113 X-Accept-Language: fr-fr, en-us, en MIME-Version: 1.0 To: CCL posting Subject: Re: CCL:freezing atoms in g03 optimizations References: <1086115899.40bcd03b1fbfc:at:webmail.unb.ca> <200406021649.02004.alessandro.contini:at:unimi.it> In-Reply-To: <200406021649.02004.alessandro.contini:at:unimi.it> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-new at up.univ-mrs.fr X-Spam-Status: No, hits=4.0 required=7.5 tests=NO_RDNS,NO_RDNS2,RM_ft_Iso8859 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, The fastest way is to use the cartesian coordinates of your system instead of the redundant internal ones. Then in order to optimize only a subset of atoms, use the following notation: Atom_i 0 X_i Y_i Z_i Atom_j -1 X_j Y_j Z_j That means that you freeze the position of atom j while atom i is free to move. Then running a standard optimization job in REDUNDANT INTERNAL COORDINATES is still possible: OPT is enough if the number of atoms is less than 50, or use OPT=REDUNDANT. The internal coordinate builder will add coordinates between active atoms, between active and frozen atoms but not between frozen atoms. Hope this helps, Nicolas Alessandro Contini a icrit : > Hi Joey, > yes, the modredundant optimization is a good choice. If you have gaussview the > procedure is pretty symple trhough the reduntant coordinate editor. If you > are not using gaussview it could be pretty challanging if your sistem is > rather big. However you have to put your redundant specifications after a > blank line at the end of the g03 input. If you need to freeze an atom > coordinate (cartesian) you'll write > > X N0 F > > where N0 is the atom number you want to freeze > > if you want to freeze a bond lenght the syntax will be > > B N1 N2 F > > for an angle > > A N1 N2 N3 F > > and for a dihedral > > D N1 N2 N3 N4 F > > where Nn are the respective atom numbers > > Hope this help > > Alessandro > > Alle 20:51, martedl 1 giugno 2004, Joey Harriman ha scritto: > >>Hi, >> >>I am trying to do a geometry optimization on a large system which contains >>some atoms that are involved in a transition-state structure. I would like >>to fix the portion of the molecule with the TS geometry and do an >>optimization on the rest of the atoms. What is the best method to freeze >>the TS atoms? I have been looking at the ModRedundant function, but am >>unaware of how to create the secondary input after the zmatrix for this. >>Any help would be greatly appreciated. >> >>Thanks in advance, >> >>Joe Harriman >> >>---------------------------------- >>Joe Harriman >>Computational Chemistry >>University of New Brunswick >>Room 228 >>Toole Hall >>s808o:at:unb.ca >>---------------------------------- >> >> >>To send e-mail to subscribers of CCL put the string CCL: on your Subject: >> >>Send your subscription/unsubscription requests to: >>CHEMISTRY-REQUEST:at:ccl.net HOME Page: http://www.ccl.net | Jobs Page: >>http://www.ccl.net/jobs >> > > -- Dr. Nicolas Ferre' Laboratoire de Chimie Theorique et de Modelisation Moleculaire UMR 6517 - CNRS Universite' de Provence Case 521 - Faculte' de Saint-Jerome Av. Esc. Normandie Niemen 13397 MARSEILLE Cedex 20 (FRANCE) Tel : (+33)4.91.28.27.33 Fax : (+33)4.91.28.87.58 From chemistry-request@ccl.net Wed Jun 2 12:24:41 2004 Received: from pohl.acpub.duke.edu (pohl.acpub.duke.edu [152.3.233.64]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i52HOfja013761 for ; Wed, 2 Jun 2004 12:24:41 -0500 Received: from godzilla.acpub.duke.edu (godzilla.acpub.duke.edu [152.3.233.25]) by pohl.acpub.duke.edu (8.12.10/8.12.10/Duke-5.0.0) with ESMTP id i52HS7hc022788 for ; Wed, 2 Jun 2004 13:28:11 -0400 Received: (from jz7@localhost) by godzilla.acpub.duke.edu (8.12.10/8.12.9/Submit) id i52HS35Z020298; Wed, 2 Jun 2004 13:28:03 -0400 (EDT) Date: Wed, 2 Jun 2004 13:28:03 -0400 (EDT) From: jz7.-at-.duke.edu Sender: jz7.-at-.duke.edu To: CHEMISTRY.-at-.ccl.net Subject: Using Amber ff in NAMD Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-PMX-Version: 4.5.0.92886, Antispam-Core: 4.0.4.93542, Antispam-Data: 2004.6.1.102231 X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_REAL_NAME 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, Has anyone used Amber force field in NAMD calculation? I feel a little bit confused: When using Charmm in NAMD, we have topology file to build structure (generate psf file), and parameter file to do calculation. But when goes to Amber, what is the corresponding topology file? And how about the format of the tcl or inp file to generate psf file? Which of the parameter files is the best for protein-DNA system? (like parm99.dat, parm99EP.dat, etc.) Thanks a lot for your kind help! Best, Jeny From chemistry-request@ccl.net Wed Jun 2 13:59:49 2004 Received: from ARLABBH01.ds.arl.army.mil (arlabbh01.ds.arl.army.mil [192.12.65.18]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i52Ixmja018289 for ; Wed, 2 Jun 2004 13:59:48 -0500 Received: from ARLABML01.DS.ARL.ARMY.MIL ([128.63.57.71]) by ARLABBH01.ds.arl.army.mil with Microsoft SMTPSVC(5.0.2195.6713); Wed, 2 Jun 2004 15:03:32 -0400 X-MimeOLE: Produced By Microsoft Exchange V6.0.6487.1 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C448D4.3C8B4F39" Subject: CCL: Use of AIM in Examining Transition States Date: Wed, 2 Jun 2004 15:03:05 -0400 Message-ID: <3DEB727CED850444BC67A65ECB26796AE8AFB1.-at-.ARLABML01.DS.ARL.ARMY.MIL> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: CCL: Use of AIM in Examining Transition States Thread-Index: AcRI1E1D/VTd4bGlT6+QTZyflLLlhw== From: "Zottola, Mark (Cont,ARL/CISD)" To: X-OriginalArrivalTime: 02 Jun 2004 19:03:32.0109 (UTC) FILETIME=[4C26BBD0:01C448D4] X-Spam-Status: No, hits=5.0 required=7.5 tests=HTML_40_50,HTML_MESSAGE, L_TITLE_MESSAGE,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 This is a multi-part message in MIME format. ------_=_NextPart_001_01C448D4.3C8B4F39 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable Can AIM be used to evaluate bonding in a transition state structure? After reading Bader's web site, he often refers to equilibrium structures. Yet it seems that there is no apparent prohibition against employing AIM to studying transition states. Since AIM is based on a physical observable and a TS is not a physical observable is it still valid to apply AIM analysis to a transition state? =20 Thanks! =20 Mark ************************************************ Dr. Mark A. Zottola Army Research Laboratory Aberdeen Proving Grounds PB #134 939-I Beards Hill Road Aberdeen, MD 21001 Voice: 410 278 7250 FAX: 410 297 9521 Email: mzottola.-at-.arl.army.mil =20 =20 ------_=_NextPart_001_01C448D4.3C8B4F39 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable Message
Can = AIM be used to=20 evaluate bonding in a transition state structure?  After=20 reading Bader's web site, he often refers to equilibrium = structures. =20 Yet it seems that there is no apparent prohibition against = employing AIM to=20 studying transition states.  Since AIM is based on a physical = observable=20 and a TS is not a physical observable is it still valid to apply = AIM=20 analysis to a transition state?
 
Thanks!
 
Mark
************************************************
Dr. Mark A. Zottola
Army Research Laboratory
Aberdeen Proving Grounds
PB #134 939-I Beards Hill Road
Aberdeen, MD 21001
Voice: 410 278 7250 =20 FAX: 410 297 9521
Email: =20 mzottola.-at-.arl.army.mil
 
 
------_=_NextPart_001_01C448D4.3C8B4F39-- From chemistry-request@ccl.net Wed Jun 2 12:52:20 2004 Received: from fujitsu2.fujitsu.com (fujitsu2.fujitsu.com [192.240.0.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i52HqJja015087 for ; Wed, 2 Jun 2004 12:52:19 -0500 Received: from fujitsu2.fujitsu.com (localhost [127.0.0.1]) by fujitsu2.fujitsu.com (8.12.10/8.12.9) with ESMTP id i52Hto9X005181 for ; Wed, 2 Jun 2004 10:55:51 -0700 (PDT) Received: from fnanic.fujitsu.com ([133.164.253.1]) by fujitsu2.fujitsu.com (8.12.10/8.12.9) with ESMTP id i52Htn7Y005107; Wed, 2 Jun 2004 10:55:49 -0700 (PDT) Received: from cachemail.fnanic.fujitsu.com (localhost [127.0.0.1]) by fnanic.fujitsu.com (8.12.11/8.12.11) with ESMTP id i52HtiTs005431; Wed, 2 Jun 2004 10:55:44 -0700 (PDT) Received: from daveg-lifebook.cachesoftware.com (localhost [127.0.0.1]) by cachemail.fnanic.fujitsu.com (8.12.11/8.12.11) with ESMTP id i52HusN0009121; Wed, 2 Jun 2004 10:57:03 -0700 (PDT) Message-Id: <6.1.0.6.0.20040602104929.01e00ec0@133.164.253.31> X-Sender: dgallagher@133.164.253.31 (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 6.1.0.6 Date: Wed, 02 Jun 2004 10:55:24 -0700 To: "Dr. Peter Burger" From: David Gallagher Subject: CCL:Unichem Cc: CHEMISTRY[at]ccl.net In-Reply-To: References: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed 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 Hi Peter, The DGauss portion of Unichem still lives on as part of the CAChe suite, and is supported by Fujitsu . Not sure about what happened to the other parts of Unichem. Regards, David Gallagher, Fujitsu. At 12:36 AM 6/2/2004, Dr. Peter Burger wrote: >Dear CCLers > >someone knows the fate of Unichem? Is it still available after >Accelrys took over Oxmol? > >Regards > >Peter From chemistry-request@ccl.net Wed Jun 2 15:46:46 2004 Received: from mx6.wvu.edu (mx6.wvu.edu [157.182.140.68]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i52Kkjja024141 for ; Wed, 2 Jun 2004 15:46:45 -0500 Received: from GWIA.HSC.WVU.EDU (gateway.hsc.wvu.edu [157.182.102.90]) by mx6.wvu.edu (8.12.10/8.12.10) with ESMTP id i52KoEZB008607 for ; Wed, 2 Jun 2004 16:50:17 -0400 (EDT) (envelope-from pgannett{at}hsc.wvu.edu) Received: from HSC-DOM5-MTA by GWIA.HSC.WVU.EDU with Novell_GroupWise; Wed, 02 Jun 2004 16:51:00 -0400 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.5.2 Beta Date: Wed, 02 Jun 2004 16:50:27 -0400 From: "Peter Gannett" To: , Subject: Re: CCL:Using Amber ff in NAMD Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Disposition: inline X-Spam-Status: No, hits=1.0 required=7.5 tests=ALUSSINAN_5 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Jeny: Yes, I've used it. I haven't used Charmm but have used amber a long time. Amber splits a molecule into a coordinate file and a topology file (I thought most programs like charmm, sybyl, insight...) also did this, but maybe I'm mistaken. You will have to construct these files. Perhaps babel will take your charmm files and write out amber files (babel will do this but i don't know how good a job it does). Alternatively, you can get moil-view ( http://morita.chem.sunysb.edu/~carlos/moil-view.html ) which can read pdb/charmm/amber files and can write amber coordinate and topology files. Which force field to use is a tough question to answer. I do DNA and use parm99. Perhaps consult the literature and see what people seem to be using for this type of problem. Pete Gannett >>> 6/2/2004 1:28:03 PM >>> Dear all, Has anyone used Amber force field in NAMD calculation? I feel a little bit confused: When using Charmm in NAMD, we have topology file to build structure (generate psf file), and parameter file to do calculation. But when goes to Amber, what is the corresponding topology file? And how about the format of the tcl or inp file to generate psf file? Which of the parameter files is the best for protein-DNA system? (like parm99.dat, parm99EP.dat, etc.) Thanks a lot for your kind help! Best, Jeny -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY{at}ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST{at}ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow{at}nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Wed Jun 2 15:41:13 2004 Received: from casbah.it.northwestern.edu (casbah.it.northwestern.edu [129.105.16.52]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i52KfCja023834 for ; Wed, 2 Jun 2004 15:41:12 -0500 Received: (from mailnull@localhost) by casbah.it.northwestern.edu (8.12.10/8.12.10) id i52KijYd009719 for ; Wed, 2 Jun 2004 15:44:45 -0500 (CDT) Received: from chief (chief.chem-eng.northwestern.edu [129.105.205.171]) by casbah.it.northwestern.edu via smap (V2.0) id xma009500; Wed, 2 Jun 04 15:44:39 -0500 From: "Jim Pfaendtner" To: Subject: Gaussian 98 file error Date: Wed, 2 Jun 2004 15:44:42 -0500 Message-ID: <006501c448e2$6e853950$abcd6981@chief> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0066_01C448B8.85AF3150" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Importance: Normal X-Spam-Status: No, hits=0.0 required=7.5 tests=HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_0066_01C448B8.85AF3150 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hi all, I am getting this message in my log file when trying to run optimization with pcm using Linda and 4 processers: FileIO operation on non-existent file. Error termination in NtrErr: NtrErr Called from FileIO. Any thoughts? My rwf files are not maxed out. ------=_NextPart_000_0066_01C448B8.85AF3150 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi all,

 

I am getting this message in my log file when trying = to run optimization with pcm using Linda and 4 = processers:

 

 

FileIO<= /span> operation on non-existent file.

 

Error termination in NtrErr:

 NtrErr Called from FileIO.

 

Any = thoughts?  My rwf files are not maxed out.

 

 

 

------=_NextPart_000_0066_01C448B8.85AF3150-- From chemistry-request@ccl.net Wed Jun 2 16:33:16 2004 Received: from LaTech.edu (selene.LaTech.edu [138.47.18.25]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i52LXFja025809 for ; Wed, 2 Jun 2004 16:33:15 -0500 Received: from localhost (localhost [127.0.0.1]) by LaTech.edu (Postfix) with ESMTP id 0B27130A376 for ; Wed, 2 Jun 2004 16:36:46 -0500 (CDT) Received: from LaTech.edu ([127.0.0.1]) by localhost (selene.latech.edu [127.0.0.1]) (amavisd-new, port 10024) with LMTP id 76822-01-39 for ; Wed, 2 Jun 2004 16:36:45 -0500 (CDT) Received: from helius.latech.edu (helius.LaTech.edu [138.47.18.18]) by LaTech.edu (Postfix) with ESMTP id 3FB0D30A361 for ; Wed, 2 Jun 2004 16:36:45 -0500 (CDT) Received: from LAPACHA (unknown [138.47.56.165]) by helius.latech.edu (Postfix) with ESMTP id 1835A99203 for ; Wed, 2 Jun 2004 16:36:45 -0500 (CDT) Message-ID: <002b01c448e9$afc4d9f0$a5382f8a@LAPACHA> Reply-To: "pderosa-Latech" From: "pderosa-Latech" To: Subject: Compiling Gaussian 03 on a Xeon cluster-part 2 Date: Wed, 2 Jun 2004 16:36:38 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0028_01C448BF.C6E2EB10" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1409 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Virus-Scanned: by amavisd-new at latech.edu X-Spam-Status: No, hits=5.0 required=7.5 tests=HTML_30_40,HTML_MESSAGE, NO_RDNS,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 This is a multi-part message in MIME format. ------=_NextPart_000_0028_01C448BF.C6E2EB10 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear all: Some time ago I requested your help due to a problem compiling = gaussian on a Xeon, basically the compilation went Ok until the end but = when I tried to run a calculation, it stops when entering link 101 = without any error messages. I received a few very useful e-mails that made me aware that = Gaussian was looking for the compiler in the wrong directory. I solved = that (I think) but I still have the same problem so I have another = question for you. In the make.log file, there are a lot of lines saying: 112, Loop not vectorized: too deeply nested 69, Loop not vectorized: multiple exits 80, Loop not vectorized: contains call Among others. Why is this happening? is this the reason for which = Gaussian does not work? how can I solve it? is this due to another = component that is the wrong directory? Please I desperately need help = with this before I have to trash the Xeon Cluster I recently acquired (I = am of course overreacting, I am starting to panic though).=20 FYI I am running Red Hat 9.0, I have the Portland compiler installed and = I am trying to install Gaussian 03 revision B.03 Thank you very much Pedro ------=_NextPart_000_0028_01C448BF.C6E2EB10 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear all:
 
        Some=20 time ago I requested your help due to a problem compiling gaussian on a = Xeon,=20 basically the compilation went Ok until the end but when I tried to = run a=20 calculation, it stops when entering link 101 without any error=20 messages.
 
        I=20 received a few very useful e-mails that made me aware that Gaussian was = looking=20 for the compiler in the wrong directory.  I solved that (I = think) but=20 I still have the same problem so I have another question for = you.
 
        = In the=20 make.log file, there are a lot of lines saying:
 
   112, Loop not vectorized: = too deeply=20 nested
    69, Loop not vectorized: multiple=20 exits
    80, Loop not vectorized: contains=20 call
Among others.  Why is this = happening? is this=20 the reason for which Gaussian does not work? how can I solve it? is this = due to=20 another component that is the wrong directory?  Please I = desperately need=20 help with this before I have to trash the Xeon Cluster I recently = acquired (I am=20 of course overreacting, I am starting to panic = though). 
 
FYI I am running Red Hat 9.0, I have = the Portland=20 compiler installed and I am trying to install Gaussian 03 revision=20 B.03
Thank you very much
 
Pedro
 
------=_NextPart_000_0028_01C448BF.C6E2EB10-- From chemistry-request@ccl.net Tue Jun 1 20:09:31 2004 Message-ID: <20040602011257.18635.qmail/at/web60305.mail.yahoo.com> Received: from [207.225.232.131] by web60305.mail.yahoo.com via HTTP; Tue, 01 Jun 2004 18:12:57 PDT Date: Tue, 1 Jun 2004 18:12:57 -0700 (PDT) From: Gustavo Mercier Reply-To: gamercier/at/yahoo.com Subject: Charge Fitting to MEP from ADF To: chemistry/at/ccl.net Hi! I am interesting in fitting atom centered charges to molecular electrostatic potentials generated with ADF (Amsterdam Density Functional Theory Package 2004/3). I know that Molden is capable of doing this with an add-on program ADFrom. Unfortunately, the link to ADFrom is broken and the version I can track down may be outdated. Gaussian and Gamess have the R.E.D. interface for doing this job with the RESP method of Kollman. Is any one aware of a similar interface for ADF? I am unable to find any in the web, except for the Molden option listed above. (Several years ago I wrote my own taking advantage of Mathematica. For several reasons I am not able to use that program. I rather not reinvent the wheel, so I am asking for your help. However, if I reprogram the stuff I'll be wiser and use Python or Java ;-) Bye! Gustavo -- Gustavo A. Mercier, Jr., MD,PhD Seattle Nuclear Medicine & U/S Associates 1229 Madison, Suite 1150 Seattle, WA 98104-1377 voice: 206-386-6300; fax: 206-386-6312 gamercier/at/yahoo.com