From S.M.Todd@chem.hull.ac.uk Mon Apr 28 09:39:17 1997 Received: from lehar.ucc.hull.ac.uk for S.M.Todd@chem.hull.ac.uk by www.ccl.net (8.8.3/950822.1) id JAA14618; Mon, 28 Apr 1997 09:36:01 -0400 (EDT) Received: from chopin.ucc.hull.ac.uk by lehar.ucc.hull.ac.uk with ESMTP; Mon, 28 Apr 1997 14:21:58 +0100 Received: from mailhub1-remote.hull.ac.uk by mailhub1.hull.ac.uk id ; Mon, 28 Apr 1997 14:21:00 +0100 Date: Mon, 28 Apr 1997 14:20:54 +0100 (BST) From: Vagabond X-Sender: chpsmt@humus1 Reply-To: S.M.Todd@chem.hull.ac.uk To: CHEMISTRY@www.ccl.net Subject: geometry information on flexible systems Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: S.M.Todd@chem.hull.ac.uk Hi there... I'm trying to find a package which will give me measurements of the dipole moment in terms of magnitude and position. I would also like to be able to calculate the centre of mass. The package would preferably run under a PC based windows environment but could also be run under SGI at a push and it would also be free/shareware. Does anyone know of any such packages. Thanks in advance mail to : S.M.Todd@chem.hull.ac.uk web-site: http://www.hull.ac.uk/php/chpsmt/ From panc@isc.kyushu-u.ac.jp Mon Apr 28 10:39:17 1997 Received: from ryugaku.isc.kyushu-u.ac.jp for panc@isc.kyushu-u.ac.jp by www.ccl.net (8.8.3/950822.1) id JAA14606; Mon, 28 Apr 1997 09:33:26 -0400 (EDT) Received: from [133.5.200.108] (pestic6.ach.agr.kyushu-u.ac.jp [133.5.200.108]) by ryugaku.isc.kyushu-u.ac.jp (8.7.5/3.4W4) with SMTP id WAA19400 for ; Mon, 28 Apr 1997 22:34:46 +0900 (JST) Message-Id: <199704281334.WAA19400@ryugaku.isc.kyushu-u.ac.jp> Date: Mon, 28 Apr 1997 22:34:38 +0900 To: CHEMISTRY@www.ccl.net From: panc@isc.kyushu-u.ac.jp (Canping Pan) Subject: help ClogP calculating MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Hi there, Please help with some ClogP calculating problem. When I use ClogP to calculate some compounds, I missed some fragment parameters. Now what and how can I do in order to make it usable? My error messages got are as follows: ---------------------------------- FRAGMENT | # 1 | --> ZNC(=NA)SA |MISSING | .000 FRAGMENT | # 2 | --> ANC(OA)=Na |MISSING | .000 FRAGMENT | # 2 | --> ZNC(=NA)OA |MISSING | .000　 (smiles for example: COc1ccccc1CNC2=NCCO2) Thanks for your help! -- Canping Pan E-mail: pan_canp@agr.kyushu-u.ac.jp Tel: 092-642-2858(O) Fax: 092-642-2864 http://133.5.200.42/pan.html Department of Agricultural Chemistry Faculty of Agriculture Kyushu University　46-02 Fukuoka 812 Japan From kamal@pharmaco.rvh.mcgill.ca Mon Apr 28 11:39:19 1997 Received: from pharmaco.rvh.mcgill.ca for kamal@pharmaco.rvh.mcgill.ca by www.ccl.net (8.8.3/950822.1) id LAA15530; Mon, 28 Apr 1997 11:37:38 -0400 (EDT) Received: from pharmaco.RVH.McGill.CA by pharmaco.rvh.mcgill.ca (AIX 3.2/UCB 5.64/4.03) id AA10045; Mon, 28 Apr 1997 11:36:47 -0400 Sender: kamal@pharmaco.rvh.mcgill.ca Message-Id: <3364C40E.167E@pharmaco.rvh.mcgill.ca> Date: Mon, 28 Apr 1997 11:36:46 -0400 From: kamal Azzaoui Organization: McGill University X-Mailer: Mozilla 3.01Gold (X11; I; AIX 2) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: Dipole moment Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi everyone I would like to display the dipole moment calculated from Mopac for a set of structures. My question is about the origin of the dipole vector, is the origin fits the centre of mass ? How can I display only the X axis dipole ? Thank you for your help please email me directly to kamal@pharmaco.rvh.mcgill.ca i'll send a summary to the list as soon as possible Regards Kamal -- _____________________________________________________________ Kamal Azzaoui, Ph.D. McGill University Oncology. Dept., Pharmacokinetics. Div. Royal Victoria Hospital 687, Pine Ave., Room M7.19 Montreal, Quebec, Canada H3A2 1A1 Tel:(514) 842-1231 ext 5841 Fax:(514) 843-1475 Email: kamal@pharmaco.rvh.mcgill ##### |\^/| ##### ##### _|\| |/|_ ##### ##### > < ##### ##### >_./|\._< ##### | ______________________________________________________________ From njh@gallium.lanl.gov Mon Apr 28 20:39:24 1997 Received: from t12mail.lanl.gov for njh@gallium.lanl.gov by www.ccl.net (8.8.3/950822.1) id UAA23936; Mon, 28 Apr 1997 20:18:43 -0400 (EDT) Received: from gallium.lanl.gov (gallium.lanl.gov [128.165.22.31]) by t12mail.lanl.gov (8.7.6/8.7.3) with SMTP id SAA02194 for <@t12mail.lanl.gov:chemistry@www.ccl.net>; Mon, 28 Apr 1997 18:18:10 -0600 (MDT) Received: (from njh@localhost) by gallium.lanl.gov (950413.SGI.8.6.12/950213.SGI.AUTOCF) id SAA26118; Mon, 28 Apr 1997 18:18:10 -0600 Date: Mon, 28 Apr 1997 18:18:10 -0600 Message-Id: <199704290018.SAA26118@gallium.lanl.gov> From: "Neil Henson (T-12)" MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit To: chemistry@www.ccl.net Subject: Running Gaussian94 on the SGI O2 workstation X-Mailer: VM 6.22 under 19.15 XEmacs Lucid Reply-To: neil.henson@lanl.gov X-Face: $4IP`G9kA83R@n!ACoX\Owysl'WE%1~E4+xTnBe}7Fw'tn4*CSUlL8s$6zL(yq^w^c0z 1kT6{O&H?aT}%:IoDtw%THW'^5AS%+BL+:Jy`M:U0%"K3pfJ0x\gR$*tZUMy.6?=)yd6)sNeorV.eW ZEQv!atR*k|x@9jAI{`)bz!?7?-c*J9md6?hKAZoKmm2i/K+5|o%~OxfrV]D8cwZ!0V|PZmSLW*~Y3 a~Set.Qenk"[]6#2e=eQ*1$Uf99DF&N%Gh2GclO3fD%pg[$Ass)d3SdIB* Dear all, I am having some problems in running Gaussian94 on an SGI O2 workstation and I am hoping that someone on the list may have some useful experiences to share. Here are some details. I can compile the program OK on an SGI Indy and then use that executable on the O2. The jobs run fine, but are rather slow as you might expect. The solution is of course to compile the program natively on the O2, and it is at this stage that I have problems. The compilation completes successfully, but :- (i) some jobs fail in link401 to correct project the guess (for example, here is an exercept from the output file :- >The smallest eigenvalue of the overlap matrix is 1.876D-04 >Leave Link 302 at Tue Apr 22 15:46:38 1997, MaxMem= 2000000 cpu: 16.7 >(Enter /usr/local/lib/g94_revE_ip32/g94/l303.exe) >DipDrv: MaxL=1. >Leave Link 303 at Tue Apr 22 15:46:41 1997, MaxMem= 2000000 cpu: 1.6 >(Enter /usr/local/lib/g94_revE_ip32/g94/l401.exe) >Projected INDO Guess. >Unable to project full set of read-in orbitals. >Projecting just the 66 occupied ones. >Unable to project read-in occupied orbitals. >Error termination via Lnk1e in /usr/local/lib/g94_revE_ip32/g94/l401.exe. >Job cpu time: 0 days 0 hours 0 minutes 33.4 seconds. >File lengths (MBytes): RWF= 10 Int= 0 D2E= 0 Chk= 1 Scr= 1 (ii) some jobs do work, but they seem to run *slower* with the natively compiled version than with the plain Indy executable. I haven't spent too long looking into this since most of the runs that I am interested are of type (i). The O2 has the second release of Irix 6.3 installed with the 7.1 release of the MIPS FORTRAN compiler. All the current SGI recommended patches to the operating system and the compilers have also been installed (1725,1759,1773,1791,1839,1932,1721,1775,1788,1816,1916,1949). Gaussian are looking into the problem, but I thought I would see if anyone else is having similar difficulties also. Thanks in advance, Neil. -- * Neil Henson Hartlepool Renaissance: a marina, * * neil.henson@lanl.gov a hung monkey and much much more * * http://www.t12.lanl.gov/~njh Tel: 505-667-7795 Fax: 505-665-3909 * * Group T-12, Mail Stop B268, Los Alamos National Laboratory, NM 87545, USA *