From chemistry-request@server.ccl.net Wed Mar 27 06:03:38 2002 Received: from mserv.itpa.lt ([193.219.53.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2RB3bp06869 for ; Wed, 27 Mar 2002 06:03:37 -0500 Received: from localhost (gicevic@localhost) by mserv.itpa.lt (8.11.6/8.11.0) with ESMTP id g2RB3KV62567 for ; Wed, 27 Mar 2002 13:03:29 +0200 (EET) (envelope-from gicevic@itpa.lt) Date: Wed, 27 Mar 2002 13:03:20 +0200 (EET) From: Jelena Tamuliene To: Subject: magnetic shielding tensors Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, We are Calculating GIAO nuclear magnetic shielding tensors using Gaussian 98 package. The obtained results are follow: SCF GIAO Magnetic shielding tensor (ppm): 1 Cu Isotropic = 2588.5256 Anisotropy = 17016.2846 XX= 2789.4653 YX= 1422.4613 ZX= 1357.1111 XY= 1307.4676 YY= -1539.9982 ZY= 2705.1311 XZ= 16030.7556 YZ= 1393.2821 ZZ= 6516.1097 Eigenvalues: -4260.1633 -1906.9752 13932.7154 2 N Isotropic = -259.6843 Anisotropy = 1580.4186 XX= -232.2097 YX= 269.0095 ZX= -149.6906 XY= -22.8555 YY= -19.4647 ZY= 42.3812 XZ= -1431.0257 YZ= 1655.9423 ZZ= -527.3784 Eigenvalues: -1556.7992 -16.1817 793.9281 I would like to know, why are non-equal symmetrical tenzors, i.e. XY non-equal to YX, ZY non-equal to YZ and so one. with respect, J. T. From chemistry-request@server.ccl.net Wed Mar 27 08:37:15 2002 Received: from web15004.mail.bjs.yahoo.com ([61.135.128.7]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g2RDbCp09699 for ; Wed, 27 Mar 2002 08:37:13 -0500 Message-ID: <20020327133701.15123.qmail@web15004.mail.bjs.yahoo.com> Received: from [202.119.32.49] by web15004.mail.bjs.yahoo.com via HTTP; Wed, 27 Mar 2002 21:37:01 CST Date: Wed, 27 Mar 2002 21:37:01 +0800 (CST) From: =?gb2312?q?yong=20pei?= Subject: A question about MD To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit dear sir I have some problems when I perform MD at constant temperature using Nose-hoover method. What I want to know is that how to set the initial values of the time-scaled factor (s) and its firsr and higher derivates in the Nose-Hoover equations of motion. Regards, Yong Pei _________________________________________________________ Do You Yahoo!? Æû³µ -- ÓÀ²»Ñá¾ëµÄ»°Ìâ http://survey.yahoo.com/cgi-bin/carsurvey/survey.cgi From chemistry-request@server.ccl.net Wed Mar 27 08:48:57 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 g2RDmvp09822 for ; Wed, 27 Mar 2002 08:48:57 -0500 Received: from mailszrz.zrz.tu-berlin.de ([130.149.4.11]) by mail2.zrz.tu-berlin.de with esmtp (exim-3.35) id 16qDnC-00071K-00; Wed, 27 Mar 2002 14:48:46 +0100 Received: from natrium.chem.tu-berlin.de ([130.149.169.143]) by mailszrz.zrz.tu-berlin.de with esmtp (exim-3.35) id 16qDnB-0003D2-00; Wed, 27 Mar 2002 14:48:45 +0100 Mime-Version: 1.0 X-Sender: chwu0531@mailszrz.zrz.tu-berlin.de (Unverified) Message-Id: In-Reply-To: References: Date: Wed, 27 Mar 2002 14:48:44 +0100 To: Jelena Tamuliene From: Christoph van =?iso-8859-1?Q?W=FCllen?= Subject: Re: CCL:magnetic shielding tensors Cc: chemistry@ccl.net 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 g2RDmvp09823 Well, a shielding tensor is a mixed second derivative of the (electronic) energy with respect to a component (x,y,z) of the external magnetic field and a component (x,y,z) of a nuclear magnetic moment. I do not understand why you expect the tensor to be symmetric. It *can* be symmetric (e.g. if symmetry dictates that it is diagonal), but in general it is not, and is not expected to be. +---------------------------------+----------------------------------+ | 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 Wed Mar 27 04:29:59 2002 Received: from web15005.mail.bjs.yahoo.com ([61.135.128.8]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g2R9Tvp03665 for ; Wed, 27 Mar 2002 04:29:58 -0500 Message-ID: <20020327092940.17568.qmail@web15005.mail.bjs.yahoo.com> Received: from [202.119.32.49] by web15005.mail.bjs.yahoo.com via HTTP; Wed, 27 Mar 2002 17:29:40 CST Date: Wed, 27 Mar 2002 17:29:40 +0800 (CST) From: =?gb2312?q?yong=20pei?= Subject: A problem about constant NVT ensemble MD simulation To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Dear Sir , I have some questions when I perform a canonical MD simulation with Nose-Hoover method.I don't know how to set the initial values of the time-scaled variable(s) and its first and higher derivates. Regards, Yong Pei _________________________________________________________ Do You Yahoo!? Æû³µ -- ÓÀ²»Ñá¾ëµÄ»°Ìâ http://survey.yahoo.com/cgi-bin/carsurvey/survey.cgi From chemistry-request@server.ccl.net Tue Mar 26 18:51:52 2002 Received: from mx.seanet.com ([199.181.164.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2QNppp19148 for ; Tue, 26 Mar 2002 18:51:52 -0500 Received: from Debug (ssl.seanet.com [199.181.164.13]) by mx.seanet.com (8.11.6/8.11.6) with SMTP id g2QNph628514; Tue, 26 Mar 2002 15:51:43 -0800 (PST) Message-Id: <200203262351.g2QNph628514@mx.seanet.com> To: Johannes Weber , chemistry@ccl.net From: Mark Thompson Subject: Re: CCL:g98: TD-DFT geometry optimizations ? Date: Tue, 26 Mar 2002 15:51:43 US/Pacific X-Mailer: Endymion MailMan Professional Edition v3.0.35 Dear Johannes, When you find out, I'd like to hear how it works. I wonder how they would handle state crossings. Mark > Dear CCL members, > > I have a Gaussian 98 related question: > > According to the g98 users manual (p. 155, TD keyword) it should be > possible to do Time Dependent DFT geometry optimizations of the N-th > excited state using the Root=N option. > > However, I can´t find a proper input. The easiest input line > > #P TD=(Root=1) B3LYP/STO-3G Test DENSITY OPT=Z-Matrix > > leads to an error in link 1002: > > (Enter /vol/chemie/libexec/g98.A9/g98/l1002.exe) > Minotr: Closed-shell wavefunction. > Cannot mix post-SCF and DFT. > Error termination via Lnk1e in /vol/chemie/libexec/g98.A9/g98/l1002.exe. > > I played around with several other options, tried to do the job in a two > step procedure, like it is described for the CIS method in > Forsman/Frisch´s "Exploring Chemistry with Electronic Structure Methods", > all without success. Is it possible to do these calculations? Anybody out > there with experience in this topic? The ultimate goal would be to perform > a normal mode frequency calculation for excited states within the TD-DFT > formalism. > > Regards, :-)ohannes. > ---------------------------------------------------------------------- > | Johannes Weber | Email: | > | Universitaet zu Koeln | Johannes.Weber@uni-koeln.de | > | Institut fuer Physikalische Chemie | | > | Lehrstuhl Prof. Dr. G. Hohlneicher | tel: 0049-(0)221-470-4812 | > | Luxemburger Str. 116 | fax: 0049-(0)221-470-5144 | > | 50939 Koeln | | > ---------------------------------------------------------------------- > > > > -= 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 > > > > > > ======================================= Mark Thompson, Ph.D. Planaria Software Seattle, WA http://www.arguslab.com ======================================= From chemistry-request@server.ccl.net Wed Mar 27 10:55:07 2002 Received: from rwcrmhc53.attbi.com ([204.127.198.39]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2RFt7p12907 for ; Wed, 27 Mar 2002 10:55:07 -0500 Received: from C1353359A ([12.228.114.158]) by rwcrmhc53.attbi.com (InterMail vM.4.01.03.27 201-229-121-127-20010626) with SMTP id <20020327155456.BYMK2951.rwcrmhc53.attbi.com@C1353359A>; Wed, 27 Mar 2002 15:54:56 +0000 Reply-To: From: "Mark Thompson" To: Cc: "Mark Thompson" Subject: PCGAMESS and RESP charges ?? Date: Wed, 27 Mar 2002 07:53:33 -0800 Message-ID: <000001c1d5a7$8c5a2fe0$0300a8c0@attbi.com> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit 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 V5.50.4807.1700 I need help with this.... I would like to generate RESP charges for some small molecules using PCGAMESS as the generator of the ESP points that are the input to the RESP program. I've found a url that gives instructions for doing this with GAMESS http://www.amber.ucsf.edu/amber/Questions/resp2.txt I've got the latest version of PCGAMESS and I've assumed that it supports this capability. The tests I ran with PCGAMESS completed successfully, but did not produce the expected set of esp charges. Here are the relevant instructions for setting up the GAMESS input that I used: **************************************************************************** ******* 1) Generate an appropiate GAMESS *.dat file which includes both the esp points and the atomic coordinates. An example of a GAMESS input file which does this is shown here: $CONTRL SCFTYP=RHF EXETYP=RUN RUNTYP=OPTIMIZE COORD=UNIQUE $END $CONTRL MOLPLT=.TRUE. $END $STATPT NSTEP=100 $END $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 $END $ELPOT IEPOT=1 WHERE=PDC OUTPUT=PUNCH $END $PDC PTSEL=CONNOLLY $END $GUESS GUESS=HUCKEL $END $DATA eg180.pdb C1 C01 6.0 -0.6388649947 0.4052483921 0.0000000000 ... ... H10 1.0 2.5277794177 0.0322897353 0.0000000000 $END **************************************************************************** ******** I'd appreciate any pointers. I already searched the CCL archives for an answer. Thanks in advance, Mark Thompson From chemistry-request@server.ccl.net Wed Mar 27 11:46:28 2002 Received: from web13501.mail.yahoo.com ([216.136.175.80]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g2RGkRp13739 for ; Wed, 27 Mar 2002 11:46:27 -0500 Message-ID: <20020327164618.59961.qmail@web13501.mail.yahoo.com> Received: from [130.74.167.22] by web13501.mail.yahoo.com via HTTP; Wed, 27 Mar 2002 08:46:18 PST Date: Wed, 27 Mar 2002 08:46:18 -0800 (PST) From: Subject: GOLD ouput files filtering To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello, I have recently started using GOLD to do database docking and I am really amazed by the results. The only think that bothers me is the number of ouput files it creates. Is there any way I can filter all the unnecessary files and retain only those which are of interest. Appreciate your help. Yogesh Sabnis __________________________________________________ Do You Yahoo!? Yahoo! Movies - coverage of the 74th Academy Awards® http://movies.yahoo.com/ From chemistry-request@server.ccl.net Wed Mar 27 20:36:15 2002 Received: from yakko.cimav.edu.mx ([148.223.46.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2S1aFp23575 for ; Wed, 27 Mar 2002 20:36:15 -0500 Received: from glossman (mild.cimav.edu.mx [148.223.46.1]) by yakko.cimav.edu.mx (8.11.6/8.11.2) with SMTP id g2S2EY225652 for ; Wed, 27 Mar 2002 19:14:36 -0700 Message-ID: <008201c1d601$4a0a87c0$2601010a@cimav.edu.mx> From: "Dr. Daniel Glossman-Mitnik" To: "Computational Chemistry List" Subject: gaussian 98 compilation on sgi Date: Wed, 27 Mar 2002 18:35:54 -0800 Organization: CIMAV - LAQUICOM MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 Disposition-Notification-To: "Dr. Daniel Glossman-Mitnik" X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Dear netters: I have trying to compile Gausssian 98 Rev. A11.2 on a Silicon Graphics O2 (R12000 - 400 MHz) with no luck. I have tried the sgi.make makefile that came with the software, and I have also tried the modified version that´s published in the WebMO.net web page. The compilers came with the machine are f77 version 7.0 and C version 7.0. Any help on how to do this work will be appreciated. As I am not an expert in UNIX, a guided step-by-step would be a must (:-) Thanks in advance Dr. Daniel Glossman-Mitnik P.S.: I have already succeded in compiling this version under Linux Red Hat 7.2 ************************************************************************** Dr. Daniel Glossman-Mitnik Centro de Investigacion en Materiales Avanzados (CIMAV) LAQUICOM - Laboratorio de Química Computacional Miguel de Cervantes 120 - Complejo Industrial Chihuahua Chihuahua, Chih. 31109 - Mexico Phone: (52) 614 4391151 FAX: (52) 614 4391112 E-mail: daniel.glossman@cimav.edu.mx glossman@hotmail.com dglossman@yahoo.com ************************************************************************** From chemistry-request@server.ccl.net Wed Mar 27 13:31:41 2002 Received: from ce.fis.unam.mx ([132.248.33.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2RIVep15374 for ; Wed, 27 Mar 2002 13:31:41 -0500 Received: from garaged.fis.unam.mx (garaged.fis.unam.mx [132.248.33.226]) by ce.fis.unam.mx (8.11.2/8.11.2) with ESMTP id g2RJYfh16637 for ; Wed, 27 Mar 2002 13:34:41 -0600 Subject: NWCHEM scf computation for a 152 atoms molecule From: Max Valdez To: chemistry@ccl.net Content-Type: text/plain Content-Transfer-Encoding: 7bit X-Mailer: Evolution/1.0.2-5mdk Date: 27 Mar 2002 12:33:13 -0600 Message-Id: <1017253993.23152.4.camel@garaged.fis.unam.mx> Mime-Version: 1.0 Dear CCL'ers I've been trying to compute a nice 152 atoms molecule in nwchem, I recall a succesful job some months ago, but now i'm trying other conformers and i cannot get the job to finish. I have this error that i dont understand: Error ---------------------------- Shell screening value no. value no. value no. value no. -------- ------ -------- ------ -------- ------ -------- ------ 0.00E+00 124458 1.00E-13 2693 1.00E-12 2966 1.00E-11 3184 1.00E-10 3379 1.00E-09 3354 1.00E-08 3520 1.00E-07 3788 1.00E-06 3910 1.00E-05 4692 1.00E-04 4357 1.00E-03 4720 1.00E-02 5804 1.00E-01 6321 1.00E+00 3154 1.00E+01 0 Forming initial guess at 20.7s 0:0:ga_diag_std allocator:: 2 0: ARMCI aborting 2 (0x2). Error -------------------------------------------------------- I've tryed to limit disk usage, it takes more than 62 GB and the crashes, or it simply crashes in the beginig like the message above. This is the type of job: scf semidirect filesize 2500000000 end task scf task esp I would appreciate any hint on this problem Thanks Max