From chemistry-request@server.ccl.net Fri Apr 6 04:09:53 2001 Received: from mail.kemi.dtu.dk ([130.225.67.150]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3689qD02293 for ; Fri, 6 Apr 2001 04:09:53 -0400 Received: from ouabain.ok.dtu.dk (tr4.ok.dtu.dk [192.38.70.74]) by mail.kemi.dtu.dk (8.9.3/8.9.1) with ESMTP id LAA31790 for ; Fri, 6 Apr 2001 11:04:10 +0200 Received: from localhost ([127.0.0.1] helo=tr4.ok.dtu.dk) by ouabain.ok.dtu.dk with esmtp (Exim 3.12 #1 (Debian)) id 14lS9p-0000An-00 for ; Fri, 06 Apr 2001 11:03:53 +0200 To: chemistry@ccl.net Subject: Re: CCL:(Sad) news about insightII on Linux In-Reply-To: Your message of "Thu, 05 Apr 2001 21:41:22 PDT." <200104060441.VAA01734@hbond.com> Date: Fri, 06 Apr 2001 11:03:53 +0200 From: Malcolm Gillies Message-Id: I'd like to respond to a couple of technical points in Dr Haney's post. > Sorry I'm late here. InsightII was never intended to work over X, > and it does not work very well between SGI's. It was somewhat of > an accident that InsightII worked between SGI's but it required the > GL service. Instead of creating true X support for InsightII they > created this stripped down version -axxess. While the GL verion > works reasonably well between SGI's, if you do any significant > screen updates, it is very slow. With 100Mbps ethernet and faster, I suspect this is less of a problem. While I admit I am accustomed to slow machines, I have regularly used Insight and Sybyl via a remote (SGI) display and been quite comfortable. For the past five years or so, Insight has supported OpenGL. As far as I know, the old SGI GL protocol (which uses a separate port for network connections) is now fully deprecated. OpenGL is supposed to be standardised (i.e., not just for SGI machines), and runs happily over an X protocol connection using the GLX protocol. This is *not* - -axxess, and is the default mode of operation when connecting remotely > from one SGI to another (and presumably to any other supported platform, if there are any). > Tripos does support full Sybyl over true X (it runs on a Linux system > fine). While this is a nice feature, it also suffers from slow > speeds if there are many screen updates. I'm not sure what you mean by "true X". Tripos supports various types of remote OpenGL displays. Last I checked Xfree86 on Linux was not mentioned explicitly, but it does seem to work pretty well. By my reasoning (and in the absence of any information from MSI), the non-compatibility of Insight with remote displays is the result of a dependence on some unusual features of the SGI OpenGL implementation, unsupported by Xfree86. That is, if it is not a simple matter of ignorance, sloppiness or obstruction... ;-) It would be nice if someone from MSI could fill the information vacuum, otherwise we will have to wait until some adventurous soul takes a debugger in hand and investigates further. cheers, Malcolm -- Malcolm Gillies Post-doctoral researcher Organic Chemistry, Dept of Chemistry, Technical University of Denmark From chemistry-request@server.ccl.net Fri Apr 6 08:53:17 2001 Received: from fluorid.ethz.ch ([129.132.126.40]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f36CrGD04892 for ; Fri, 6 Apr 2001 08:53:16 -0400 Received: from igc.phys.chem.ethz.ch (fluorid [129.132.126.40]) by fluorid.ethz.ch (8.8.8/8.8.8) with ESMTP id PAA03811 for ; Fri, 6 Apr 2001 15:45:08 +0200 (CEST) Sender: portmann@igc.phys.chem.ethz.ch Message-ID: <3ACDC864.BAD89F26@igc.phys.chem.ethz.ch> Date: Fri, 06 Apr 2001 15:45:08 +0200 From: Stefan Portmann X-Mailer: Mozilla 4.61 [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: SCF=restart with G98A9 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello it seems to be impossible to restart any SCF calculation, that terminated either because of reaching the MAXCYCLE limit or was kicked out of a queue because the job reached the max CPU limit. All attempts failed with: >-- Leave Link 303 at Fri Apr 6 15:19:58 2001, MaxMem= 6291456 cpu: 0.5 > (Enter /usr/c4/sw/chempool/g98.a9/l401.exe) > FileIO operation on non-existent file. >FileIO: IOper= 2 IFilNo(1)=-20670 Len= 4 IPos= 0 Q= 4397981628936 If I try to read the geometry from the same checkpoint file with geom=allcheckpoint the job crashes already in link l101 with the same message which makes no sense to me: > Leave Link 1 at Fri Apr 6 15:13:09 2001, MaxMem= 0 cpu: 0.2 > (Enter /usr/c4/sw/chempool/g98.a9/l101.exe) > FileIO operation on non-existent file. >FileIO: IOper= 2 IFilNo(1)=-20502 Len= 100 IPos= 40000 Q= 4398041538016 god knows which file is non existing, the checkpoint file is touched by gaussian and gets a new date. It looks more like the checkpoint file is not written properly every SCF iteration step. Does anybody have a solution to the problem, or at least experienced the same thing, so I can be sure not trying to do something which is hopeless. The problem occurs on HP-UX, OSF/1, SUPER-UX (NEC SX4/5) with G98 Rev. A9 but used to work with G94!!! Any comments or suggestions are very welcome Stefan Dr. Stefan Portmann Laboratory of Physical Chemistry ETH-Zurich Universitaetsstr. 65 CH-8092 Zurich Switzerland Phone: +41 (0) 1 632 57 82 Fax: +41 (0) 1 632 16 15 e-mail: portmann@igc.phys.chem.ethz.ch WWW: http://igc.ethz.ch/portmann/ From chemistry-request@server.ccl.net Fri Apr 6 10:52:39 2001 Received: from rzumail2.unizh.ch ([130.60.128.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f36EqdD05891 for ; Fri, 6 Apr 2001 10:52:39 -0400 Received: from zisgi.unizh.ch (zisgi.unizh.ch [130.60.19.17]) by rzumail2.unizh.ch (8.9.3/8.9.3/08) with ESMTP id RAA08908 for ; Fri, 6 Apr 2001 17:46:51 +0200 (MET DST) Date: Fri, 6 Apr 2001 17:46:51 +0200 From: "Dr. Peter Burger" To: CHEMISTRY@ccl.net Subject: CCL = G98 userlist Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, I do not want to upset anyone and I know how bad it is if one has a problem and how I appreciated all help I received previously from CCL. Nevertheless, it is more and more occuring to me that CCL is a G98 usergroup list. So I was wondering - isn't there any support provided by Gaussian? Are there no G98 usergroups? Best wishes Peter From chemistry-request@server.ccl.net Fri Apr 6 11:29:46 2001 Received: from hotmail.com ([64.4.17.80]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f36FTkD06299 for ; Fri, 6 Apr 2001 11:29:46 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Fri, 6 Apr 2001 09:20:58 -0700 Received: from 130.83.244.129 by lw11fd.law11.hotmail.msn.com with HTTP; Fri, 06 Apr 2001 16:20:58 GMT X-Originating-IP: [130.83.244.129] From: "Dr.H. Can" To: chemistry@ccl.net Subject: Natural Hybrid Orbitals Date: Fri, 06 Apr 2001 16:20:58 -0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 06 Apr 2001 16:20:58.0351 (UTC) FILETIME=[902B9FF0:01C0BEB5] Dear All, When I performed the NBO calculations by using Gaussian94, I obtained NHO(Natural Hybrid Orbitals) directionality and bond bending (deviations > from line of nulear center). What for can I use these deviation values? My second question is about the orbital interactinsas donor- acceptor interactions in NBO results. What is the meaning of high stabilization energy (E2)? All the suggestions and helps will be appriciated, thank you in advance. Regards, Hatice _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. From chemistry-request@server.ccl.net Fri Apr 6 13:15:55 2001 Received: from onsager.cop.uop.edu (IDENT:root@[138.9.50.194]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f36HFsD07497 for ; Fri, 6 Apr 2001 13:15:54 -0400 Received: (from mccallum@localhost) by onsager.cop.uop.edu (8.9.3/8.9.3) id KAA03181 for chemistry@ccl.net; Fri, 6 Apr 2001 10:09:31 -0700 Date: Fri, 6 Apr 2001 10:09:31 -0700 From: "C. Michael McCallum" To: chemistry@ccl.net Subject: creating a new residue in charmm Message-ID: <20010406100931.A3141@onsager.cop.uop.edu> Reply-To: "C. Michael McCallum" Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2i I am trying to prepare a .pdb file for charmm. This protein has a heme and ruthenium-bipy-his fragment ligands within it. I can prepare the heme part no problem, but the ru/bipy part is called 'CMB' in the .pdb file, and I'm not quite sure how to prepare it in order for charmm to generate a full .psf file. If it were defined in my top_all22_XXX.inp files, that would be no problem. I don't want to just guess at all the charges. Just how should I go about doing this so I may include this Ru complex in my protein? I'm not actually using CHARMm; I'm using NAMDs 'psfgen' to generate the imput files. I've attached the pertinent .pdb file. There is a ruthenium, two BIPYs and a HIS fragment. thanks, Mike McCallum --- HETATM 1842 RU1 CMB 143 -17.961 37.653 11.665 HETATM 1843 N11 CMB 143 -19.797 37.955 10.919 HETATM 1844 N11' CMB 143 -17.426 38.325 9.853 HETATM 1845 N12 CMB 143 -17.625 39.544 12.238 HETATM 1846 N12' CMB 143 -16.110 37.404 12.387 HETATM 1847 C21 CMB 143 -19.795 38.476 9.620 HETATM 1848 C31 CMB 143 -21.071 38.743 8.994 HETATM 1849 HC31 CMB 143 -21.133 39.126 8.051 HETATM 1850 C41 CMB 143 -22.264 38.457 9.729 HETATM 1851 HC41 CMB 143 -23.157 38.663 9.280 HETATM 1852 C51 CMB 143 -22.237 37.904 11.044 HETATM 1853 HC51 CMB 143 -23.089 37.695 11.564 HETATM 1854 C61 CMB 143 -20.963 37.644 11.629 HETATM 1855 HC61 CMB 143 -20.904 37.233 12.561 HETATM 1856 C21' CMB 143 -18.512 38.698 9.055 HETATM 1857 C31' CMB 143 -18.233 39.266 7.754 HETATM 1858 HC31 CMB 143 -18.983 39.570 7.133 HETATM 1859 C41' CMB 143 -16.869 39.397 7.346 HETATM 1860 HC41 CMB 143 -16.686 39.808 6.431 HETATM 1861 C51' CMB 143 -15.781 38.976 8.170 HETATM 1862 HC51 CMB 143 -14.809 39.062 7.874 HETATM 1863 C61' CMB 143 -16.091 38.420 9.444 HETATM 1864 HC61 CMB 143 -15.342 38.093 10.054 HETATM 1865 C22 CMB 143 -15.537 38.585 12.871 HETATM 1866 C32 CMB 143 -14.200 38.512 13.418 HETATM 1867 HC32 CMB 143 -13.723 39.341 13.772 HETATM 1868 C42 CMB 143 -13.547 37.241 13.456 HETATM 1869 HC42 CMB 143 -12.603 37.203 13.840 HETATM 1870 C52 CMB 143 -14.172 36.051 12.980 HETATM 1871 HC52 CMB 143 -13.706 35.145 13.019 HETATM 1872 C62 CMB 143 -15.485 36.154 12.439 HETATM 1873 HC62 CMB 143 -15.961 35.321 12.094 HETATM 1874 C22' CMB 143 -16.348 39.744 12.772 HETATM 1875 C32' CMB 143 -15.987 41.084 13.178 HETATM 1876 HC32 CMB 143 -15.066 41.295 13.562 HETATM 1877 C42' CMB 143 -16.956 42.126 13.031 HETATM 1878 HC42 CMB 143 -16.686 43.067 13.317 HETATM 1879 C52' CMB 143 -18.261 41.887 12.506 HETATM 1880 HC52 CMB 143 -18.952 42.631 12.407 HETATM 1881 C62' CMB 143 -18.585 40.557 12.114 HETATM 1882 HC62 CMB 143 -19.512 40.346 11.745 ATOM 1883 CB CMB 143 -19.026 35.143 16.494 ATOM 1884 HCB CMB 143 -19.984 35.024 16.754 ATOM 1885 HCB CMB 143 -18.672 34.284 16.125 ATOM 1886 HCB CMB 143 -18.492 35.405 17.298 ATOM 1887 CG CMB 143 -18.923 36.190 15.477 ATOM 1888 ND1 CMB 143 -19.301 37.461 15.623 ATOM 1889 HND1 CMB 143 -19.675 37.946 16.336 ATOM 1890 CD2 CMB 143 -18.419 36.023 14.196 ATOM 1891 HCD2 CMB 143 -18.018 35.218 13.715 ATOM 1892 CE1 CMB 143 -19.050 38.072 14.454 ATOM 1893 HCE1 CMB 143 -19.201 39.047 14.194 ATOM 1894 NE2 CMB 143 -18.528 37.206 13.556 -- C. Michael McCallum | "That may be one tough nut to crack, Associate Professor | but I am one determined Chemistry, UOP | little squirrel" mmccallum@uop.edu | (209) 946-2393 | fax (209) 946-2607 From chemistry-request@server.ccl.net Fri Apr 6 13:41:42 2001 Received: from smtp.popsite.net ([216.126.128.16]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f36HffD07665 for ; Fri, 6 Apr 2001 13:41:42 -0400 Received: from Hppav (09-121.008.popsite.net [198.173.195.121]) by smtp.popsite.net (Postfix) with SMTP id 7CB20FEA7; Fri, 6 Apr 2001 13:35:49 -0500 (CDT) Message-ID: <007d01c0bec8$69816c00$0100a8c0@icdc.com> From: "Jim Kress" To: "Dr. Peter Burger" Cc: "CCL" References: Subject: Re: CCL:CCL = G98 userlist Date: Fri, 6 Apr 2001 14:35:52 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 CCL provides information on many topics, not just Gaussian. However, having said that I should point out that Gaussian is notorious for its lack of support. Its documentation also is very poor, especially with respect to error messages. CCL is the only resource (that I know) that offers the users of Gaussian any hope of having their questions answered and problems resolved. Jim ----- Original Message ----- From: "Dr. Peter Burger" To: Sent: Friday, April 06, 2001 11:46 AM Subject: CCL:CCL = G98 userlist > Dear netters, > > I do not want to upset anyone and I know how bad > it is if one has a problem and how I appreciated all help > I received previously from CCL. > > Nevertheless, it is more and more occuring to me that CCL is a G98 > usergroup list. So I was wondering - isn't there any support provided by > Gaussian? Are there no G98 usergroups? > > Best wishes > > Peter > > > > -= 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 > > > > From chemistry-request@server.ccl.net Fri Apr 6 15:21:58 2001 Received: from onsager.cop.uop.edu (IDENT:root@[138.9.50.194]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f36JLwD07920 for ; Fri, 6 Apr 2001 15:21:58 -0400 Received: (from mccallum@localhost) by onsager.cop.uop.edu (8.9.3/8.9.3) id LAA03262 for chemistry@ccl.net; Fri, 6 Apr 2001 11:21:23 -0700 Date: Fri, 6 Apr 2001 11:21:22 -0700 From: "C. Michael McCallum" To: chemistry@ccl.net Subject: Re: CCL:creating a new residue in charmm Message-ID: <20010406112122.A3254@onsager.cop.uop.edu> Reply-To: "C. Michael McCallum" References: <20010406100931.A3141@onsager.cop.uop.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2i In-Reply-To: <20010406100931.A3141@onsager.cop.uop.edu>; from mmccallum@uop.edu on Fri, Apr 06, 2001 at 10:09:31AM -0700 * C. Michael McCallum (mmccallum@uop.edu) [010406 11:15]: > As a follow-up to this, I see this nice page: http://www.psc.edu/general/software/packages/charmm/tutorial/crowley/protein_index.html which includes: * Initial decisions and analysis (N.B. Read the pdb file carefully) * Titratable groups * Xray waters * Missing residues * bound ions and coordination complexes * Unknown ligands and odd residues ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Which looks like a discussion that I need, but only the first subject is linked. Cheers, Mike -- C. Michael McCallum | "That may be one tough nut to crack, Associate Professor | but I am one determined Chemistry, UOP | little squirrel" mmccallum@uop.edu | (209) 946-2393 | fax (209) 946-2607 From chemistry-request@server.ccl.net Fri Apr 6 16:09:57 2001 Received: from mail.rpi.edu (root@[128.113.22.40]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f36K9vD08365 for ; Fri, 6 Apr 2001 16:09:57 -0400 Received: from extreme.chem.rpi.edu (extreme.chem.rpi.edu [128.113.21.133]) by mail.rpi.edu (8.11.3/8.11.3) with ESMTP id f36K9vo113200; Fri, 6 Apr 2001 16:09:57 -0400 Received: (from nagams@localhost) by extreme.chem.rpi.edu (8.8.5/8.8.6) id QAA72376; Fri, 6 Apr 2001 16:09:56 -0400 (EDT) From: "N. Sukumar" Message-Id: <1010406160955.ZM74516@extreme.chem.rpi.edu> Date: Fri, 6 Apr 2001 16:09:55 -0400 In-Reply-To: shen Lingling "CCL:X-mailer: FoxMail 3.0 beta 2 [cn]" (Apr 5, 11:16am) References: <200104050324.LAA28697@mail.shcnc.ac.cn> X-Mailer: Z-Mail (4.0.1 13Jan97) To: shen Lingling , "chemistry@ccl.net " Subject: CHELPG charges for Br MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Lingling, You can use the ReadRadii keyword in the route card (in Gaussian) to specify radii to be read from the com file. Sample com file looks like this: #HF/... POP=(chelpg,ReadRadii) ... ... 53, 2.500000 This specifies that radius of Br is to be taken as 2.5 -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ / Dr. N. SUKUMAR / / Department of Chemistry / / Rensselaer Polytechnic Institute / / Troy, NY 12180-3590 / ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Fri Apr 6 13:02:45 2001 Received: from Mercury.acs.unt.edu ([129.120.220.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f36H2jD07420 for ; Fri, 6 Apr 2001 13:02:45 -0400 Received: from jove.acs.unt.edu (10759@jove.acs.unt.edu [129.120.220.41]) by Mercury.acs.unt.edu (8.8.8/8.8.8) with ESMTP id MAA05018 for ; Fri, 6 Apr 2001 12:56:57 -0500 (CDT) Received: from localhost (tdp0006@localhost) by jove.acs.unt.edu (8.8.8/8.8.8) with ESMTP id MAA25182 for ; Fri, 6 Apr 2001 12:56:56 -0500 (CDT) Date: Fri, 6 Apr 2001 12:56:56 -0500 (CDT) From: TREVOR D POWER To: CHEMISTRY@ccl.net Subject: Re: CCL:CCL = G98 userlist In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Peter, Yes, in fact the people at Gaussian, Inc. are very helpful. Those persons posting at ccl with a valid program license could alternatively just ask the folks at Gaussian. I have learned a great deal from reading questions and answers on the ccl (and I am sure this cuts down on quite a lot of simple questions directed to Gaussian, Inc). I have also noticed that Gaussian people answer questions here as well. I believe that the reason that so many questions are directed to Gaussian people reflects the popularity of this program amongst the ccl subscribers. David Power Dept. of Chemistry University of North Texas NT Station, Box 305070 Denton, Texas 76203-5070 tdp0006 On Fri, 6 Apr 2001, Dr. Peter Burger wrote: > Dear netters, > > I do not want to upset anyone and I know how bad > it is if one has a problem and how I appreciated all help > I received previously from CCL. > > Nevertheless, it is more and more occuring to me that CCL is a G98 > usergroup list. So I was wondering - isn't there any support provided by > Gaussian? Are there no G98 usergroups? > > Best wishes > > Peter > > > > -= 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 > > > > > > From chemistry-request@server.ccl.net Fri Apr 6 14:04:16 2001 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f36I4GD07798 for ; Fri, 6 Apr 2001 14:04:16 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id OAA12328; Fri, 6 Apr 2001 14:58:28 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Fri, 06 Apr 2001 13:58:06 -0400 (Eastern Daylight Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GBD00BDYWIH6Z@lvlmail.unitedcatalysts.com> for chemistry@ccl.net; Fri, 06 Apr 2001 14:54:17 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Fri, 06 Apr 2001 14:58:29 -0400 Content-return: allowed Date: Fri, 06 Apr 2001 14:58:24 -0400 From: "Shobe, Dave" Subject: RE: CCL = G98 userlist To: "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629DDAADF2@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) 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 f36I4GD07799 I am against splitting a Gaussian users' group off from CCL. Yes, it's probably the program that gets mentioned the most, but people also discuss here the use of Gamess, Molden, various molecular mechanics programs, etc. --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com -----Original Message----- From: Dr. Peter Burger [mailto:chburger@aci.unizh.ch] Sent: Friday, April 06, 2001 11:47 AM To: CHEMISTRY@ccl.net Subject: CCL:CCL = G98 userlist Dear netters, I do not want to upset anyone and I know how bad it is if one has a problem and how I appreciated all help I received previously from CCL. Nevertheless, it is more and more occuring to me that CCL is a G98 usergroup list. So I was wondering - isn't there any support provided by Gaussian? Are there no G98 usergroups? Best wishes Peter -= 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 From chemistry-request@server.ccl.net Fri Apr 6 13:29:16 2001 Received: from localhost.localdomain (IDENT:root@[132.248.33.226]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f36HTED07600 for ; Fri, 6 Apr 2001 13:29:15 -0400 Received: from correo.fc.uaem.mx (IDENT:max@garaged [127.0.0.1]) by localhost.localdomain (8.11.0/8.11.0) with ESMTP id f25IUCs30458 for ; Mon, 5 Mar 2001 12:30:15 -0600 Sender: max@localhost.localdomain Message-ID: <3AA3DB33.455DD4A8@correo.fc.uaem.mx> Date: Mon, 05 Mar 2001 12:30:11 -0600 From: maxvalde@servm.fc.uaem.mx X-Mailer: Mozilla 4.76 [en] (X11; U; Linux 2.2.16-22smp i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Questions about NWChem Content-Type: multipart/mixed; boundary="------------1337C78107FA18381DDB8D0F" This is a multi-part message in MIME format. --------------1337C78107FA18381DDB8D0F Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'rs Again, I have a couple of questions, we've been running some "real life" test with NWChem in a 20 nodes cluster connected by fast ethernet, and 2 problems have come from this: 1) In the MP2/cc-pvdz computation of a 36 atoms molecule we found a significant difference between Gaussian 98 and NWchem 2) In the computation of a 163 atoms at the HF/6-31G* level, we haven't been able to do any computation because always crashes with the next error : ------------------------------------------------------------------------ Arrgggghh 0 ------------------------------------------------------------------------ ------------------------------------------------------------------------ current input line : 183: task scf ------------------------------------------------------------------------ 0:0:Arrgggghh:: 0 -10001(s):armci_rcv_req: failed to receive header : 0 0: ARMCI aborting 0 (0). -10002(s):armci_rcv_req: failed to receive header : 0 2:Child process terminated prematurely, status=: 256 ************* Can anybody give us some help on this two issues?? Is there any signifficant difference between the MP2 methods of NWChem and Gaussian?? and what kind of problem are we facing with the communication of the nodes with the larger job ?? Thanks in advance ! Max --------------1337C78107FA18381DDB8D0F Content-Type: text/x-vcard; charset=us-ascii; name="maxvalde.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Content-Disposition: attachment; filename="maxvalde.vcf" begin:vcard n:Valdéz González;Max x-mozilla-html:TRUE org:FC-UAEM;CCF-UNAM adr:;;;;;; version:2.1 email;internet:maxvaldez@yahoo.com title:Estudiante x-mozilla-cpt:;640 fn:Max Valdéz González end:vcard --------------1337C78107FA18381DDB8D0F-- From chemistry-request@server.ccl.net Fri Apr 6 17:58:01 2001 Received: from lauca.usach.cl ([158.170.64.28]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f36LvxD09172 for ; Fri, 6 Apr 2001 17:58:00 -0400 Received: from lauca.usach.cl ([158.170.51.105]) by lauca.usach.cl (8.10.0.Beta12/8.10.0.Beta10) with ESMTP id f36LtoA24410 for ; Fri, 6 Apr 2001 17:55:50 -0400 (CST) Message-ID: <3ACE2E94.DC30257A@lauca.usach.cl> Date: Fri, 06 Apr 2001 17:01:08 -0400 From: Danilo Gonzalez X-Mailer: Mozilla 4.73 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Bilayer Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Folks! I'm working with a protein inserted in a bilayer. But when I try to optimize the bilayer, it calculation is too big for my computer,..so,... Anybody have this system optimized?,... I will appreciate if anybody give me the coordinate file (car, pdb, etc.) of a bilayer (DPPC, POPC, etc....). Thanks a lot! Danilo Gonzalez-Nilo Faculty of Chemistry and Biology University of Santiago of Chile. From chemistry-request@server.ccl.net Fri Apr 6 19:01:38 2001 Received: from jasper.uor.edu ([192.251.139.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f36N1aD09594 for ; Fri, 6 Apr 2001 19:01:36 -0400 Received: by jasper.uor.edu id QAA0000028172; Fri, 6 Apr 2001 16:08:49 -0700 (PDT) Message-ID: <3ACE4BF6.A8E0B7A6@uor.edu> Date: Fri, 06 Apr 2001 16:06:30 -0700 From: Barbara Murray Reply-To: bmurray@jasper.uor.edu Organization: University of Redlands X-Mailer: Mozilla 4.76 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 CC: CHEMISTRY@ccl.net Subject: Re: CCL = G98 userlist References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit In 1997 Andy Dustman created a gaussian userlist called G. I don't know whether it is still operational but it was mentioned on CCL at the end of May in '97. Never was very active. People would rather post to CCL I think. -- *********************************************************** Barbara Murray, Director bmurray@uor.edu Center for Science and Mathematics Phone: 909-793-2121 University of Redlands FAX: 909-793-2029 PO Box 3080, 1200 E. Colton Redlands, CA 92373-0999 From chemistry-request@server.ccl.net Fri Apr 6 19:08:09 2001 Received: from sunflare.ccs.yorku.ca ([130.63.236.128]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f36N89D09655 for ; Fri, 6 Apr 2001 19:08:09 -0400 Received: from curl.gkcl.yorku.ca (curl.gkcl.yorku.ca [130.63.232.224]) by sunflare.ccs.yorku.ca (8.9.3/8.9.3) with ESMTP id TAA18066 for ; Fri, 6 Apr 2001 19:08:08 -0400 (EDT) Received: (from chan@localhost) by curl.gkcl.yorku.ca (8.10.0/8.10.0) id f36N89R18243 for chemistry@ccl.net; Fri, 6 Apr 2001 19:08:09 -0400 (EDT) From: Wai-To Chan Message-Id: <200104062308.f36N89R18243@curl.gkcl.yorku.ca> Subject: Re: CCL:symmetry change To: chemistry@ccl.net Date: Fri, 6 Apr 2001 19:08:08 -0400 (EDT) X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit <<<<<<<<<<<<<<<<<< The following simple job dies as stated. I am using G98W A.9. Phillip has a H2O input file that also fails. I am curious if his also completes a complete iteration after the symmetry change is detected before crashing with x=2. >>>>>>>>>>>>>>>>>> I ran this job with an added keyword and got it completed with the symmetry advantage apparently retained. Here is the input file: -------------------------------------- # b3lyp/3-21g opt=verytight symmetry=loose h2o freq 0 1 ..... z-matrix snipped .... -------------------------------------- I did not use exactly the unrestricted method as you did but the reason your job crashed was the slight distortion from the Cs symmetry. In your case the initial geometry in your is actually C1. It also happened to me that in the course of DFT geometry optimization distortion from a Cs symmetry of the starting geometry to C1 could set in and abort the job. To get around this follow these steps: Lift the cartesian coordinates of the geometry from the last optimization step and edit it to a gaussian input format. Here are the coordinates taken from the aborted job starting > from your original job input 1 -0.813997 0.000001 -1.864364 7 -0.764606 0.000001 -0.863704 6 0.024411 0.000000 0.037382 8 0.770027 -0.000001 0.971039 You then zero all of the nearly-zero coordinates in the middle column to force the symmetry back to Cs from C1 and restart the job with or without the 'symmetry=loose' option. The option may not work for large distortion. Wai-To Chan From chemistry-request@server.ccl.net Fri Apr 6 20:22:23 2001 Received: from onsager.cop.uop.edu (IDENT:root@[138.9.50.194]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f370MND10113 for ; Fri, 6 Apr 2001 20:22:23 -0400 Received: (from mccallum@localhost) by onsager.cop.uop.edu (8.9.3/8.9.3) id QAA03653; Fri, 6 Apr 2001 16:21:29 -0700 Date: Fri, 6 Apr 2001 16:21:29 -0700 From: "C. Michael McCallum" To: Danilo Gonzalez , CCL List Subject: Re: CCL:Bilayer Message-ID: <20010406162129.A3647@onsager.cop.uop.edu> Reply-To: "C. Michael McCallum" References: <3ACE2E94.DC30257A@lauca.usach.cl> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2i In-Reply-To: <3ACE2E94.DC30257A@lauca.usach.cl>; from fgonzale@lauca.usach.cl on Fri, Apr 06, 2001 at 05:01:08PM -0400 * Danilo Gonzalez (fgonzale@lauca.usach.cl) [010406 15:41]: > Hi Folks! > > I'm working with a protein inserted in a bilayer. But when I try to > optimize the bilayer, it calculation is too big for my computer,..so,... > > Anybody have this system optimized?,... I will appreciate if anybody > give me the coordinate file (car, pdb, etc.) of a bilayer (DPPC, POPC, > etc....). > Do you have the time or the wherewithal to do it in chunks? Make a patch of bilayer, relax it, replicate it, make a hole, put in the protein, then "freeze" the outer portion of the bilayer? I think something like this was done in: Irailev, etc., Biophys. J. _77_, 1753 (1999) Hope this helps, --Mike > Thanks a lot! > > Danilo Gonzalez-Nilo > Faculty of Chemistry and Biology > University of Santiago of Chile. -- C. Michael McCallum | "That may be one tough nut to crack, Associate Professor | but I am one determined Chemistry, UOP | little squirrel" mmccallum@uop.edu | (209) 946-2393 | fax (209) 946-2607 From chemistry-request@server.ccl.net Fri Apr 6 20:35:40 2001 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f370ZdD10214 for ; Fri, 6 Apr 2001 20:35:39 -0400 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id UAA06230; Fri, 6 Apr 2001 20:27:50 -0400 (EDT) Date: Fri, 6 Apr 2001 20:27:50 -0400 From: Rick Venable To: "C. Michael McCallum" cc: chemistry@ccl.net Subject: Re: CCL:creating a new residue in charmm In-Reply-To: <20010406100931.A3141@onsager.cop.uop.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In large part because of the ruthenium, this is actually a fairly difficult problem. You will probably need to develop and test ligand bond parameters for Ru based on the binding geometry of the metal complex, as well as ab initio studies to determine the charges on Ru and nearby atoms. The methods used to develop CHARMM parameters are puplished, and you can find a fair number of key references at the URL http://www.pharmacy.umaryland.edu/~alex/research.html On Fri, 6 Apr 2001, C. Michael McCallum wrote: > I am trying to prepare a .pdb file for charmm. This protein has a > heme and ruthenium-bipy-his fragment ligands within it. I can > prepare the heme part no problem, but the ru/bipy part is called > 'CMB' in the .pdb file, and I'm not quite sure how to prepare it in > order for charmm to generate a full .psf file. If it were defined > in my top_all22_XXX.inp files, that would be no problem. I don't > want to just guess at all the charges. > > Just how should I go about doing this so I may include this Ru > complex in my protein? I'm not actually using CHARMm; I'm using > NAMDs 'psfgen' to generate the imput files. > > I've attached the pertinent .pdb file. There is a ruthenium, two > BIPYs and a HIS fragment. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@server.ccl.net Fri Apr 6 17:07:15 2001 Received: from narnia5.rutgers.edu ([165.230.180.170]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f36L7FD08830 for ; Fri, 6 Apr 2001 17:07:15 -0400 Received: from eden.rutgers.edu (molly.envsci.rutgers.edu [165.230.5.148]) by narnia5.rutgers.edu (8.8.8/8.8.8) with ESMTP id RAA11085 for ; Fri, 6 Apr 2001 17:07:15 -0400 (EDT) Message-ID: <3ACE30D4.28F04973@eden.rutgers.edu> Date: Fri, 06 Apr 2001 17:10:45 -0500 From: "Mary O'Connor" X-Mailer: Mozilla 4.08 [en] (Win98; I) MIME-Version: 1.0 To: chemistry@ccl.net Subject: re:Docking Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, again. Can anyone provide information on web based tutorials or good books in order to familiarize myself with docking molecules at receptors? Is this a subject that can be self-taught? Mary O'Connor Doctoral Candidate Rutgers University New Brunswick, NJ, 08903 From chemistry-request@server.ccl.net Fri Apr 6 18:16:12 2001 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f36MGBD09312 for ; Fri, 6 Apr 2001 18:16:11 -0400 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id SAA07394 for ; Fri, 6 Apr 2001 18:08:54 -0400 (EDT) Date: Fri, 6 Apr 2001 18:08:53 -0400 From: Rick Venable To: "'CCL'" Subject: Re: CCL:CCL = G98 userlist In-Reply-To: <157A51F55AAAD3119CD70008C7B1629DDAADF2@lvlxch01.unitedcatalysts.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII This topic has come up a couple of times before on CCL. I also feel the number of Gaussian specific questions and answers is too high for what is supposed to be a GENERAL discussion list, and not a Gaussian help desk. The main problems seem to be: (1) there isn't a good Gaussian mailing list already (2) product support for Gaussian is not very good I value the breadth of contributions to CCL as well, but don't see how that relates to whether or not there should be a specific Gaussian list. I happen to think a Gaussian specific list would be an excellent idea. IMHO, that would be the proper place to discuss nuances such as memory usage as a consequence of symmetry changes in G98. Attempts to create such a list in the past, however, haven't been very successful, which is why this topic has come up again. Fortunately, the message volume on CCL is reasonable, and it's easy to delete messages with G98 in the Subject: line with most mail programs. On Fri, 6 Apr 2001, Shobe, Dave wrote: > I am against splitting a Gaussian users' group off from CCL. Yes, > it's probably the program that gets mentioned the most, but people > also discuss here the use of Gamess, Molden, various molecular > mechanics programs, etc. > -----Original Message----- > From: Dr. Peter Burger [mailto:chburger@aci.unizh.ch] > Sent: Friday, April 06, 2001 11:47 AM > To: CHEMISTRY@ccl.net > Subject: CCL:CCL = G98 userlist > > I do not want to upset anyone and I know how bad > it is if one has a problem and how I appreciated all help > I received previously from CCL. > > Nevertheless, it is more and more occuring to me that CCL is a G98 > usergroup list. So I was wondering - isn't there any support provided by > Gaussian? Are there no G98 usergroups? =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@server.ccl.net Fri Apr 6 20:04:53 2001 Received: from web13405.mail.yahoo.com ([216.136.175.63]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f3704rD10017 for ; Fri, 6 Apr 2001 20:04:53 -0400 Message-ID: <20010407000453.66630.qmail@web13405.mail.yahoo.com> Received: from [169.232.140.246] by web13405.mail.yahoo.com; Fri, 06 Apr 2001 17:04:53 PDT Date: Fri, 6 Apr 2001 17:04:53 -0700 (PDT) From: eric hu Subject: question about molden To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi, all I wonder how to find converged geometries in g98 coordinate driving output with molden. Here is what I did. I click the button geom conv. and it shows three plots. One is the energy to points, then steps to points and force constant to points. i)However, by looking at the first plot, I can't identify the 26 converged geometries( accounted manully in g98 output) in the curve. ii)Which one represents the most possible transition state? iii)How to prove that one reaction is barrierless(not just limited to molden)? Thanks! Eric __________________________________________________ Do You Yahoo!? Get email at your own domain with Yahoo! Mail. http://personal.mail.yahoo.com/