From chemistry-request@ccl.net Tue Aug 26 09:59:22 2003 Received: from glaurung.gpcc.itd.umich.edu (glaurung.gpcc.itd.umich.edu [141.211.2.181]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7QDxMYj003981 for ; Tue, 26 Aug 2003 09:59:22 -0400 Received: from millipede.gpcc.itd.umich.edu (millipede.gpcc.itd.umich.edu [141.211.2.204]) by glaurung.gpcc.itd.umich.edu (8.9.3p2/4.3-mailhub) with ESMTP id JAA24052 for ; Tue, 26 Aug 2003 09:59:14 -0400 (EDT) Received: from localhost (scai@localhost) by millipede.gpcc.itd.umich.edu (8.9.3p2/5.1-client) with ESMTP id JAA22958 for ; Tue, 26 Aug 2003 09:59:13 -0400 (EDT) Precedence: first-class Date: Tue, 26 Aug 2003 09:59:13 -0400 (EDT) From: Sheng Cai X-X-Sender: scai)at(millipede.gpcc.itd.umich.edu To: chemistry)at(ccl.net Subject: Re: curvilinear step not converged in G98 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL'ers I got several suggestions from people in CCL. Unfortunately, none of them worked for me. I think the problem may be that I use reduntant coordinates for OPT. My input file looks like following: _______________________________ #P HF/STO-3G Opt=AddRedundant test 0 1 C 0. 0. 0. C 0. 1. 1. O 0. 1. 2. ...(continue xyz coordinates) 3 4 1.1 F 2 5 6 180. F 3 8 1 9 180. F ...(continue z-matirx constrains) ________________________________ This is a ploypeptide with several water molecules. I use xyz as starting structure and add z-matrix constrains as reduntant coordinates. I fix all relative water positions, all backbone dihedral angles and all side chain conformation and orientations by putting constrains on distances, angles or dihedral angles. I add too many constrains (which is required, however) so that there may be some conflicts in those coordinates. Another method is to do OPT in internal coordinates (by variables and constants). However, for this large system (about 120 atoms),it is too difficult (it is a really tedious work) to built a z-matrix which gives the right distance, angles and dihedral angle which I want to add constrains on. Even if I change the order of the atoms very carefully, there are still some constrains which are not in the variable and constant list. The Gaussian company claims that OPT using reduntant coordinates is better than using internal coordinates. For my case here, it is not true. I think at least the calculation will not crash if I can built the right z-matrix. Does anybody have any idea for my problem? Thanks. Sincerely Sheng Cai Biophysics Research Division University of Michigan email: scai)at(umich.edu From chemistry-request@ccl.net Mon Aug 25 20:24:18 2003 Received: from p08.es.uci.edu (p08.es.uci.edu [128.200.73.148]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7Q0OHYj010755 for ; Mon, 25 Aug 2003 20:24:17 -0400 Received: from uci.edu (dhcp-204148.bio.uci.edu [128.200.204.148]) by p08.es.uci.edu (8.11.6/8.11.6) with ESMTP id h7Q0OB927743 for ; Mon, 25 Aug 2003 17:24:16 -0700 Message-ID: <3F4AA8AA.7000706)at(uci.edu> Date: Mon, 25 Aug 2003 17:24:10 -0700 From: Qiang Lu Reply-To: qiangl)at(uci.edu Organization: Biology and Biochemistry Department User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: zh-cn, en-us, en MIME-Version: 1.0 To: chemistry)at(ccl.net Subject: g03 books Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear CCLers I need books about GAUSSIAN 03. Any suggestion would be helpful. Qiang Lu From chemistry-request@ccl.net Tue Aug 26 12:46:50 2003 Received: from berlin.ucdavis.edu (berlin.ucdavis.edu [169.237.104.158]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7QGkoYj010006 for ; Tue, 26 Aug 2003 12:46:50 -0400 Received: from andrena.ucdavis.edu (andrena.ucdavis.edu [169.237.104.181]) by berlin.ucdavis.edu (8.12.9/8.12.9/it-defang-5.1.2) with ESMTP id h7QGkh2w003639 for ; Tue, 26 Aug 2003 09:46:48 -0700 (PDT) Received: (from www@localhost) by andrena.ucdavis.edu (8.11.7/8.11.0/UCD4.1.0) id h7QGkhp14335; Tue, 26 Aug 2003 09:46:43 -0700 (PDT) Date: Tue, 26 Aug 2003 09:46:43 -0700 (PDT) Message-Id: <200308261646.h7QGkhp14335)at(andrena.ucdavis.edu> To: chemistry)at(ccl.net Subject: autodock v.3.0 question From: "Dustin Nouri" X-Errors-To: dhnouri)at(bronze.ucdavis.edu X-Mailer: Geckomail-b16 X-Originating-IP: [169.237.38.151] X-User-Agent: Mozilla/4.0 (compatible; MSIE 5.0; Mac_PowerPC) X-Scanned-By: MIMEDefang 2.35 Good morning everyone, I am using Autodock v.3.0 and can't seem to get an image of the protein. I am able to view the .dpf files of the ligands no problem once I convert them to .pdb files for macromodel v.7.0. Is there a way to view the protein as well once the docking is completed, and how would I extract this data? Thank-you so much for your time, Dustin Nouri University of California--Davis From chemistry-request@ccl.net Tue Aug 26 11:26:58 2003 Received: from pat.uio.no (pat.uio.no [129.240.130.16]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7QFQvYj007237 for ; Tue, 26 Aug 2003 11:26:57 -0400 Received: from mail-mx4.uio.no ([129.240.10.45]) by pat.uio.no with esmtp (Exim 4.20) id 19rfij-0006oM-2Z for chemistry)at(ccl.net; Tue, 26 Aug 2003 17:26:57 +0200 Received: from snapp.uio.no ([129.240.130.64]) by mail-mx4.uio.no with esmtp (Exim 4.14) id 19rfih-0003mv-QG for chemistry)at(ccl.net; Tue, 26 Aug 2003 17:26:55 +0200 Received: from bio89162.uio.no ([129.240.89.162] helo=bio89162.ulrik.uio.no) by snapp.uio.no with esmtp (Exim 2.12 #7) id 19rfih-0007I4-00 for chemistry)at(ccl.net; Tue, 26 Aug 2003 17:26:55 +0200 Message-Id: <5.1.0.14.2.20030826172435.00b979a8)at(uio-pop.uio.no> X-Sender: sergioma)at(uio-pop.uio.no X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Tue, 26 Aug 2003 17:25:09 +0200 To: chemistry)at(ccl.net From: Sergio Manzetti Subject: AUTODOCK Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-MailScanner-Information: This message has been scanned for viruses/spam. Contact postmaster)at(uio.no if you have questions about this scanning. X-UiO-MailScanner: No virus found Hello, how can I increase the number of resulting conformations of the ligand that I wish to dock to the receptor? many thanks Sergio From chemistry-request@ccl.net Tue Aug 26 04:50:51 2003 Received: from socrates.cc.uoi.gr (socrates.cc.uoi.gr [195.130.119.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7Q8onYj025432 for ; Tue, 26 Aug 2003 04:50:50 -0400 Received: from prokopis (pc216.dialup.uoi.gr [195.130.119.216]) by socrates.cc.uoi.gr (8.9.3/8.9.3) with SMTP id LAA79632 for ; Tue, 26 Aug 2003 11:43:45 +0300 (EEST) Message-ID: <006b01c36baf$22984840$0200a8c0@prokopis> From: "George Papamokos" To: Subject: CCL: Re to formchk problem Date: Tue, 26 Aug 2003 11:50:12 +0300 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0060_01C36BC8.3522CC10" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2720.3000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0060_01C36BC8.3522CC10 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello Yixuan, One way to solve this problem is to follow the steps below: 1. Find the file of the program (formchk.F) that decides the size of the = array for this capability. 2. Change the size of the array in the code 3. Recompile gaussian 4. ready to do the job George Papamokos Ph. D. Student University of Ioannina Dept. of Chemistry Sector of Physical Chemistry ------=_NextPart_000_0060_01C36BC8.3522CC10 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello Yixuan,
One way to solve this problem is to = follow the=20 steps below:
1. Find the file of the program=20 (formchk.F) that decides the size of the array for this=20 capability.
2. Change the  size of the array in the code
3. Recompile gaussian
4. ready to do the job
 
George Papamokos
Ph. D. Student
 
University of Ioannina
Dept. of Chemistry
Sector of Physical=20 Chemistry
------=_NextPart_000_0060_01C36BC8.3522CC10-- From chemistry-request@ccl.net Wed Aug 27 06:51:57 2003 Received: from mbu.iisc.ernet.in (mail.mbu.iisc.ernet.in [144.16.74.32]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7RAphYj004346 for ; Wed, 27 Aug 2003 06:51:51 -0400 Received: from mbu.iisc.ernet.in (localhost.localdomain [127.0.0.1]) by mbu.iisc.ernet.in (8.12.8/8.12.5) with ESMTP id h7RBeEGF028712; Wed, 27 Aug 2003 17:10:14 +0530 Received: from localhost (gyan@localhost) by mbu.iisc.ernet.in (8.12.8/8.12.5/Submit) with ESMTP id h7RBe03E028708; Wed, 27 Aug 2003 17:10:08 +0530 Date: Wed, 27 Aug 2003 17:10:00 +0530 (IST) From: Gyanendra kumar To: Sergio Manzetti cc: chemistry-.at.-ccl.net Subject: Re: CCL:AUTODOCK In-Reply-To: <5.1.0.14.2.20030826172435.00b979a8-.at.-uio-pop.uio.no> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII hi sergio, in ur .dpf file, you can change the no. of ga_runs. by default it is 10. gyan. On Tue, 26 Aug 2003, Sergio Manzetti wrote: > Hello, how can I increase the number of resulting conformations of the > ligand that I wish to dock to the receptor? > > > many thanks > > Sergio > > > > -= This is automatically added to each message by 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, jkl-.at.-ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > -- ******************************************** Gyanendra Kumar (Research Student), Prof. A. Surolia's Lab, #204, Molecular Biophysics Unit, Indian Institute Of Science, Bangalore, PIN-560012.INDIA, Phone 91-80-293-2389,-2714(Lab), -2539(Res). http://mbu.iisc.ernet.in/~surolia/gyan.html ******************************************** Residence: R-17, Students Hostel, IISc. ******************************************** From chemistry-request@ccl.net Wed Aug 27 06:57:55 2003 Received: from mbu.iisc.ernet.in (mbu.iisc.ernet.in [144.16.74.32]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7RAugYj004489 for ; Wed, 27 Aug 2003 06:57:53 -0400 Received: from mbu.iisc.ernet.in (localhost.localdomain [127.0.0.1]) by mbu.iisc.ernet.in (8.12.8/8.12.5) with ESMTP id h7RBjgGF028938; Wed, 27 Aug 2003 17:15:42 +0530 Received: from localhost (gyan@localhost) by mbu.iisc.ernet.in (8.12.8/8.12.5/Submit) with ESMTP id h7RBjVw5028930; Wed, 27 Aug 2003 17:15:42 +0530 Date: Wed, 27 Aug 2003 17:15:31 +0530 (IST) From: Gyanendra kumar To: Dustin Nouri cc: chemistry=at=ccl.net Subject: Re: CCL:autodock v.3.0 question In-Reply-To: <200308261646.h7QGkhp14335=at=andrena.ucdavis.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII hi dustin, you can cat the pdb file of the receptor to the pdb file containing the co-ordinates of the ligands. you will be able to view the ligands docked with receptor. you can use the comand: cat recpt.pdbqs >> lig.dlg.pdb hope this helps you. On Tue, 26 Aug 2003, Dustin Nouri wrote: > > Good morning everyone, > > I am using Autodock v.3.0 and can't seem to get an image of the > protein. I am able to view the .dpf files of the ligands no problem > once I convert them to .pdb files for macromodel v.7.0. Is there a way > to view the protein as well once the docking is completed, and how > would I extract this data? > > Thank-you so much for your time, > Dustin Nouri > University of California--Davis > > > > -= This is automatically added to each message by 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, jkl=at=ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > -- ******************************************** Gyanendra Kumar (Research Student), Prof. A. Surolia's Lab, #204, Molecular Biophysics Unit, Indian Institute Of Science, Bangalore, PIN-560012.INDIA, Phone 91-80-293-2389,-2714(Lab), -2539(Res). http://mbu.iisc.ernet.in/~surolia/gyan.html ******************************************** Residence: R-17, Students Hostel, IISc. ******************************************** From chemistry-request@ccl.net Wed Aug 27 04:17:00 2003 Received: from parker.howard.edu ([138.238.147.154]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7R8GwYj000658 for ; Wed, 27 Aug 2003 04:16:59 -0400 Received: by PARKER with Internet Mail Service (5.5.2653.19) id ; Wed, 27 Aug 2003 04:16:56 -0400 Message-ID: From: "Ferber, Steven D" To: "'CHEMISTRY/at/ccl.net'" Subject: re: CCL:curvilinear step not converged in G98-clarifications Date: Wed, 27 Aug 2003 04:16:54 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain Dear Joslyn Kravitz, Shen Cai & anybody else interested, I quickly presumed the original question was referring to coordinates input in CARTESIAN's - after Joslyn's note I went back to see that Shen may have been working in INTERNAL coordinates => Z-matrix input. I work on rather large molecules (Nucleotides ~ 40 atoms) starting from crystal structures (Cartesians) so I found a way to freeze atoms accordingly. I ran into the exact same error message as Shen & found this way around it. Conceptually it may be more tedious - but pragmatic-ly it would work to re-input your peptide (& associated water molecules) in Cartesians for the "fake" optimization & subsequent real one as per my first note. The real problem may be how to "tether" your hydration molecules to the peptide as IT optimizes - ya may have to do a quasi-Step opt "crawl" of your own over a few cycles (i.e. opt the peptide w/hydration frozen, then vice-versa). A bit "brute force" though it should work - or maybe write a macro doing the same. Steve Ferber Howard U. Chemistry sferber/at/howard.edu From chemistry-request@ccl.net Wed Aug 27 07:29:43 2003 Received: from pat.uio.no (pat.uio.no [129.240.130.16]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7RBTgYj005258 for ; Wed, 27 Aug 2003 07:29:43 -0400 Received: from mail-mx3.uio.no ([129.240.10.44]) by pat.uio.no with esmtp (Exim 4.20) id 19ryUg-00008r-OF; Wed, 27 Aug 2003 13:29:42 +0200 Received: from snapp.uio.no ([129.240.130.64]) by mail-mx3.uio.no with esmtp (Exim 4.14) id 19ryUb-0006AC-2N; Wed, 27 Aug 2003 13:29:37 +0200 Received: from bio89162.uio.no ([129.240.89.162] helo=bio89162.ulrik.uio.no) by snapp.uio.no with esmtp (Exim 2.12 #7) id 19ryUa-0004Ko-00; Wed, 27 Aug 2003 13:29:36 +0200 Message-Id: <5.1.0.14.2.20030827132745.00b47990/at/uio-pop.uio.no> X-Sender: sergioma/at/uio-pop.uio.no X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Wed, 27 Aug 2003 13:27:51 +0200 To: Gyanendra kumar , Sergio Manzetti From: Sergio Manzetti Subject: Re: CCL:AUTODOCK Cc: chemistry/at/ccl.net In-Reply-To: References: <5.1.0.14.2.20030826172435.00b979a8/at/uio-pop.uio.no> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-MailScanner-Information: This message has been scanned for viruses/spam. Contact postmaster/at/uio.no if you have questions about this scanning. X-UiO-MailScanner: No virus found THANK YOU! At 17:10 27.08.2003 +0530, Gyanendra kumar wrote: >hi sergio, >in ur .dpf file, you can change the no. of ga_runs. by default it is 10. > >gyan. > > >On Tue, 26 Aug 2003, Sergio Manzetti wrote: > > > Hello, how can I increase the number of resulting conformations of the > > ligand that I wish to dock to the receptor? > > > > > > many thanks > > > > Sergio > > > > > > > > -= This is automatically added to each message by 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, jkl/at/ccl.net (read about it on CCL Home Page) > > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > > > > > >-- >******************************************** >Gyanendra Kumar (Research Student), >Prof. A. Surolia's Lab, >#204, Molecular Biophysics Unit, >Indian Institute Of Science, >Bangalore, PIN-560012.INDIA, >Phone 91-80-293-2389,-2714(Lab), -2539(Res). >http://mbu.iisc.ernet.in/~surolia/gyan.html >******************************************** >Residence: R-17, Students Hostel, IISc. >******************************************** From chemistry-request@ccl.net Wed Aug 27 09:22:46 2003 Received: from webmail.mta.ca (postal.mta.ca [138.73.1.51]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7RDMkYj007986 for ; Wed, 27 Aug 2003 09:22:46 -0400 Received: from nobody by webmail.mta.ca with local (Exim 4.20) id 19s0Fo-0007Vr-QV for chemistry/at/ccl.net; Wed, 27 Aug 2003 10:22:28 -0300 Received: from 138.73.24.247 ( [138.73.24.247]) as user arussell/at/mailserv.mta.ca by webmail.mta.ca with HTTP; Wed, 27 Aug 2003 10:22:28 -0300 Message-ID: <1061990548.3f4cb094c26c7/at/webmail.mta.ca> Date: Wed, 27 Aug 2003 10:22:28 -0300 From: Aaron Russell To: chemistry/at/ccl.net Subject: Question about gaussian installation MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Originating-IP: 138.73.24.247 Hello Do you use Gaussian G98 and G03 on your cluster or do you know anyone who does? I am trying to install Gaussian G98 and G03 and not having much success keeping it stable. I am looking to know how other people have installed Gaussian on a cluster and the special tricks they did to get it working. I am very interested in things like using are you using a stratch/ directory on the NFS file system or a stratch/ directory on each compute node. Did you install Gaussian on each compute node? What version of Linux and kernal version are you using? Do you have any problems with Linda and running Gaussian in parallel? Sincerely Aaron Russell Research Technologist Mount Allison University 67 York Street Sackville, New Brunswick, Canada E4L 1E6 Phone: (506) 364-2162 Fax: (506) 364-2313 E-mail: arussell/at/mta.ca From chemistry-request@ccl.net Wed Aug 27 01:06:24 2003 Received: from p08.es.uci.edu (p08.es.uci.edu [128.200.73.148]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7R56OYj028935 for ; Wed, 27 Aug 2003 01:06:24 -0400 Received: from 192.168.0.100 (vp087184.reshsg.uci.edu [128.195.87.184]) by p08.es.uci.edu (8.11.6/8.11.6) with ESMTP id h7R56K906751 for ; Tue, 26 Aug 2003 22:06:20 -0700 Date: Tue, 26 Aug 2003 22:06:17 -0700 From: Qiang Lu X-Mailer: The Bat! (v1.62r) Reply-To: Qiang Lu Organization: UCI MBB X-Priority: 3 (Normal) Message-ID: <1364804561.20030826220617/at/uci.edu> To: chemistry/at/ccl.net Subject: gaussian normal mode projection MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi I need to project gaussian98/03 normal mode vibrations onto inner coordinates. Does anyone knows any software that can do it. That would be very helpful. -- Best regards, Qiang Lu mailto:qiangl/at/uci.edu From chemistry-request@ccl.net Wed Aug 27 05:35:09 2003 Received: from socrates.cc.uoi.gr (socrates.cc.uoi.gr [195.130.119.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7R9Z8Yj002721 for ; Wed, 27 Aug 2003 05:35:08 -0400 Received: from prokopis (pc251.dialup.uoi.gr [195.130.119.251]) by socrates.cc.uoi.gr (8.9.3/8.9.3) with SMTP id MAA147419 for ; Wed, 27 Aug 2003 12:28:02 +0300 (EEST) Message-ID: <002f01c36c7e$7d38cf20$0200a8c0@prokopis> From: "George Papamokos" To: Subject: CCL: Re to formchk problems (plus) Date: Wed, 27 Aug 2003 12:34:30 +0300 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0028_01C36C97.8FC7E6D0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2720.3000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0028_01C36C97.8FC7E6D0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi again Yixuan, You need not recompile the whole program. G98 can recompile only part of its self if needed. You can find details in the manuals. George Papamokos Ph. D. Student University of Ioannina Department of Chemistry Sector of Physical Chemistry ------=_NextPart_000_0028_01C36C97.8FC7E6D0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi again Yixuan,
 
You need not recompile the whole=20 program.
G98 can recompile only part of its self = if=20 needed.
You can find details in the = manuals.
 
George Papamokos
Ph. D. Student
 
University of Ioannina
Department of Chemistry
Sector of Physical = Chemistry
 
 
------=_NextPart_000_0028_01C36C97.8FC7E6D0-- From chemistry-request@ccl.net Wed Aug 27 10:42:55 2003 Received: from aquarius.ime.eb.br (aquarius.ime.eb.br [200.20.120.44]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7REgsYj010183 for ; Wed, 27 Aug 2003 10:42:55 -0400 Received: from epq.ime.eb.br (epq.ime.eb.br [200.20.120.217]) by aquarius.ime.eb.br (8.12.8/8.12.8) with ESMTP id h7REgrI5005622 for ; Wed, 27 Aug 2003 11:42:53 -0300 Received: from EPQ/SpoolDir by epq.ime.eb.br (Mercury 1.48); 27 Aug 03 11:52:46 -0300 Received: from SpoolDir by EPQ (Mercury 1.48); 27 Aug 03 11:52:19 -0300 Received: from epq.ime.eb.br (200.20.123.218) by epq.ime.eb.br (Mercury 1.48) with ESMTP; 27 Aug 03 11:52:17 -0300 Message-ID: <3F4CC34B.1010006_at_epq.ime.eb.br> Date: Wed, 27 Aug 2003 11:42:19 -0300 From: Teodorico Ramalho User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.3) Gecko/20030313 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry_at_ccl.net Subject: IEF/PCM Question Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear CCL's I carried out optimization using IEF/PCM (solvent= aniline) in G98A.11. The same job run using B3lyp/6-31G**, but it does not run with HF/6-31G**. The error message is the following: Hint: increase the number of tesserae or change the molecule orientation. Could anyone help me to know what occurred? Thanks very much, Teodorico From chemistry-request@ccl.net Wed Aug 27 10:05:05 2003 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7RE54Yj009386 for ; Wed, 27 Aug 2003 10:05:04 -0400 Received: from chem.utoronto.ca (slip2 [142.150.224.87]) by alchemy.chem.utoronto.ca (8.11.6/8.11.6) with ESMTP id h7RE54E31463 for ; Wed, 27 Aug 2003 10:05:04 -0400 Message-ID: <3F4CBB89.427ADFE7_at_chem.utoronto.ca> Date: Wed, 27 Aug 2003 10:09:14 -0400 From: "Nam A. Nguyen" X-Mailer: Mozilla 4.8 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry_at_ccl.net Subject: Oscillator strength Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear colleagues, I need oscillator strengths for the transitions from the 5 ^2D state of Rb atom. Since I didn't find the data in the literature so I've decided to calculate them myself. My questions are: 1-Since I can determine the excited state wave functions using Gaussian CASSCF, is there anyway to calculate the oscillator strengths using Gaussian output files ? 2-Is there any program that is able to calculate excited states and oscillator strengths of ATOMS ? Thank you for your help Nam Nguyen University of Toronto From chemistry-request@ccl.net Wed Aug 27 17:38:10 2003 Received: from ultra.chem.ucsb.edu (ultra.chem.ucsb.edu [128.111.114.119]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7RLcAUH020425 for ; Wed, 27 Aug 2003 17:38:10 -0400 Received: from localhost (localhost [127.0.0.1]) by ultra.chem.ucsb.edu (Postfix) with ESMTP id BDC0A502CF; Wed, 27 Aug 2003 14:38:08 -0700 (PDT) Received: from ultra.chem.ucsb.edu ([127.0.0.1]) by localhost (ultra [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 12347-07; Wed, 27 Aug 2003 14:38:06 -0700 (PDT) Received: by ultra.chem.ucsb.edu (Postfix, from userid 3016) id 2A813502CB; Wed, 27 Aug 2003 14:38:06 -0700 (PDT) Received: from localhost (localhost [127.0.0.1]) by ultra.chem.ucsb.edu (Postfix) with ESMTP id 21BC5170726; Wed, 27 Aug 2003 14:38:06 -0700 (PDT) Date: Wed, 27 Aug 2003 14:38:06 -0700 (PDT) From: John Bushnell To: Aaron Russell Cc: chemistry-.at.-ccl.net Subject: Re: CCL:Question about gaussian installation In-Reply-To: <1061990548.3f4cb094c26c7-.at.-webmail.mta.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by amavisd-new We have g98 installed in /usr/local which is nfs mounted by all the compute nodes. Users use the local /scratch directory on the compute nodes for the scratch files (the .inp, .d2e, .rwf and .scr files) and checkpoint files. So they have to copy over the checkpoint file after the job completes if they need it. The job output (.log file) is written to their home directory (/home is also nfs mounted). We haven't had any noticeable problems, though if users run a lot of jobs that don't finish normally, the scratch files collect on the compute nodes. But they aren't hard to clean out, and things haven't gotten out of hand with a 32 node dual cpu cluster. We haven't run Gaussian in parallel. BTW, we are using fast ethernet which has been fine running like this. HTH - John On Wed, 27 Aug 2003, Aaron Russell wrote: > Hello > > Do you use Gaussian G98 and G03 on your cluster or do you know anyone > who does? I am trying to install Gaussian G98 and G03 and not having > much success keeping it stable. I am looking to know how other people > have installed Gaussian on a cluster and the special tricks they did > to get it working. I am very interested in things like using are you > using a stratch/ directory on the NFS file system or a stratch/ > directory on each compute node. Did you install Gaussian on each > compute node? What version of Linux and kernal version are you using? > Do you have any problems with Linda and running Gaussian in parallel? > > Sincerely > > Aaron Russell > Research Technologist > Mount Allison University > 67 York Street > Sackville, New Brunswick, Canada > E4L 1E6 > Phone: (506) 364-2162 > Fax: (506) 364-2313 > E-mail: arussell-.at.-mta.ca From chemistry-request@ccl.net Wed Aug 27 15:32:14 2003 Received: from p08.es.uci.edu (p08.es.uci.edu [128.200.73.148]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7RJWEUH018166 for ; Wed, 27 Aug 2003 15:32:14 -0400 Received: from 128.200.204.148 (dhcp-204148.bio.uci.edu [128.200.204.148]) by p08.es.uci.edu (8.11.6/8.11.6) with ESMTP id h7RJWE902899 for ; Wed, 27 Aug 2003 12:32:14 -0700 Date: Wed, 27 Aug 2003 12:32:11 -0700 From: Qiang Lu X-Mailer: The Bat! (v1.62r) Reply-To: Qiang Lu Organization: UCI MBB X-Priority: 3 (Normal) Message-ID: <1301030585.20030827123211^at^uci.edu> To: chemistry^at^ccl.net Subject: install g03 on redhat 7.2 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi CCLers, Can g03 be installed on Redhat 7.2? -- Best regards, Qiang mailto:qiangl^at^uci.edu From chemistry-request@ccl.net Wed Aug 27 20:07:23 2003 Received: from ultra.chem.ucsb.edu (ultra.chem.ucsb.edu [128.111.114.119]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7S07MUH022932 for ; Wed, 27 Aug 2003 20:07:23 -0400 Received: from localhost (localhost [127.0.0.1]) by ultra.chem.ucsb.edu (Postfix) with ESMTP id DD512502D2; Wed, 27 Aug 2003 17:07:21 -0700 (PDT) Received: from ultra.chem.ucsb.edu ([127.0.0.1]) by localhost (ultra [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 21237-07; Wed, 27 Aug 2003 17:07:19 -0700 (PDT) Received: by ultra.chem.ucsb.edu (Postfix, from userid 3016) id 3375F502CF; Wed, 27 Aug 2003 17:07:19 -0700 (PDT) Received: from localhost (localhost [127.0.0.1]) by ultra.chem.ucsb.edu (Postfix) with ESMTP id 2D8C2170726; Wed, 27 Aug 2003 17:07:19 -0700 (PDT) Date: Wed, 27 Aug 2003 17:07:19 -0700 (PDT) From: John Bushnell To: Qiang Lu Cc: chemistry:at:ccl.net Subject: Re: CCL:install g03 on redhat 7.2 In-Reply-To: <1301030585.20030827123211:at:uci.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by amavisd-new Somebody posted that g03 could be installed on Redhat 7.3 by downloading a patched libpgthread.so from the Portland Group ftp server (ftp.pgroup.com). I have no idea whether this works, or more importantly whether it works for Redhat 7.2 - John On Wed, 27 Aug 2003, Qiang Lu wrote: > Hi CCLers, > > Can g03 be installed on Redhat 7.2? > > > -- > Best regards, > Qiang mailto:qiangl:at:uci.edu > > > > -= This is automatically added to each message by 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, jkl:at:ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > >