From chemistry-request@server.ccl.net Wed Jul 7 03:35:36 1999 Received: from mgw1.merck.com (taz.merck.com [155.91.6.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA10084 for ; Wed, 7 Jul 1999 03:35:36 -0400 Message-Id: <199907070735.DAA10084@server.ccl.net> Date: Wed, 07 Jul 1999 03:31:05 -0400 From: "Mackey, Mark" Subject: Java molecule viewer To: "'chemistry@ccl.net'" MIME-version: 1.0 Content-type: text/plain Content-transfer-encoding: 7BIT Hi everyone. For various reasons I would like a Java applet for viewing molecules in 3D. My requirements are reasonably specific, and include the ability to display and independently rotate numerous molecules in the same window. I've looked around, and have yet to see anything that will fit my requirements off the shelf, so am left with the task of writing my own :). I'm not that good at Java yet, and would prefer to avoid reinventing the wheel. So, does anyone know if there is source code available for even a simple molecule viewer? For portability reasons I would prefer code that works with Java 1.1 or older: I've found a few molecule viewers (such as the publically-released viewer from Tripos) but these all seem to require the JDK 1.2 and Java3D extension. All help appreciated :) Mark Mackey. From chemistry-request@server.ccl.net Wed Jul 7 05:14:42 1999 Received: from alpha.luc.ac.be (alpha.luc.ac.be [193.190.2.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA11149 for ; Wed, 7 Jul 1999 05:14:42 -0400 Received: from sbg-ts (sbg-ts.luc.ac.be [193.190.1.15]) by alpha.luc.ac.be (8.9.3/8.9.3) with SMTP id LAA20603 for ; Wed, 7 Jul 1999 11:11:44 +0200 (MET DST) Date: Wed, 7 Jul 1999 11:11:44 +0200 (MET DST) Message-Id: <199907070911.LAA20603@alpha.luc.ac.be> X-Sender: skwasnie@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: sergiusz kwasniewski Subject: TD-RHF Hi all, I would like to ask you if anyone knows a reference for TD-RHF as implemented in Gaussian 98. The only references that I seem to find are for TD-DFT. I would like to know how the Excitation Energies are calculated in TD-RHF. Thanks in advance. Serge K. _________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 011/268315 fax : 011/268301 email : sergiusz.kwasniewski@luc.ac.be _________________________________________________ From chemistry-request@server.ccl.net Wed Jul 7 05:42:20 1999 Received: from matavnet.hu (matavnet.hu [145.236.224.246]) by server.ccl.net (8.8.7/8.8.7) with SMTP id FAA11545 for ; Wed, 7 Jul 1999 05:42:19 -0400 Received: (qmail 2898 invoked from network); 7 Jul 1999 11:37:05 +0200 Received: from line-209-160.dial.matav.net (HELO chemaxon.com) (145.236.209.160) by mail.matav.hu with SMTP; 7 Jul 1999 11:37:05 +0200 Message-ID: <37831FD3.15970C3@chemaxon.com> Date: Wed, 07 Jul 1999 11:37:23 +0200 From: Ferenc Csizmadia Organization: ChemAxon X-Mailer: Mozilla 4.51 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: "Mackey, Mark" CC: chemistry@ccl.net Subject: Re: CCL:Java molecule viewer References: <199907070735.DAA10084@server.ccl.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Mark, We have a product called Marvin that contains applets for drawing and viewing structures. (See http://www.chemaxon.com/products.html) It supports the display of numerous structures and works with all Java versions. Our policy doesn't allow to provide the source code, but since our company is interested in custom development, we would be glad to develop a product that meets your expectations. We are about to finish version 2 that has more support for 3D than the present version. It will also work with with all Java versions (Swing is also supported). It can be previewed at http://www.jchem.com/marvin/ . (Unfortunately the 3D example is not yet ready, but we are working on it) Regards, Ferenc -- Ferenc Csizmadia, Ph.D. Managing Director ChemAxon Ltd. Valyog u. 7, H-1032 Budapest, Hungary http://www.chemaxon.com T:+3620 9570988 Fax: +361 3875944 mailto:fcsiz@chemaxon.com "Mackey, Mark" wrote: > Hi everyone. > > For various reasons I would like a Java applet for viewing molecules in 3D. > My requirements are reasonably specific, and include the ability to display > and independently rotate numerous molecules in the same window. I've looked > around, and have yet to see anything that will fit my requirements off the > shelf, so am left with the task of writing my own :). I'm not that good at > Java yet, and would prefer to avoid reinventing the wheel. > > So, does anyone know if there is source code available for even a simple > molecule viewer? For portability reasons I would prefer code that works with > Java 1.1 or older: I've found a few molecule viewers (such as the > publically-released viewer from Tripos) but these all seem to require the > JDK 1.2 and Java3D extension. > > All help appreciated :) > > Mark Mackey. > > -= 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 Wed Jul 7 06:23:59 1999 Received: from mail.rwth-aachen.de (mail.RWTH-Aachen.DE [137.226.144.9]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA12098 for ; Wed, 7 Jul 1999 06:23:55 -0400 Received: from zosia (zosia.dorf.RWTH-Aachen.DE) by mail.rwth-aachen.de (PMDF V5.1-12 #D3869) with SMTP id <01JDA6TZM9M40005RA@mail.rwth-aachen.de> for chemistry@ccl.net; Wed, 7 Jul 1999 12:19:09 +0200 Date: Wed, 07 Jul 1999 12:18:29 +0200 From: Krzysztof Radacki Subject: Summary: isosurface X-Sender: kradacki@mail.rwth-aachen.de To: chemistry@ccl.net Message-id: <3.0.6.32.19990707121829.007debf0@mail.rwth-aachen.de> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Content-type: text/plain; charset="us-ascii" Hello all, below are answers that I received for my question: Can somebody sugest me free or working-demo program that can plot 3d-isosurfaces from discrete data (not just functions)? The best would be if I could choose value of F(x,y,z) that I want to plot. Martin Leboeuf --------------------- Look at VU : http://www.cerca.umontreal.ca/vu. It works with data and functions. "Tatyana E. Shubina" ---------------------------- What do you think about HyperChem 5.0? Fuad Abdallah -------------------- you could try to use vtk to produce the isosurface plots you are interested in. It has got many interesting features and interfaces to tcl/java/python/c++ but you would have to implement the application yourself because it is mainly a set of libraries. You can find more informations at http://www.kitware.com/vtk.html Another very interesting option would by IBM's dataexplorer. It has all the functionality you need, a brilliant graphical interface for constructing the visualization pipeline and it is free. You can find more information at http://www.research.ibm.com/dx/ Thorsten Klein --------------------- I think that gnuplot 3.7 is able to fit for this task. it is a lot of command-line working, but it generates very nice graphs and has a great data-parsing ability. http://ntfreeware.zdv.uni-tuebingen.de/NTSOFT/UG010017.htm#364 as a possible starting point. Lev Gorenstein ---------------------- Looks like gnuplot is what you need. Take a look at http://www.cs.dartmouth.edu/gnuplot_info.html. The program is _very_ powerful. If all you need is to plot the stuff from a data table (rather than an analytical expression), you could use the nice program PlotMTV (available for download from many places, e.g. http://aixpdslib.seas.ucla.edu/plot-tools/plotmtv4.html , see an overview at http://www.vis.colostate.edu/software/plotmtv/ ). In my work I use PlotMTV a lot with a separate program that generates the proper data file. "David F. Green" ----------------------- RLaB should be able to do what you want. It's a math program with strong matrix capabilities available under the GNU Public License (it's not really a Matlab clone, but alot of the syntax, etc. is Matlab-like, and it is a matrix-math program). You can find out more at the homepage: http://www.eskimo.com/~ians/rlab.html I run it under Linux, but it should be fine under any system running X. If you run KDE with Linux, there is also a new (functional but still being developed) extension available for the GUI. It's called KLab and can be found at: http://www.chaos.umd.edu/~dsweet/KDE/KLab/ I hope this helps. Ryszard Czerminski --------------------------- Try also http://root.cern.ch Richard Gillilan --------------------- Check out this web site: OpenDX.org Alexander Klinsky ------------------------- Search the net for DrawP3D ! I would like to thank for all answers. From my side I want to add ChemPlus (add-on for HyperChem) - it can produce molecular orbitals but use very easy to hack format (start-xyz, grid-size, grid-step and than valuse through awhole grid). One can insert his own values, which can have nothing to do with electron density of orbitals. regards Krzys Radacki _________________________---------------------------------------------------- ------------------------- e-mail: Krys.Radacki@ac.RWTH-Aachen.DE --- ---------------------------------------------------------------------------- - From chemistry-request@server.ccl.net Wed Jul 7 09:57:14 1999 Received: from mail.rwth-aachen.de (mail.RWTH-Aachen.DE [137.226.144.9]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA16294 for ; Wed, 7 Jul 1999 09:57:07 -0400 Received: from ac.rwth-aachen.de (pae102.ac.RWTH-Aachen.DE) by mail.rwth-aachen.de (PMDF V5.1-12 #D3869) with ESMTP id <01JDAEA71YBS0006WP@mail.rwth-aachen.de> for CHEMISTRY@ccl.net; Wed, 7 Jul 1999 15:52:16 +0200 Date: Wed, 07 Jul 1999 15:51:46 +0200 From: Krzysztof Radacki Subject: imagin frequency & TS search Sender: krzys@mail.rwth-aachen.de To: CCL Message-id: <37835B72.C55C38BF@ac.rwth-aachen.de> Organization: Inst. Inorg. Chem., RWTH Aachen, Germany MIME-version: 1.0 X-Mailer: Mozilla 4.51 [en] (X11; I; Linux 2.2.5-15 i586) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en HI all, I'm a little confused. Actualy I'm calculating reaction path where in last steo hydrogen is shifted between two borons: A & B. I found local Min(1) with hydrogen on A-atom (g9* log: SCF Done: E(RHF) = -106.086888589 A.U. after 14 cycles Low frequencies --- -18.2607 -5.9591 0.0007 0.0008 0.0009 3.7707 Low frequencies --- 132.6392 164.4866 455.8743) Transition state which points on it has hydroge a little shifted in direction of B-atom (log: SCF Done: E(UHF) = -106.086219321 A.U. after 13 cycles Low frequencies --- -233.5116 -8.0197 -3.0854 0.0006 0.0010 0.0010 Low frequencies --- 1.2505 325.0280 496.2008). Frequence -233.5 is conected to further shift of H in direction of B-atom. When from this TS(1) I started IRC calculation I got (what I suspected) in one direction Min(1) in other Min(2). For this second minimum Freq-part of log looks like: SCF Done: E(UHF) = -106.100979851 A.U. after 13 cycles Low frequencies --- -267.2175 -61.0431 -0.0010 -0.0008 0.0006 26.4452 Low frequencies --- 321.8358 344.4124 608.7472 so in vibrational part Gaussian writes that the lowest frequency of vibration is 321.8... Also here this freq=321 points further at translation of hydrogen. Because I don't specialy like rot.freq=-261 I started for Min(2) once more optimalization, trying both opt=tight and opt=verytight. results were very similar. What I got is geometry which has nothing to do with Min(2) but with end-product of this reaction Min(End). Coming to my confusion. I copied from log-file first six geometries found by SCF-steps and calculated freq.anal. Parts of first 3 logs are below: ======== Min(3) SCF Done: E(UHF) = -106.111693951 A.U. after 13 cycles ... Low frequencies --- -253.8169 -83.3521 -0.0005 0.0007 0.0008 46.3181 Low frequencies --- 193.3072 346.7127 448.5709 Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering activities (A**4/AMU), Raman depolarization ratios, reduced masses (AMU), force constants (mDyne/A) and normal coordinates: 1 2 3 A' A" A' Frequencies -- 185.2393 344.2092 448.2177 ======== Min(4) SCF Done: E(UHF) = -106.120239108 A.U. after 13 cycles ... Low frequencies --- -425.0755 -179.1839 -99.7147 -0.0009 -0.0008 -0.0008 Low frequencies --- 139.1175 299.3142 484.2108 Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering activities (A**4/AMU), Raman depolarization ratios, reduced masses (AMU), force constants (mDyne/A) and normal coordinates: 1 2 3 A' A" A" Frequencies -- 40.5275 287.4488 473.4673 ======== Min(5) SCF Done: E(UHF) = -106.123411791 A.U. after 13 cycles ... Low frequencies --- -205.9984 -65.3112 -0.0004 0.0005 0.0007 78.8174 Low frequencies --- 288.0438 323.8774 433.4241 Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering activities (A**4/AMU), Raman depolarization ratios, reduced masses (AMU), force constants (mDyne/A) and normal coordinates: 1 2 3 A' A" A" Frequencies -- 287.1555 299.3749 431.4945 ========= As one can see both Min(1) and TS(1) have nearly the same energy however difference in geometry is quite big. What is funny is that this some points that I found through reoptimalization of Min(2) (I labeled them Min(3)--Min(5)), however they have very big forces, are found to be minima with frequence analysis. What I disslike is that they have quite low rotational frequence. Also what I realy disslike that I can't realy find any TS which leads from Min(2) to Min(End). Even if I found such geometry that freq.analysis shows one negative frequency connected to shift of hydrogen I'm fninishing in both forward & reverse direction in Min(End). What I thing is that gradient of energy between Min(2) and Min(End) can be to small to find it with freq.analysis. Another idea I want to try is changing level of theory to higher but I realy appreciate any comments and advices. Regards Krzysztof Radacki From chemistry-request@server.ccl.net Tue Jul 6 16:31:03 1999 Received: from mail.chat.ru (gnu.chat.ru [212.24.32.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA03689 for ; Tue, 6 Jul 1999 16:30:26 -0400 Received: from [62.76.11.197] (helo=chat.ru) by mail.chat.ru with smtp (Exim 2.12 #3) id 111bn4-000OEZ-00 for CHEMISTRY@ccl.net; Wed, 7 Jul 1999 00:26:09 +0400 Date: Wed, 7 Jul 1999 02:24:33 +0500 From: "Qadir K. Timerghazin" X-Mailer: The Bat! (v1.036) S/N B2B97075 Reply-To: "Qadir K. Timerghazin" Priority: Normal Message-ID: <0100.990707@chat.ru> To: CHEMISTRY@ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, Using G98w I often get such error during hi-level calcualtions (MP4, QCISD(T), etc.): Erroneous write. write -1 instead of 50250000. fd = 2 writwa What's is this? How to fix this problem? Best regards, Qadir Timerghazin mailto:qt@chat.ru From chemistry-request@server.ccl.net Wed Jul 7 03:48:18 1999 Received: from mserv.rug.ac.be (mserv.rug.ac.be [157.193.40.37]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA10211 for ; Wed, 7 Jul 1999 03:48:17 -0400 Received: from allserv.rug.ac.be (allserv.rug.ac.be [157.193.40.42]) by mserv.rug.ac.be (8.9.0/8.9.0) with ESMTP id JAA07691; Wed, 7 Jul 1999 09:43:09 +0200 (MET DST) Received: from houston (houston.rug.ac.be [157.193.89.160]) by allserv.rug.ac.be (8.9.0/8.9.0) with SMTP id JAA09300; Wed, 7 Jul 1999 09:43:07 +0200 (MET DST) Received: by localhost with Microsoft MAPI; Wed, 7 Jul 1999 09:43:23 +0200 Message-ID: <01BEC85D.2762C250.jeanluc.verschelde@rug.ac.be> From: Administrator To: "'cytoskel@listbot.com'" , "'chemistry@ccl.net'" Subject: functional domains Date: Wed, 7 Jul 1999 09:43:21 +0200 X-Mailer: Microsoft Internet E-mail/MAPI - 8.0.0.4211 Encoding: 17 TEXT Dear all, I am looking for a review or other source of information on functional domains like WW, PH ,SH3, C2 and PDZ. I appreciate your help. ------------------------------------------------------------------------------------------------------------------- Verschelde Jean-Luc Department of Medical Protein Research (VIB 09) and Department of Biochemistry, Faculty of Medicine, University Ghent, K.L. Ledeganckstraat 35 Ghent. Tel. 32 (9) 2645306 Fax. 32 (9) 2645279 E-mail: jeanluc.verschelde@rug.ac.be ---------------------------------------------------- From chemistry-request@server.ccl.net Wed Jul 7 11:34:57 1999 Received: from sirio.cineca.it (sirio.cineca.it [193.204.121.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA17998 for ; Wed, 7 Jul 1999 11:34:55 -0400 Received: (from abc0@localhost) by sirio.cineca.it (8.8.5/8.7) id RAA12488; Wed, 7 Jul 1999 17:32:39 +0200 (MDT) Date: Wed, 7 Jul 1999 17:32:39 +0200 (MDT) From: Sigismondo Boschi Reply-To: Sigismondo Boschi To: "Qadir K. Timerghazin" cc: CHEMISTRY@ccl.net Subject: Erroneous write. write -1 instead of 50250000 In-Reply-To: <0100.990707@chat.ru> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, I have got some similar errors with g98 (A6) on an IBM SP Power3, compiled with compiler version xlf 5.1. Is it an error due to the impossibility of writing some files, or is it a gaussian error? I'm recompiling g98 (A7) with the new compiler, in order to see it changes something. Thanks in advance. kind regards Sigismondo Boschi -------------------------- ------------------------- -------------------- | | http://incm.cineca.it | | | ------------ ------------ | |Sigismondo Boschi |tel: +39 051 6171559 | |CINECA (High Performance Systems) |fax: +39 051 6132198 | |via Magnanelli, 6/3 |e-mail: s.boschi@cineca.it | |40033 Casalecchio di Reno (BO)-ITALY | | --------------------------------------- --------------------------------- On Wed, 7 Jul 1999, Qadir K. Timerghazin wrote: > Dear CCLers, > > Using G98w I often get such error during hi-level calcualtions (MP4, > QCISD(T), etc.): > > Erroneous write. write -1 instead of 50250000. > fd = 2 > writwa > > What's is this? How to fix this problem? > > > Best regards, > Qadir Timerghazin mailto:qt@chat.ru > From chemistry-request@server.ccl.net Wed Jul 7 13:05:37 1999 Received: from ce.fis.unam.mx (ce.fis.unam.mx [132.248.33.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA19257 for ; Wed, 7 Jul 1999 13:05:34 -0400 Received: from ce.fis.unam.mx ([132.248.33.121]) by ce.fis.unam.mx with ESMTP (8.7.1/8.7.1) id LAA28619; Wed, 7 Jul 1999 11:57:52 -0700 (PDT) Message-ID: <3783951E.150C8E6E@ce.fis.unam.mx> Date: Wed, 07 Jul 1999 11:57:51 -0600 From: Max Valdez Organization: Centro de Ciencias Fisicas, UNAM X-Mailer: Mozilla 4.6 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: Sigismondo Boschi , CHEMISTRY@ccl.net Subject: Re: CCL:Erroneous write. write -1 instead of 50250000 References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi everybody That kind of error is due because the disc has no more space to write on it. Make sure you will have enough space before you send that kind of calculation (or when the molecule is too large). i had the same problem a few days ago. I hope this helps Waves Max Sigismondo Boschi wrote: > Hi all, > > I have got some similar errors with g98 (A6) on an IBM SP Power3, > compiled with compiler version xlf 5.1. Is it an error due to the > impossibility of writing some files, or is it a gaussian error? > > I'm recompiling g98 (A7) with the new compiler, in order to see it changes > something. > > Thanks in advance. > > kind regards > > Sigismondo Boschi > > -------------------------- ------------------------- -------------------- > | | http://incm.cineca.it | | > | ------------ ------------ | > |Sigismondo Boschi |tel: +39 051 6171559 | > |CINECA (High Performance Systems) |fax: +39 051 6132198 | > |via Magnanelli, 6/3 |e-mail: s.boschi@cineca.it | > |40033 Casalecchio di Reno (BO)-ITALY | | > --------------------------------------- --------------------------------- > > On Wed, 7 Jul 1999, Qadir K. Timerghazin wrote: > > > Dear CCLers, > > > > Using G98w I often get such error during hi-level calcualtions (MP4, > > QCISD(T), etc.): > > > > Erroneous write. write -1 instead of 50250000. > > fd = 2 > > writwa > > > > What's is this? How to fix this problem? > > > > > > Best regards, > > Qadir Timerghazin mailto:qt@chat.ru > > > > -= 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 Wed Jul 7 14:38:55 1999 Received: from dedalus.lcc.ufmg.br (dedalus.lcc.ufmg.br [150.164.65.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA20600 for ; Wed, 7 Jul 1999 14:38:53 -0400 Received: from localhost (rkrocha@localhost) by dedalus.lcc.ufmg.br (8.9.3/8.9.3) with SMTP id PAA17518 for ; Wed, 7 Jul 1999 15:33:22 -0300 Date: Wed, 7 Jul 1999 15:33:22 -0300 (BSC) From: ramon kleber da rocha To: Computational Chemistry Mailing List Subject: Problems with Autodock 3.0 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers I am a new user of AutoDock 3.0 and I found some problems to get start it. The first one concern to my receptor, it is DNA molecule. When I run addsol, it gaves me a .pdbqs file with the last two coluns filled by ZEROS. It seems that addsol dont know the residues in DNA molecule. In fact, sol_par.dat file dont have any parameter for DNA atoms. I tried to follow the Methology described in AutoDock User Guide and when I run mkgpf3, it returns the following error message: ________________________________________________________________________________ mkgpf3 Version 3.0 (C) 1996, Garrett Morris, TSRI. Ligand = "berenil.pdbq", Macromolecule = "dna.pdbqs". Making "dna.gpf", based on the atom types found in "berenil.pdbq" gpf3gen[19]: /usr/bin/nawk: arg list too long /gridcenter - Out of range Cannot open xx02: No such file or directory Completed making grid parameter file: "dna.gpf" ________________________________________________________________________________ I dont know if that problem is because the lacks of solvation parameters or not. Please, could anybody help me? Best regards. Ramon ________________________________________________________________________________ Ramon Kleberda Rocha, MSc. VOICE +55-31-499-5765 e-mail rkrocha@dedalus.lcc.ufmg.br FAX +55-31-499-5700 Laboratorio de QSAR e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal - NEQUIM - http://www.qui.ufmg.br/~nequim Departamento de Quimica - Instituto de Ciencias Exatas Universidade Federal de Minas Gerais Av. Presidente Antonio Carlos, 6627 Campus Pampulha CEP 31-270-901 - Belo Horizonte - Minas Gerais - Brasil ________________________________________________________________________________ From chemistry-request@server.ccl.net Wed Jul 7 14:47:21 1999 Received: from ccshst09.cs.uoguelph.ca (ccshst09.cs.uoguelph.ca [131.104.96.18]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA20895 for ; Wed, 7 Jul 1999 14:47:21 -0400 Received: from ccshst01 (ccshst01.cs.uoguelph.ca [131.104.96.14]) by ccshst09.cs.uoguelph.ca (8.8.6 (PHNE_17135)/8.8.6) with SMTP id OAA17500; Wed, 7 Jul 1999 14:40:34 -0400 (EDT) Date: Wed, 7 Jul 1999 14:40:34 -0400 (EDT) From: WeiQuan Tian X-Sender: wtian@ccshst01 To: Max Valdez cc: Sigismondo Boschi , CHEMISTRY@ccl.net Subject: Re: CCL:Erroneous write. write -1 instead of 50250000 In-Reply-To: <3783951E.150C8E6E@ce.fis.unam.mx> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Maybe it is not only the problem for disk space. I did a calculation C26H12O with 6-31G* by BLYP. I have 2 GB disk space for scratch file and I am sure that this calculation doesn't need more than 2GB disk space. However the job stopped at l1002 for the frequency calculation. So I guess it is due to memory, however, I have 128MB memory in PII350 and I included 120MB for the calculation. I was confused with this error. As in fact I met the similar problem with UNIX, while I can't remember how I solved such a problem. Wei Quan Tian Univ. of GUelph Canada On Wed, 7 Jul 1999, Max Valdez wrote: > Hi everybody > That kind of error is due because the disc has no more space to write on it. > Make sure you will have enough space before you send that kind of calculation (or > when the molecule is too large). i had the same problem a few days ago. > > I hope this helps > Waves > Max > > Sigismondo Boschi wrote: > > > Hi all, > > > > I have got some similar errors with g98 (A6) on an IBM SP Power3, > > compiled with compiler version xlf 5.1. Is it an error due to the > > impossibility of writing some files, or is it a gaussian error? > > > > I'm recompiling g98 (A7) with the new compiler, in order to see it changes > > something. > > > > Thanks in advance. > > > > kind regards > > > > Sigismondo Boschi > > > > -------------------------- ------------------------- -------------------- > > | | http://incm.cineca.it | | > > | ------------ ------------ | > > |Sigismondo Boschi |tel: +39 051 6171559 | > > |CINECA (High Performance Systems) |fax: +39 051 6132198 | > > |via Magnanelli, 6/3 |e-mail: s.boschi@cineca.it | > > |40033 Casalecchio di Reno (BO)-ITALY | | > > --------------------------------------- --------------------------------- > > > > On Wed, 7 Jul 1999, Qadir K. Timerghazin wrote: > > > > > Dear CCLers, > > > > > > Using G98w I often get such error during hi-level calcualtions (MP4, > > > QCISD(T), etc.): > > > > > > Erroneous write. write -1 instead of 50250000. > > > fd = 2 > > > writwa > > > > > > What's is this? How to fix this problem? > > > > > > > > > Best regards, > > > Qadir Timerghazin mailto:qt@chat.ru > > > > > > > > -= 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 Wed Jul 7 17:19:13 1999 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA22985 for ; Wed, 7 Jul 1999 17:19:13 -0400 Received: from elvis.scripps.edu (elvis.scripps.edu [137.131.130.25]) by relay1.scripps.edu (8.9.3/TSRI-3.0.2r) with ESMTP id OAA02444 for ; Wed, 7 Jul 1999 14:13:56 -0700 (PDT) Received: from scripps.edu (localhost [127.0.0.1]) by elvis.scripps.edu (8.9.2/TSRI-3.0) with ESMTP id OAA19784 for ; Wed, 7 Jul 1999 14:13:56 -0700 (PDT) Sender: yadavm@scripps.edu Message-ID: <3783C313.E4EA18DF@scripps.edu> Date: Wed, 07 Jul 1999 14:13:55 -0700 From: Maneesh Yadav X-Mailer: Mozilla 4.07C-SGI [en] (X11; I; IRIX64 6.5 IP30) MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: SDF->MOL2 via Babel? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Has anyone here been succesfful in converting an SDF format database to a mol2 database using babel? I use the keywords 'all' and it just tells me that my database doesn't contain any compunds..any help would be appreciated; I can't seem to reach the babel team.. P.S. There are tools that come with DOCK4.0, but I don't have SYBL (which is required by them), so an alternate solution would be nice. From chemistry-request@server.ccl.net Wed Jul 7 18:06:21 1999 Received: from cosmos.cosm.sc.edu (cosmos.cosm.sc.edu [129.252.40.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA23420 for ; Wed, 7 Jul 1999 18:06:21 -0400 Received: from localhost (jorge@localhost) by cosmos.cosm.sc.edu (8.9.3/8.9.3) with SMTP id SAA19296 for ; Wed, 7 Jul 1999 18:01:05 -0400 (EDT) Date: Wed, 7 Jul 1999 18:01:04 -0400 (EDT) From: Jorge Seminario To: chemistry@ccl.net Subject: gold vapor on hydrocarbons Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Can anyone provide information about gold vapor deposited on hydrocarbons like CH4, C2H6, C2H4, C2H2, and especially on benzene. The question is how the gold atoms would combine with the hydrocarbon atoms. Any pointers to theoretical or experimental studies is appreciated. Please send replies to me or to CCL. I will summarize. -------------------------------------------- Jorge M. Seminario Department of Chemistry and Biochemistry University of South Carolina Columbia, South Carolina 29208 Tel: 803-777-9567 Fax: 803-777-9521 email: jorge@psc.sc.edu jorge@cosmos.cosm.sc.edu --------------------------------------------