From chemistry-request@server.ccl.net Wed Jul 24 08:03:02 2002 Received: from vimg1.rdg.ac.uk ([134.225.112.81]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6OC32r02299 for ; Wed, 24 Jul 2002 08:03:02 -0400 Received: from vimv1.rdg.ac.uk ([134.225.16.87]) by vimg1.rdg.ac.uk (Exim: gateway) with esmtp id 17XKr4-0004hv-00 for chemistry@ccl.net; Wed, 24 Jul 2002 13:02:58 +0100 Received: from vimh1.rdg.ac.uk ([134.225.16.83]) by vimv1.rdg.ac.uk (Exim: virusscanner) with esmtp id 17XKqw-0004hn-00 for chemistry@ccl.net; Wed, 24 Jul 2002 13:02:50 +0100 Received: from scpc146.rdg.ac.uk ([134.225.169.246] helo=scpc146) by vimh1.rdg.ac.uk (Exim: host) with esmtp id 17XKqr-000724-00 for chemistry@ccl.net; Wed, 24 Jul 2002 13:02:45 +0100 From: "Tris Youngs" To: chemistry@ccl.net Date: Wed, 24 Jul 2002 12:54:49 +0100 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: DL_POLY Total Energy Reply-to: t.g.a.youngs@reading.ac.uk Message-ID: <3D3EA399.26465.141863DE@localhost> Priority: normal X-mailer: Pegasus Mail for Win32 (v3.12c) X-Scanner: exiscan *17XKqw-0004hn-00*oOrqjfjxXVM* (The University of Reading) Hi. Could somebody out there who uses DL_POLY please enlighten me on how the total energy of the system (eng_tot) in the OUTPUT file is calculated? One would normally assume it is a simple combination of the other energy contributions given, but this seems not to be the case. So... 1) Are there some further energy terms that are not shown? 2) Am I missing something else obvious (not unlikely), or.... 3) Am I just being ignorant? :-) Any help would be greatly appreciated. Regards, Tris Youngs Department of Chemistry University of Reading UK From chemistry-request@server.ccl.net Wed Jul 24 04:39:28 2002 Received: from ciamserv.ciam.unibo.it (postfix@[137.204.214.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6O8dRr29457 for ; Wed, 24 Jul 2002 04:39:27 -0400 Received: from ciamserv.ciam.unibo.it (elim.ciam.unibo.it [137.204.117.29]) by ciamserv.ciam.unibo.it (Postfix) with ESMTP id 8F4643ADF for ; Wed, 24 Jul 2002 10:38:39 +0200 (CEST) Sender: luca@ciam.unibo.it Message-ID: <3D3E681E.C38E38B7@ciamserv.ciam.unibo.it> Date: Wed, 24 Jul 2002 10:41:02 +0200 From: eoin galligan X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.2.16-22smp i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: PBC'S and TINKER Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello I am building some new forcefield terms within tinker. The functions (angle,bond etc) work fine with PBC's - i get correct breathing frequencies. However, without PBC's - I cant get it to work. Can any experts in TINKER drop me a line about what I could be doing wrong? Any ideas gratefully received! Many thanks for your time. Regards, E Galligan From chemistry-request@server.ccl.net Wed Jul 24 07:25:32 2002 Received: from clmboh1-smtp3.columbus.rr.com ([65.24.0.112]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6OBPWr01083 for ; Wed, 24 Jul 2002 07:25:32 -0400 Received: from kent.edu (dhcp065-025-054-078.neo.rr.com [65.25.54.78]) by clmboh1-smtp3.columbus.rr.com (8.11.2/8.11.2) with ESMTP id g6OBPSU02747; Wed, 24 Jul 2002 07:25:29 -0400 (EDT) Message-ID: <3D3E8F01.D9AE8A88@kent.edu> Date: Wed, 24 Jul 2002 07:26:57 -0400 From: Steve Cabaniss X-Mailer: Mozilla 4.07 [en] (Win98; U) MIME-Version: 1.0 To: "Shobe, Dave" CC: "'knauerc'" , chemistry@ccl.net Subject: Re: CCL:Equilibrium constants References: <157A51F55AAAD3119CD70008C7B1629D01C15EC2@lvlxch01.unitedcatalysts.com> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Sorry to be late in responding, but I may have missed an important point. Do you need gas-phase or aqueous-phase equilibrium constants? The answers (and necessary data sets) will differ considerably. Shobe, Dave wrote: > The NIST WebBook (http://webbook.nist.gov/chemistry/) has thermochemical > data as a function of temperature, and you can calculate equilibrium > constants in the usual way. > > --David Shobe > Süd-Chemie Inc. > phone (502) 634-7409 > fax (502) 634-7724 > email dshobe@sud-chemieinc.com > > Don't bother flaming me: I'm behind a firewall. > > -----Original Message----- > From: knauerc [mailto:knauerc@georgetown.edu] > Sent: Friday, July 19, 2002 8:14 PM > To: chemistry@ccl.net > Subject: CCL:Equilibrium constants > > Does anyone know where I can find good data for the equilibrium constants, > (as a > function of temperature), for the reactions: > > H2 + Cl2 = 2HCL > > and > > H2 + Br2 = 2HBr > > Thank you. > > Connie Knauer > Georgetown University > knauerc@georgetown.edu > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Wed Jul 24 02:37:42 2002 Received: from moutvdomng2.kundenserver.de ([195.20.224.149]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6O6bfr25895 for ; Wed, 24 Jul 2002 02:37:41 -0400 Received: from [195.20.224.220] (helo=mrvdomng1.kundenserver.de) by moutvdomng2.kundenserver.de with esmtp (Exim 3.35 #2) id 17XFmB-0003Ja-00; Wed, 24 Jul 2002 08:37:35 +0200 Received: from [213.23.28.163] (helo=dsl-213-023-028-163.arcor-ip.net) by mrvdomng1.kundenserver.de with esmtp (Exim 3.35 #2) id 17XFmB-0003xX-00; Wed, 24 Jul 2002 08:37:35 +0200 Subject: Re: CCL:Swiss PDB Viewer in Red Hat 7.3 From: Thomas Wein To: Sergio Cc: CCL In-Reply-To: <200207240014.00900.sergio@proinformatix.com> References: <200207240014.00900.sergio@proinformatix.com> Content-Type: text/plain; charset=ISO-8859-15 X-Mailer: Ximian Evolution 1.0.3 (1.0.3-6) Date: 24 Jul 2002 08:37:25 +0200 Message-Id: <1027492646.2923.23.camel@linux> Mime-Version: 1.0 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g6O6bgr25896 Hi Sergio, for me the procedure described in the Install FAQs worked fine. I'm running RedHat 7.3 (downloaded fomr RedHat as ISO images) on a PIII box with Nvidia graphics card and Nvidia Linux drivers (Versions: NVIDIA_kernel-1.0-2960.rh73up and NVIDIA_GLX-1.0-2960). When starting Swiss-Prot-Viewer is says "Swiss PDB Viewer accellerated with OpenGL". Find them here: http://us.expasy.org/spdbv/text/faq.htm#linux And the text is: 1. error in loading shared libraries: libMesaGL.so.3. ... Why this The simple reason for this is that the newer Mesa now uses different names for the libraries than those with which SPDBV has been linked with. Apparently they are now called libGL.so and libGLU.so instead of libMesaGL.so and libMesaGLU.so. How to solve it The new Mesa is completly backward compatible and should not harm SPDBV from working properly. So there is no need to install an old Mesa version. Just a little hack is needed to get it work: if you can get root access to your linux box, make the following symbolic links from the new libraries to the old names: ln -s /usr/X11R6/lib/libGL.so.1.2.0 /usr/X11R6/lib/libMesaGL.so.3 ln -s /usr/X11R6/lib/libGLU.so.1.2.0 /usr/X11R6/lib/libMesaGLU.so.3 then run /sbin/ldconfig to make the system remember this changes. (I assumed that the libraries are installed under /usr/X11R6/lib. If this is not correct, please adjust the above commands with the correct location.) Good luck Thomas Wein On Wed, 2002-07-24 at 00:14, Sergio wrote: > Hi, has anyone managed to install SPDBV in Red Hat 7.3 in redirect the old > Mesa library to the new OpenGL library? > > I haven't... > > Anyone has, please let me know! > > Sergio > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > -- --- T2-Consult Dr. Thomas Wein, Executive Partner Steinachtalweg 6 81549 München Germany Fon: +49 (0)89 21 58 87 55 Fax: +49 (0)89 21 58 16 82 http://www.t2-consult.de From chemistry-request@server.ccl.net Wed Jul 24 08:46:32 2002 Received: from mail-a.bcc.ac.uk ([144.82.100.21]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6OCkWr03487 for ; Wed, 24 Jul 2002 08:46:32 -0400 Received: from ucl.ac.uk (actually host chlorine.chem.ucl.ac.uk) by mail-a.bcc.ac.uk with SMTP (Mailer) with ESMTP; Wed, 24 Jul 2002 13:46:13 +0100 Sender: mb@ucl.ac.uk Message-ID: <3D3E9F9D.2068DFF3@ucl.ac.uk> Date: Wed, 24 Jul 2002 13:37:49 +0100 From: M Brunsteiner Organization: UCL X-Mailer: Mozilla 4.76C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Tris Youngs CC: chemistry@ccl.net Subject: Re: CCL:DL_POLY Total Energy References: <3D3EA399.26465.141863DE@localhost> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Tris Youngs wrote: > > Could somebody out there who uses DL_POLY please enlighten > me on how the total energy of the system (eng_tot) in the OUTPUT > file is calculated? > > One would normally assume it is a simple combination of the other > energy contributions given, This should the case for a microcnonical ensemble (NVE-simulation) > but this seems not to be the case. > 1) Are there some further energy terms that are not shown? for NVT or NPT dynamics (at least for the Nose-Hoover versions) the total energy term is actually the conserved quantity rather than the total energy. For details see some of the papers by W.G. Hoover (as probably referenced in the DLPOLY docu) or node70.html in the online documentation. hope that helps! mic ========================================================================== According to convention there is a sweet and a bitter, a hot and a cold, and according to convention, there is an order. In truth, there are atoms and a void. -- Democritus, 400 B.C. -------------------------------------------------------------------------- Michael Brunsteiner Centre for Theoretical and Computational Chemistry University College London mailto:m.brunsteiner@ucl.ac.uk http://www.ucl.ac.uk/~uccambr/ -------------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Jul 24 10:39:04 2002 Received: from paradox.harvard.edu ([128.103.96.164]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6OEd4r07492 for ; Wed, 24 Jul 2002 10:39:04 -0400 Received: by paradox.harvard.edu (Postfix, from userid 1159) id E0F3E1BCEC; Wed, 24 Jul 2002 09:47:51 -0400 (EDT) Received: from localhost (localhost [127.0.0.1]) by paradox.harvard.edu (Postfix) with ESMTP id B99098F6C for ; Wed, 24 Jul 2002 09:47:51 -0400 (EDT) Date: Wed, 24 Jul 2002 09:47:51 -0400 (EDT) From: Liu Zhijie To: Computational Chemistry List Subject: Data of protien-peptide complexes Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I am developing a potential to evaluate the binding affinity of protein-peptide complexes only based on structual information, but I found it is difficult to find enough experimental protein-peptide dissociation constants data to examine my potential. Could any of you give me some references on the protein-ligand database (which includes the dissociation constant data and related complex structure, and has more protein-peptide data)? Thanks in advance Zhijie Liu From chemistry-request@server.ccl.net Wed Jul 24 10:55:51 2002 Received: from paradox.harvard.edu ([128.103.96.164]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6OEtpr08092 for ; Wed, 24 Jul 2002 10:55:51 -0400 Received: by paradox.harvard.edu (Postfix, from userid 1159) id 114051BCEC; Wed, 24 Jul 2002 10:04:38 -0400 (EDT) Received: from localhost (localhost [127.0.0.1]) by paradox.harvard.edu (Postfix) with ESMTP id E6BF08F6C for ; Wed, 24 Jul 2002 10:04:38 -0400 (EDT) Date: Wed, 24 Jul 2002 10:04:38 -0400 (EDT) From: Liu Zhijie To: Computational Chemistry List Subject: Data of protien-peptide complexes (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I am developing a potential to evaluate the binding affinity of protein-peptide complexes only based on structual information, but I found it is difficult to find enough experimental protein-peptide dissociation constants data to examine my potential. Could any of you give me some references on the protein-ligand database (which includes the dissociation constant data and related complex structure, and has more protein-peptide data)? Thanks in advance Zhijie Liu ___________________________________________________________________ Name : Zhijie Liu Email : lzj@paradox.harvard.edu URL : http://www-shakh.harvard.edu/~lzj ____________________________________________________________________ From chemistry-request@server.ccl.net Wed Jul 24 12:25:12 2002 Received: from localhost.localdomain ([130.67.54.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6OGP9r11430 for ; Wed, 24 Jul 2002 12:25:09 -0400 Received: from localhost (localhost [[UNIX: localhost]]) by localhost.localdomain (8.11.6/8.11.6) id g6OGOR613158; Wed, 24 Jul 2002 18:24:27 +0200 Content-Type: text/plain; charset="iso-8859-1" From: Sergio To: Liu Zhijie Subject: Re: CCL:Data of protien-peptide complexes Date: Wed, 24 Jul 2002 18:24:26 +0200 User-Agent: KMail/1.4.1 References: In-Reply-To: Cc: CCL MIME-Version: 1.0 Message-Id: <200207241824.26992.sergio@proinformatix.com> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g6OGPCr11441 Dear Liu, check out these papers and please notify me if you get something out of your program, I would like to use it if possible. Ding L, Coombs GS, Strandberg L, Navre M, Corey DR, Madison EL., 1995. Origins of the specificity of tissue-type plasminogen activator. Proc Natl Acad Sci 15:7627-7631. Coombs GS, Dang AT, Madison EL, Corey DL, 1996. Distinct mechanisms contribute to stringent substrate specificity of tissue-type plasminogen activator. J Biol Chem. 23:4461-4467. Coombs GS, Rao MS, Olson AJ, Dawson PE, Madison EL, 1998. Revisiting catalysis by chymotrypsin family serine proteases using peptide substrates and inhibitors with unnatural main chains. J Biol Chem. 20:24074-24709. Corey DR, Willett WS, Coombs GS, Craik CS, 1995. Trypsin specificity increased through substrate-assisted catalysis. Biochemistry 34:11521-7. These have all Km/Kcat constants between trypsin and a series of peptide substrates, no synthetic stuff used here, all natural. Best Regards Sergio From chemistry-request@server.ccl.net Wed Jul 24 12:00:56 2002 Received: from web12302.mail.yahoo.com ([216.136.173.100]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6OG0ur09994 for ; Wed, 24 Jul 2002 12:00:56 -0400 Message-ID: <20020724160055.90426.qmail@web12302.mail.yahoo.com> Received: from [202.141.64.236] by web12302.mail.yahoo.com via HTTP; Wed, 24 Jul 2002 09:00:55 PDT Date: Wed, 24 Jul 2002 09:00:55 -0700 (PDT) From: Anirban Subject: DL_POLY : initial configuration generation!! To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii hi!! I need initial configuration for doing MD with DL_POLY for water (TIP4P , SPC/E etc.).How do I generate coordinates for say 256 molecules keeping them in a box with a particular density ? There are methods like starting with fcc lattice or skew start method but I dont know how to go about using them for generating the coordinates in case of polyatomic(e.g. water) systems because apart from positions we have to keep in mind their orientations and that they dont overlap. Could someone throw some light in this direction ?? Thanks !! Anirban Mudi IIT Delhi INDIA __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com From chemistry-request@server.ccl.net Wed Jul 24 13:14:28 2002 Received: from netc-1v.grolier.fr ([194.158.97.217]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6OHERr18233 for ; Wed, 24 Jul 2002 13:14:28 -0400 Received: from netcourrier.com (localhost [127.0.0.1]) by netc-1v.grolier.fr (8.9.3+Sun/8.9.3) with SMTP id TAA28393; Wed, 24 Jul 2002 19:14:25 +0200 (CEST) Date: Wed, 24 Jul 2002 19:14:25 +0200 (CEST) From: eric.vangrevelinghe@netcourrier.com Received: from [194.191.169.72] by netcourrier-1v.netcourrier.com via html interface; To: lzj@paradox.harvard.edu Cc: chemistry@ccl.net Subject: Re: CCL:Data of protien-peptide complexes (fwd) Mime-Version: 1.0 X-Mailer: Medianet/v2.0 Message-Id: Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g6OHESr18237 Hi! Maybe you can take a look on the work of Lavigne et al. http://www.pence.ca/ftp/stc/ You should find some links towards experimental data. Best Regards, Eric. >Dear CCLers, > > I am developing a potential to evaluate the binding affinity of >protein-peptide complexes only based on structual information, but I >found it is difficult to find enough experimental protein-peptide >dissociation constants data to examine my potential. Could any of you >give me some references on the protein-ligand database (which includes >the dissociation constant data and related complex structure, and has more >protein-peptide data)? > > Thanks in advance > > Zhijie Liu > > > >___________________________________________________________________ > Name : Zhijie Liu > Email : lzj@paradox.harvard.edu > URL : http://www-shakh.harvard.edu/~lzj >____________________________________________________________________ > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > ------------------------------------------------------------- NetCourrier, votre bureau virtuel sur Internet : Mail, Agenda, Clubs, Toolbar... Web/Wap : www.netcourrier.com Téléphone/Fax : 08 92 69 00 21 (0,34 € TTC/min) Minitel: 3615 NETCOURRIER (0,15 € TTC/min) From chemistry-request@server.ccl.net Wed Jul 24 12:38:54 2002 Received: from hotmail.com ([207.68.163.176]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6OGcsr13507 for ; Wed, 24 Jul 2002 12:38:54 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Wed, 24 Jul 2002 09:38:49 -0700 Received: from 158.227.161.44 by sea1fd.sea1.hotmail.msn.com with HTTP; Wed, 24 Jul 2002 16:38:48 GMT X-Originating-IP: [158.227.161.44] From: "Mus Musculus" To: CHEMISTRY@ccl.net Subject: opt=(StepSize=N) Does it work? Date: Wed, 24 Jul 2002 18:38:48 +0200 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1; format=flowed Message-ID: X-OriginalArrivalTime: 24 Jul 2002 16:38:49.0187 (UTC) FILETIME=[963DBB30:01C23330] Dear CCL's Just a short question. I've searched the ccl files and I found two messages > from people who had had the same problem, but unfortunately no answers. I'm trying to reduce the step size of a geometry optimization (I want to find a minimum) using the keyword opt(StepSize=N) as written in the g98 manual, but any time I try this, the calculation breaks with a syntax error. Is there a maximum or minimum value for N? What am I doing wrong? Thank you very much for your kind attention. Regards Viv _________________________________________________________________ Charle con sus amigos online usando MSN Messenger: http://messenger.msn.com From chemistry-request@server.ccl.net Wed Jul 24 11:46:10 2002 Received: from web12307.mail.yahoo.com ([216.136.173.105]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6OFk9r09456 for ; Wed, 24 Jul 2002 11:46:10 -0400 Message-ID: <20020724154609.3197.qmail@web12307.mail.yahoo.com> Received: from [202.141.64.236] by web12307.mail.yahoo.com via HTTP; Wed, 24 Jul 2002 08:46:09 PDT Date: Wed, 24 Jul 2002 08:46:09 -0700 (PDT) From: Anirban Subject: Re: CCL:DL_POLY Total Energy To: Tris Youngs Cc: chemistry@ccl.net In-Reply-To: <3D3EA399.26465.141863DE@localhost> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii hi!! I dont know whether this would help.But still I would like to share this . After going through the DL_POLY manual regarding the output file and its contents it seems that the total energy is not a sum of kinetic and potential energy only but there are contributions from other sources like the thermostats being used to regulate the temperature.May be you will get to understand things better if you go through the DL_POLY manual which is downloadable from the url http://www.dl.ac.uk/TCSC/Software/DL_POLY/main.html Yours sincerely Anirban Mudi Research student, IIT Delhi, Delhi, India __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com From chemistry-request@server.ccl.net Wed Jul 24 14:09:33 2002 Received: from zephyr.meteo.McGill.CA ([132.206.43.13]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6OI9Wr24251 for ; Wed, 24 Jul 2002 14:09:32 -0400 Received: from kinetic.Meteo.McGill.CA by zephyr.meteo.McGill.CA (AIX 4.1/UCB 5.64/4.03) id AA20846; Wed, 24 Jul 2002 14:01:01 -0400 Date: Wed, 24 Jul 2002 14:09:35 -0400 From: Andrew Ryzhkov X-Mailer: The Bat! (v1.53d) Reply-To: Andrew Ryzhkov Organization: Dep. of Atm. & Oc. Sci. McGill Univ. X-Priority: 3 (Normal) Message-Id: <172309826126.20020724140935@zephyr.meteo.mcgill.ca> To: "Mus Musculus" Cc: CHEMISTRY@ccl.net Subject: Re: CCL:opt=(StepSize=N) Does it work? In-Reply-To: References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello Mus, Wednesday, July 24, 2002, 12:38:48 PM, you wrote: MM> Dear CCL's MM> Just a short question. I've searched the ccl files and I found two messages >> from people who had had the same problem, but unfortunately no answers. MM> I'm trying to reduce the step size of a geometry optimization (I want to MM> find a minimum) using the keyword opt(StepSize=N) as written in the g98 MM> manual, but any time I try this, the calculation breaks with a syntax error. MM> Is there a maximum or minimum value for N? What am I doing wrong? MM> Thank you very much for your kind attention. MM> Regards MM> Viv This keyword does not work. You should use instead it the following command: "IOP(1/8=N)" You can read about this IOP at http://www.gaussian.com/iops1.htm#1_8 Best regards, Andrew Dr. Andrei Ryjkov Departments of Chemistry, and Atmospheric and Oceanic Sciences, McGill University, 805 Sherbrooke St. West #808 Montreal, Quebec, CANADA, H3A 2K6. ---------------------------------------------------------------- E-mail: Andrew@Zephyr.Meteo.McGill.Ca Internet: http://RedAndr.tripod.com From chemistry-request@server.ccl.net Wed Jul 24 14:47:28 2002 Received: from pcserver.iqm.unicamp.br ([143.106.51.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6OIlRr28316 for ; Wed, 24 Jul 2002 14:47:27 -0400 Received: from localhost (localhost.iqm.unicamp.br [127.0.0.1]) by pcserver.iqm.unicamp.br (Postfix) with ESMTP id D36633E2D for ; Wed, 24 Jul 2002 15:47:25 -0300 (BRT) Received: from iqm.unicamp.br (luxor.iqm.unicamp.br [143.106.51.146]) by pcserver.iqm.unicamp.br (Postfix) with ESMTP id B32233E22 for ; Wed, 24 Jul 2002 15:47:23 -0300 (BRT) Message-ID: <3D3EF632.2030805@iqm.unicamp.br> Date: Wed, 24 Jul 2002 15:47:14 -0300 From: Milton Taidi Sonoda User-Agent: Mozilla/5.0 (X11; U; FreeBSD i386; en-US; rv:0.9.7) Gecko/20020123 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry@ccl.net Subject: Rigid + flexible molecule under TIKER Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: by AMaViS perl-11 Hi CCLers Does anybody know how to perform classical md simulation under TINKER, with some rigid molecules plus others flexible? Thank you all in advance Milton Taidi Sonoda From chemistry-request@server.ccl.net Wed Jul 24 13:58:35 2002 Received: from cardinal5.Stanford.EDU ([171.64.15.253]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6OHwZr23422 for ; Wed, 24 Jul 2002 13:58:35 -0400 Received: (from liviu@localhost) by cardinal5.Stanford.EDU (8.11.6/8.11.6) id g6OHwMh17579; Wed, 24 Jul 2002 10:58:22 -0700 Date: Wed, 24 Jul 2002 10:58:22 -0700 (PDT) From: Liviu Mihail Mirica To: chemistry@ccl.net Subject: Error in Freq job Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi everybody, I have a question regarding a G98 Freq job. When i do a UBP86 Freq calculation on an already geomery optimized Cu complex, with the wavefunction already in the .chk file, i get this error message: "Not enough memory in AlgDDF. Error termination via Lnk1e in /afs/ir.stanford.edu/class/chemeng444a/programs$ Job cpu time: 0 days 16 hours 0 minutes 10.8 seconds. File lengths (MBytes): RWF= 336 Int= 0 D2E= 0 Chk= 9 Scr= 1" Is this due to the memory limit on the folder i have my temp files, or is some problem in the calculation. Does anyone have an idea how i can solve this problem? thanks. Sincerely, Liviu Mirica ************************** Liviu Mihail Mirica tel: 650-497-3188 Escondido Village, 35 B email: liviu@leland.stanford.edu Stanford, CA 94305, USA From chemistry-request@server.ccl.net Wed Jul 24 15:57:02 2002 Received: from ws4-4.us4.outblaze.com ([205.158.62.105]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6OJv1r30943 for ; Wed, 24 Jul 2002 15:57:01 -0400 Received: (qmail 24042 invoked by uid 1001); 24 Jul 2002 19:56:46 -0000 Message-ID: <20020724195646.24041.qmail@linuxmail.org> Content-Type: text/plain; charset="iso-8859-1" Content-Disposition: inline Content-Transfer-Encoding: 7bit MIME-Version: 1.0 X-Mailer: MIME-tools 5.41 (Entity 5.404) Received: from [129.69.145.79] by ws4-4.us4.outblaze.com with http for bimo7@linuxmail.org; Wed, 24 Jul 2002 21:56:46 +0200 From: "Bimo Ario Tejo" To: chemistry@ccl.net Cc: jkl@ccl.net Date: Wed, 24 Jul 2002 21:56:46 +0200 Subject: C sp3 or sp? X-Originating-Ip: 129.69.145.79 X-Originating-Server: ws4-4.us4.outblaze.com Dear CCLers, I have a C* atom bound to three O atoms and 1 C atom. Which one is the proper model for the C* atom: as sp3 or sp? I need the model regarding of its bond length and its angles. For example, some people put C* as sp in the CHCl3 molecule. Best regards, Bimo ITB-Stuttgart -- Get your free email from www.linuxmail.org Powered by Outblaze From chemistry-request@server.ccl.net Wed Jul 24 16:03:55 2002 Received: from web12303.mail.yahoo.com ([216.136.173.101]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6OK3tr31192 for ; Wed, 24 Jul 2002 16:03:55 -0400 Message-ID: <20020724200355.89312.qmail@web12303.mail.yahoo.com> Received: from [202.141.64.236] by web12303.mail.yahoo.com via HTTP; Wed, 24 Jul 2002 13:03:55 PDT Date: Wed, 24 Jul 2002 13:03:55 -0700 (PDT) From: Anirban Subject: DL_POLY : initial configuration + A PROBLEM To: chemistry@ccl.net In-Reply-To: <000b01c2334a$59b8b970$0401a8c0@kressworks.com> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii HI!! Thanks to everyone for the help and overwhelming response to my mail.I will definitely try out the suggestions one by one. At present what I have tried is that I have taken the coordinates of SPC water molecules and scaled the coordinates to so as to fit the molecules in a cubic cell of a particular dimension(as governed by the density of the liquid) knowing that the cell dimension of the original SPC system was different. Now my system contains flexible water molecules .After running the MD I find that various quantities like total energy, coordinates and others show NaNQ ( not a number) instead of any reasonable values. There was no error message at all.I havent able to figure out why I am getting an output like that. Help in this regard will be appreciated. Thanks Anirban Mudi __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com From chemistry-request@server.ccl.net Wed Jul 24 15:41:23 2002 Received: from web13507.mail.yahoo.com ([216.136.175.86]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6OJfNr30425 for ; Wed, 24 Jul 2002 15:41:23 -0400 Message-ID: <20020724194123.16177.qmail@web13507.mail.yahoo.com> Received: from [130.74.167.22] by web13507.mail.yahoo.com via HTTP; Wed, 24 Jul 2002 12:41:23 PDT Date: Wed, 24 Jul 2002 12:41:23 -0700 (PDT) From: Subject: Database scan for salts To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello, I am looking for a program or a script which will allow me to pick those molecules from a database which are present as salts (i.e. no connectivity between the molecule and the respective salt). This will allow me to free my database of salts. Thank you Sincerely, Yogesh Sabnis __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com From chemistry-request@server.ccl.net Wed Jul 24 14:52:56 2002 Received: from mail-d.bcc.ac.uk ([144.82.100.24]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6OIqur28901 for ; Wed, 24 Jul 2002 14:52:56 -0400 Received: from ucl.ac.uk (actually host chlorine.chem.ucl.ac.uk) by mail-d.bcc.ac.uk with SMTP (Mailer) with ESMTP; Wed, 24 Jul 2002 19:52:55 +0100 Sender: mb@ucl.ac.uk Message-ID: <3D3EF590.A64FF4B@ucl.ac.uk> Date: Wed, 24 Jul 2002 19:44:32 +0100 From: M Brunsteiner Organization: UCL X-Mailer: Mozilla 4.76C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Anirban CC: chemistry@ccl.net Subject: Re: CCL:DL_POLY : initial configuration generation!! References: <20020724160055.90426.qmail@web12302.mail.yahoo.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Anirban wrote: > > hi!! > > I need initial configuration for doing MD with DL_POLY > for water (TIP4P , SPC/E etc.).How do I generate > coordinates for say 256 molecules keeping them in a > box with a particular density ? > There are methods like starting with fcc lattice or > skew start method but I dont know how to go about > using them for generating the coordinates in case of > polyatomic(e.g. water) systems because apart from > positions we have to keep in mind their orientations > and that they dont overlap. As for water molecules ... these are "nearly" spherical So you can still use fcc or skew start and the coordinates generated with one of these algorithms are simply taken to be the center of mass or the oxigen position of the waters. You don't have to care about the orientations either since you can choose these randomly or even let all the waters have the same orientation. After a few picoseconds equilibration the average total dipole moment of the unit cell will vanish anyway (for an isotropic fluid). If you use a protocol starting with a very short time step (<< 1 fs) (and possibly the directive "shake 0.001" in DL_POLY) that you increase gradually over a few ps you can even start with considerable overlaps unless you have molecules of a very peculiar shape. regards mic ps: on my homepage (below) you can find a small program that you can use for this purpose provided your molecules are roughly spherical ========================================================================== According to convention there is a sweet and a bitter, a hot and a cold, and according to convention, there is an order. In truth, there are atoms and a void. -- Democritus, 400 B.C. -------------------------------------------------------------------------- Michael Brunsteiner Centre for Theoretical and Computational Chemistry University College London mailto:m.brunsteiner@ucl.ac.uk http://www.ucl.ac.uk/~uccambr/ --------------------------------------------------------------------------