From chemistry-request@server.ccl.net Fri May 10 04:07:58 2002 Received: from mr3.cc.ic.ac.uk ([155.198.5.113]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4A87wU24134 for ; Fri, 10 May 2002 04:07:58 -0400 Received: from origin.ch.ic.ac.uk ([155.198.224.252] helo=chcmga.ch.ic.ac.uk) by mr3.cc.ic.ac.uk with esmtp (Exim 3.35 #1) id 1765RW-0008JD-03 for chemistry@ccl.net; Fri, 10 May 2002 09:07:58 +0100 Received: from hbtower.ch.ic.ac.uk ([155.198.226.132] helo=ic.ac.uk) by chcmga.ch.ic.ac.uk with esmtp (Exim 2.02 #1) id 1765Sa-00GFmY-00; Fri, 10 May 2002 09:09:04 +0100 Sender: krzys@ic.ac.uk Message-ID: <3AFA3D82.25204ABF@ic.ac.uk> Date: Thu, 10 May 2001 08:04:34 +0100 From: Krzysztof Radacki Organization: Imperial College, London X-Mailer: Mozilla 4.78 [en] (X11; U; Linux 2.4.7-10smp i686) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: redhat7.2 question Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'ers probably somebody can help me with a bit of know-how. During instalation of redhat 7.2 I've choose to login in "old&good" text modus and it was what I've seen after first restart. For unknown reason during the 2nd start Linux has loaded graphical login. Can somebody tell me how to make redhat not to load gdm on the start-up? MfG Krzysztof -- Dr. K.Radacki Department of Chemistry Catalysis and Advanced Materials Section Imperial College, London From chemistry-request@server.ccl.net Fri May 10 04:23:26 2002 Received: from crisvm.univ-pau.fr ([194.167.156.216]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4A8NPU24391 for ; Fri, 10 May 2002 04:23:26 -0400 Received: from localhost (crisvm [127.0.0.1]) by crisvm.univ-pau.fr (Postfix) with ESMTP id 0D962743D9 for ; Fri, 10 May 2002 10:23:19 +0200 (CEST) Received: from etud.univ-pau.fr (etud.univ-pau.fr [194.167.156.219]) by crisvm.univ-pau.fr (Postfix) with ESMTP id 5A8EA743C5 for ; Fri, 10 May 2002 10:23:18 +0200 (CEST) Received: (from nobody@localhost) by etud.univ-pau.fr (8.9.3/8.9.3) id KAA08346; Fri, 10 May 2002 10:23:16 +0200 Date: Fri, 10 May 2002 10:23:16 +0200 From: v.lemierre@etud.univ-pau.fr Message-Id: <200205100823.KAA08346@etud.univ-pau.fr> X-Authentication-Warning: etud.univ-pau.fr: nobody set sender to v.lemierre@etud.univ-pau.fr using -f To: chemistry@ccl.net Errors-To: v.lemierre@etud.univ-pau.fr Reply-To: v.lemierre@etud.univ-pau.fr MIME-Version: 1.0 Content-Type: text/plain Content-Transfer-Encoding: 7bit X-Mailer: IMP/PHP3 Imap webMail Program 2.0.2 Sender: v.lemierre@etud.univ-pau.fr X-Originating-IP: 194.167.156.15 Subject: MOLEKEL X-Virus-Scanned: by AMaViS perl-11 Hello, I write you because I have some problems with the utilisation of molekel. Indeed, I look for a good visualization of molecular orbitals. So in menu compute, I select an orbital from the list, I save the data in a macu file and I set the job priority. At this moment, in log info it is written : "can't read the basis-set. I don't understand why I can't visualize molecular orbitals. Best regards PS: I work with Gaussian 98 VIRGINIE LEMIERRE (v.lemierre@etud.univ-pau.fr) VIRGINIE LEMIERRE (v.lemierre@etud.univ-pau.fr) From chemistry-request@server.ccl.net Fri May 10 05:34:00 2002 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4A9Y0U26033 for ; Fri, 10 May 2002 05:34:00 -0400 Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 1766jE-00011w-00; Fri, 10 May 2002 09:30:20 +0000 Date: Fri, 10 May 2002 09:30:20 +0000 (GMT) From: Szilveszter Juhos To: Krzysztof Radacki cc: CCL Subject: Re: CCL:redhat7.2 question In-Reply-To: <3AFA3D82.25204ABF@ic.ac.uk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 10 May 2001, Krzysztof Radacki wrote: > Linux has loaded graphical login. Can somebody tell me > how to make redhat not to load gdm on the start-up? Comment out in the /etc/inittab the line corresponding to the preferred xdm like: # Run xdm in runlevel 5 # xdm is now a separate service #x:5:respawn:/etc/X11/prefdm -nodaemon than: $ init q (as root) of course you have to kill the just running gdm ('killall gdm' or something similar) Szilva From chemistry-request@server.ccl.net Fri May 10 06:03:12 2002 Received: from lgsx01.lg.ehu.es ([158.227.2.34]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4AA3AU26510 for ; Fri, 10 May 2002 06:03:11 -0400 Received: from lgdx04.lg.ehu.es (lgdx04.lg.ehu.es [158.227.1.36]) by lgsx01.lg.ehu.es (8.11.6/8.11.6) with ESMTP id g4AA1jJ21105; Fri, 10 May 2002 12:01:45 +0200 (MET DST) Date: Fri, 10 May 2002 12:01:45 +0200 (MET DST) From: VITORIA GARCIA Pablo To: v.lemierre@etud.univ-pau.fr cc: chemistry@ccl.net Subject: Re: CCL:MOLEKEL In-Reply-To: <200205100823.KAA08346@etud.univ-pau.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Virginie, In order to visualize MO, you should run your Gaussian job with the keywords GFPRINT and POP=REG or POP=FULL, so that Molekel can read the basis sets and the coefficients of the MOs. Best regards Pablo On Fri, 10 May 2002 v.lemierre@etud.univ-pau.fr wrote: > Hello, > > I write you because I have some problems with the utilisation of molekel. > Indeed, I look for a good visualization of molecular orbitals. So in menu > compute, I select an orbital from the list, I save the data in a macu file and > I set the job priority. At this moment, in log info it is written : "can't read > the basis-set. I don't understand why I can't visualize molecular orbitals. > > > Best regards > > PS: I work with Gaussian 98 > > > VIRGINIE LEMIERRE > (v.lemierre@etud.univ-pau.fr) > > > > > > VIRGINIE LEMIERRE > (v.lemierre@etud.univ-pau.fr) > > -= 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 > > > > > > -------------------------------------------------------------------------------- Pablo Vitoria Garcia Address: Dpto. Quimica Inorganica, Facultad de Ciencias Universidad del Pais Vasco (UPV/EHU) Apartado 644, E-48080 Bilbao SPAIN e-mail: qibvigap@lg.ehu.es Phone: +34 94 6012000 Ext. 5529 Fax: +34 94 4648500 -------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri May 10 04:25:58 2002 Received: from mailstudenti.unimi.it ([159.149.10.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4A8PwU24488 for ; Fri, 10 May 2002 04:25:58 -0400 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailstudenti.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0GVV00AGGZE1WO@mailstudenti.unimi.it> for chemistry@ccl.net; Fri, 10 May 2002 10:25:14 +0200 (MEST) Received: from vega (vega.farma.unimi.it [159.149.79.32]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with SMTP id <0GVV008AMZE301@smtp.unimi.it> for chemistry@ccl.net; Fri, 10 May 2002 10:25:15 +0200 (MEST) Date: Fri, 10 May 2002 10:25:35 +0200 From: Giulio Vistoli Subject: Re: question about charmm To: Mao Xiang , CCL Message-id: <004701c1f7fc$4253ec20$204f959f@farma.unimi.it.farma.unimi.it> Organization: Ist. Chimica Farmaceutica MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-Mailer: Microsoft Outlook Express 6.00.2600.0000 Content-type: text/plain; charset=gb2312 Content-transfer-encoding: 7BIT X-Priority: 3 X-MSMail-priority: Normal References: <3CD9BBF2.1379B8F4@iris.sipp.ac.cn> Dear Mao Xiang Vega is able to solvate any molecule with any solvent and can save it in several formats Try it (http://users.unimi.it/~ddl) Best regards Giulio Vistoli -- Dr. Giulio Vistoli Ist. di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano (Italy) Tel. +39 02 503 17522 Fax +39 02 503 17565 E-Mail: giulio.vistoli@unimi.it WWW: http://users.unimi.it/~ddl ----- Original Message ----- From: "Mao Xiang" To: Sent: Thursday, May 09, 2002 1:59 AM Subject: question about charmm > pdb-l > > Hello everyone: > Here is some questions that I need your help. I wonder if > anyone could tell me how to generate any size of water sphere using > charmm. And When I generated a large box(90A), and want to cut it to the > sphere, Charmm would not read in the coordinate file, I think it is > because it could not differ the first and the second coloum in the > coordinate like the following: > > ----------------------------- > 8099126997 TIP3 H2 -42.02900 -42.78300 -32.56100 ABC 997 0.00000 > 8099226998 TIP3 OH2 -17.48700 -32.81400 -42.10200 ABC 998 0.00000 > 8099326998 TIP3 H1 -17.43100 -32.94900 -41.15600 ABC 998 0.00000 > 8099426998 TIP3 H2 -18.18400 -33.40500 -42.38800 ABC 998 0.00000 > 8099526999 TIP3 OH2 -28.39600 -45.51900 -16.52900 ABC 999 0.00000 > 8099626999 TIP3 H1 -28.88800 -46.30300 -16.28500 ABC 999 0.00000 > 8099726999 TIP3 H2 -27.63500 -45.85300 -17.00500 ABC 999 0.00000 > 8099827000 TIP3 OH2 -37.27900 -37.63700 -39.21200 ABC 1000 0.00000 > 8099927000 TIP3 H1 -37.93700 -37.80100 -38.53500 ABC 1000 0.00000 > 8100027000 TIP3 H2 -37.51000 -38.24000 -39.91900 ABC 1000 0.00000 > ----------------------------- > So I wonder if you have some good ways to generate large water sphere, > for example 50A in the radius. > > Another question is how to generate the TIP3P deformable boundary force > for a water sphere . > > Thanks in advance. > > > Regards, > mao xiang > > > > > *** Details on how to be removed from this list as well as an *** > *** archive of recent postings are available at *** > *** http://www.rcsb.org/pdb/forum.html *** > From chemistry-request@server.ccl.net Fri May 10 08:53:13 2002 Received: from netmaster.kds.com.ua ([194.44.106.42]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4ACrAU30316 for ; Fri, 10 May 2002 08:53:11 -0400 Received: from akhavr by netmaster.kds.com.ua with local (Exim 3.22 #1) id 1769sw-0004nx-00; Fri, 10 May 2002 15:52:34 +0300 To: Szilveszter Juhos Cc: Krzysztof Radacki , CCL Subject: Re: redhat7.2 question References: From: Andrey Khavryuchenko Organization: KDS Software Group X-Attribution: AVK Date: 10 May 2002 15:52:34 +0300 In-Reply-To: Message-ID: Lines: 25 User-Agent: Gnus/5.0808 (Gnus v5.8.8) XEmacs/21.4 (Academic Rigor) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Szilveszter, "SJ" == Szilveszter Juhos wrote: SJ> On Thu, 10 May 2001, Krzysztof Radacki wrote: >> Linux has loaded graphical login. Can somebody tell me >> how to make redhat not to load gdm on the start-up? SJ> Comment out in the /etc/inittab the line corresponding to the preferred SJ> xdm like: >> Run xdm in runlevel 5 >> xdm is now a separate service >> x:5:respawn:/etc/X11/prefdm -nodaemon More clean way is to select 3rd runlevel. To do this, just make sure that the line, starting with 'id' looks like: id:3:initdefault: And then, of course, do `init q'. Or just restart your system. -- Andrey V Khavryuchenko http://www.kds.com.ua/ Offshore Software Development From chemistry-request@server.ccl.net Fri May 10 09:45:46 2002 Received: from hotmail.com ([207.68.163.93]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4ADjjZ31523 for ; Fri, 10 May 2002 09:45:46 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Fri, 10 May 2002 06:45:41 -0700 Received: from 193.146.42.31 by sea1fd.sea1.hotmail.msn.com with HTTP; Fri, 10 May 2002 13:45:40 GMT X-Originating-IP: [193.146.42.31] From: "Mus Musculus" To: CHEMISTRY@ccl.net Subject: Gaussian error Date: Fri, 10 May 2002 15:45:40 +0200 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1; format=flowed Message-ID: X-OriginalArrivalTime: 10 May 2002 13:45:41.0104 (UTC) FILETIME=[F97ACF00:01C1F828] Dear all, I'm trying to locate some transition states with g98, and I find quite often an error message that reads so: Item Value Threshold Converged? Maximum Force 0.030792 0.000450 NO RMS Force 0.009409 0.000300 NO Maximum Displacement 0.000000 0.001800 YES RMS Displacement 0.000000 0.001200 YES Predicted change in Energy= 0.000000D+00 (...) Error termination request processed by link 9999. Error termination via Lnk1e in C:\G98W\l9999.exe. Does it have any meaning to have forces but no associated displacement? (What kind of point is this? What is happening, do the displacements cancel each other or something like that? ) Should I do something besides trying a new geometry guess? I will thank any kind of help provided, and by the way, does anyone know if there is a place where the gaussian errors are explained? Thank you all, Regards, Viv _________________________________________________________________ Hable con sus amigos en línea, pruebe MSN Messenger: http://messenger.msn.es