From chemistry-request@server.ccl.net Thu Jul 15 03:44:48 1999 Received: from modeling.farma.unige.it (modeling.farma.unige.it [130.251.75.66]) by server.ccl.net (8.8.7/8.8.7) with SMTP id DAA26837 for ; Thu, 15 Jul 1999 03:44:46 -0400 Received: (from lopresti@localhost) by modeling.farma.unige.it (940816.SGI.8.6.9/950213.SGI.AUTOCF) id JAA21355 for chemistry@www.ccl.net; Thu, 15 Jul 1999 09:35:56 +0200 From: "lo presti eleonora" Message-Id: <9907150935.ZM21353@modeling.farma.unige.it> Date: Thu, 15 Jul 1999 09:35:50 -0600 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: chemistry@server.ccl.net Subject: CCL: MonteCarlo search Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers, I am working with a set of flexible molecules containing a ciclopentyloxy residue and I am getting thousands of conformers from MonteCarlo search. By cluster analysis these conformers are grouped in two or three big families instead of being uniformely grouped. Is this something that could happen with very flexible molecules? Shall I take into consideration only the lead of the most populated groups or all conformers selected by cluster analysis? Thank you very much for your answers, -- ******************************************************************* Dr. Eleonora Lo Presti PhD-Student Dip. Scienze Farmaceutiche - Facolta' di Farmacia Universita' di Genova - Viale Benedetto XV, 3 - 16145 Genova Italy lopresti@modeling.farma.unige.it ******************************************************************* From chemistry-request@server.ccl.net Thu Jul 15 04:37:43 1999 Received: from pump2.york.ac.uk (pump2.york.ac.uk [144.32.128.12]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA27747 for ; Thu, 15 Jul 1999 04:37:30 -0400 Received: from mailer.york.ac.uk (mailer.york.ac.uk [144.32.128.96]) by pump2.york.ac.uk (8.8.7/8.8.7) with SMTP id JAA22413 for ; Thu, 15 Jul 1999 09:05:50 +0100 (BST) Date: Thu, 15 Jul 1999 09:06:02 +0100 (BST) From: "M.Reinhold" To: chemistry newsgroup Subject: ADF under Linux Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCl'ers, I am currently running ADF calculations on a Linux platform (PII, 350MHZ). Ever so often calculations stop with a 'memory fault' message or similar. Things seem to have improved since I switched to ADF 1999 and applied using the memoryusage key. Still, a lot of jobs abort. Looking with xosview on the memory usage on my PC it looks like the memory is not completely given back, after one job has finished. Has anybody experienced similar problems or can offer some help? Many thanks in advance, Meike Reinhold P.S. Same jobs on similar PC, but 450 MHZ = no problemo reply to: mr113@york.ac.uk M. Reinhold Chemistry Department University of York room B013 From chemistry-request@server.ccl.net Thu Jul 15 04:52:00 1999 Received: from stark.udg.es (stark.udg.es [130.206.128.61]) by server.ccl.net (8.8.7/8.8.7) with SMTP id EAA27988 for ; Thu, 15 Jul 1999 04:51:55 -0400 Received: from stark.udg.es (akenaton.udg.es [130.206.128.125]) by stark.udg.es (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id KAA16810 for ; Thu, 15 Jul 1999 10:48:05 -0200 Message-ID: <378DA103.4404DBD7@stark.udg.es> Date: Thu, 15 Jul 1999 10:51:15 +0200 From: Emili =?iso-8859-1?Q?Besal=FA?= Organization: IQC-UdG X-Mailer: Mozilla 4.51 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Hosoya's Z Index computation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all! I'm interested into finding an efficient computer algorithm which, for any kind of topological graph G, is capable to compute the Hosoya's Z index value and ALSO all the related p(G,k) contributions. Emili Besalu, Ph. D. Dept of Chemistry & Institute of Computational Chemistry University of Girona Campus de Montilivi 17071 Girona, CATALONIA (Spain) From chemistry-request@server.ccl.net Thu Jul 15 05:24:22 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA28280 for ; Thu, 15 Jul 1999 05:24:22 -0400 Received: from techunix.technion.ac.il (mailer@techunix.technion.ac.il [132.68.1.28]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id FAA04668 for ; Thu, 15 Jul 1999 05:17:21 -0400 (EDT) Received: from tx.technion.ac.il (cedl09.technion.ac.il [132.68.80.95]) by techunix.technion.ac.il (Postfix) with ESMTP id DD6A6865B for ; Thu, 15 Jul 1999 12:17:13 +0300 (IDT) Message-ID: <378DA2AB.4F6D5CE9@tx.technion.ac.il> Date: Thu, 15 Jul 1999 11:58:20 +0300 From: Irena Efremenko Organization: Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa 32000 X-Mailer: Mozilla 4.03 [en] (Win95; I) MIME-Version: 1.0 To: CCL Computational Chemistry List Subject: ECP in ONIOM Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Dear All, I tried to do ONIOM(Becke3LYP/Gen:PM3) in Gaussian98 and received the following error message: QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE. #T ONIOM(BECKE3LYP/GEN:PM3) SCF(CAMP-KIN ' Last state="GCL" TCursr= 2644 LCursr= 3 Error termination via Lnk1e in /usr/local/g94/l1.exe. Job cpu time: 0 days 0 hours 0 minutes 0.7 seconds. File lengths (MBytes): RWF= 1 Int= 0 D2E= 0 Chk= 1 Scr= 1 Error termination via Lnk1e. Error termination via Lnk1e. What is wrong here? Does ONIOM in G98 allow to use ECP? If yes, where do I have to insert "Pseudo=Read"? Any help will be very appreciated. Thank in advance!! Irena From chemistry-request@server.ccl.net Wed Jul 14 09:27:02 1999 Received: from fringe.vpharm.com (fringe.vpharm.com [198.114.232.2]) by server.ccl.net (8.8.7/8.8.7) with SMTP id JAA15598 for ; Wed, 14 Jul 1999 09:27:02 -0400 Received: from portal.vpharm.com by fringe.vpharm.com via smtpd (for server.ccl.net [192.153.40.39]) with SMTP; 14 Jul 1999 13:20:15 UT Received: (private information removed) Message-ID: <378C8DE5.C9BD2E52@vpharm.com> Date: Wed, 14 Jul 1999 09:17:25 -0400 From: Pat Walters Organization: Vertex Pharmaceuticals X-Mailer: Mozilla 4.6 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: visualizing docking output Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit There have a been a few recent posts regarding visualization of the output from docking calculations so thought I'd throw in my 0.02. While it is relatively easy to visualize a single protein ligand complex with any of a number of tools, most of us are not interested in looking at just one ligand. Typically the user of a docking program will want to examine dozens or even hundreds of docked ligands. To my knowledge there is currently no commercial or academic software which adequately addresses this problem. Before software vendors get upset and start flaming me, let me specify what I think is necessary. The program should be able to 1. Read a protein as a PDB file. 2. Read a multi-structure file containing a set of ligands in a file format appropriate for small molecules (SDF,mol2, not PDB). 3. Allow facile creation and display of a protein surface colored by electrostatic potential. It should also be easy to toggle the surface on and off. 4. Be capable of displaying hydrogen bonds between the protein and ligand. 5. Allow the user to easily scroll through the set of ligands, displaying each ligand in the active site of the protein. 6. Provide adequate performance with macromolecular systems. It would also be nice to be able to 7. Mark interesting compounds and save the marked compounds to a file. 8. Display a 2D ligand structure along with the 3D structure. 9. Display docking scores along with 3D strucutres. 10. Filter structures - e.g. show me only those structure which make a hydrogen bond with ASP 87. 11. Visualize close contacts. None of this is rocket science, but I have yet to find a package which satisfies all the requirements. Our solution was to write our own viewer. Unfortunately this viewer relies on Molecular Inventor which has been orphaned by SGI I'd be happy if anyone could prove me wrong and point me to software which fulfills the requirements above. I'd also be interested in any toolkits, Active-X/COM/WhateverMicrosoftIsCallingItToday components for doing molecular graphics. I'll gladly summarize for the list. Pat -- W. Patrick Walters, Ph.D. Vertex Pharmaceuticals, Inc., 130 Waverley St., Cambridge, MA 02139 Voice: (617)577-6242 FAX: (617)577-6400 -------------------------------------------------------------------- friends don't let friends write FORTRAN code. From chemistry-request@server.ccl.net Wed Jul 14 10:57:07 1999 Received: from pollux.chem.umn.edu (pollux.chem.umn.edu [128.101.156.56]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA16901 for ; Wed, 14 Jul 1999 10:57:07 -0400 Received: (from cramer@localhost) by pollux.chem.umn.edu (8.9.3/8.9.3) id JAA13476; Wed, 14 Jul 1999 09:46:45 -0500 (CDT) From: Christopher Cramer Message-Id: <199907141446.JAA13476@pollux.chem.umn.edu> Subject: Re: CCL:Solvation energies of iodide organic compounds To: claudio@itqb.unl.pt (=?iso-8859-1?Q?Cl=E1udio?= Soares) Date: Wed, 14 Jul 1999 09:46:45 -0500 (CDT) Cc: CHEMISTRY@ccl.net, truhlar@chem.umn.edu (Don Truhlar) In-Reply-To: <3.0.6.32.19990713160616.0086e910@brutus.itqb.unl.pt> from "=?iso-8859-1?Q?Cl=E1udio?= Soares" at Jul 13, 99 04:06:16 pm X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dr. Soares, The SM5.0 model is a surface-area-only solvation model with iodine parameters. You can find the aqueous model described in Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. "Parameterized Model for Aqueous Free Energies of Solvation using Geometry-dependent Atomic Surface Tensions with Implicit Electrostatics" J. Phys. Chem. B 1997, 101, 7147. and the same model for all organic solvents in Hawkins, G. D.; Liotard, D. A.; Cramer, C. J.; Truhlar, D. G. "OMNISOL: Fast Prediction of Free Energies of Solvation and Partition Coefficients" J. Org. Chem. 1998, 63, 4305. Moreover, the model is available in the free code OMNISOL, distributed under license from Minnesota. See http://comp.chem.umn.edu/WWW/OMNISOL/OMNISOL.html Best regards, Chris =?iso-8859-1?Q?Cl=E1udio?= Soares > > Dear CClers > > We need solvation parameters for iodine to apply in molecular docking > methods (G=alpha*SAS like methods). So far we did not find any parameter > for iodine in the literature. Is anyone aware of these parameters for > iodine somewhere? > > Alternatively, we can try to derive these parameters for iodine ourselves, > but for that we need solvation energies (in water) of organic molecules > containing iodine and that hasn't been easy either. > > Regards, > > Cláudio Soares > > -------------------------------------------------------------------- > Cláudio Soares | > Instituto de Tecnologia | > Química e Biológica |Phone:(351-1)4469610/4469100 > 6º Piso, Av. da Republica | Fax :(351-1)4411277 > Apartado 127 |email:claudio@itqb.unl.pt > 2781-901 OEIRAS Portugal |http://www.itqb.unl.pt/~claudio > > -= 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 > > > > > -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-2006 cramer@pollux.chem.umn.edu http://pollux.chem.umn.edu/~cramer From chemistry-request@server.ccl.net Thu Jul 15 11:15:23 1999 Received: from cerberus.ulaval.ca (cerberus.ulaval.ca [132.203.250.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA01040 for ; Thu, 15 Jul 1999 11:15:22 -0400 Received: from promethium.chm.ulaval.ca (promethium.chm.ulaval.ca [132.203.70.61]) by cerberus.ulaval.ca (8.8.7/8.7.3) with ESMTP id LAA12950 for ; Thu, 15 Jul 1999 11:17:56 -0400 (EDT) Received: (from anh@localhost) by promethium.chm.ulaval.ca (8.6.12/8.6.12) id CAA15678 for chemistry@ccl.net; Thu, 15 Jul 1999 02:12:39 -0400 From: "Nguyen Nam Anh" Message-Id: <9907150212.ZM15676@promethium.chm.ulaval.ca> Date: Thu, 15 Jul 1999 02:12:38 -0400 X-Mailer: Z-Mail (3.2.1 6apr95 MediaMail) To: chemistry@ccl.net Subject: Large rotations in CASSCF Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear experts, I'm doing CASSCF calculations using G94 and getting several warning messages of this type: WARNING! : large rotation I J = 110 5 Step scaled by 7.0061957246605036E-02 Often the job ends up not being converged. What does the warning message mean? Is there a way around to overcome this difficulty Thank you very much -- Nguyen Nam Anh Quebec, Canada E-mail: anh@chm.ulaval.ca WWW: http://promethium.chm.ulaval.ca/~anh/ From chemistry-request@server.ccl.net Thu Jul 15 15:47:56 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 PAA04255 for ; Thu, 15 Jul 1999 15:47:54 -0400 Received: from localhost (rkrocha@localhost) by dedalus.lcc.ufmg.br (8.9.3/8.9.3) with SMTP id QAA36618 for ; Thu, 15 Jul 1999 16:40:46 -0300 Date: Thu, 15 Jul 1999 16:40:45 -0300 (BSC) From: ramon kleber da rocha To: Computational Chemistry Mailing List Subject: AutoDock 3.0 in DNA simulations Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I'm wondering if anyone have experience in DNA simulations using AutoDock 3.0? My problem is when I run "addsol" in order to get the solvations parameters on DNA molecule, it add two coluns filled by ZEROS on the .pdbqs file. It seems that AutoDock 3.0 hasn't solvation parameters to DNA. In fact, the sol_par.dat file dont shows that parameters to DNA bases, even the AutoDock's autors insure that it can do DNA simulations. Does anybody know how/where can I get that parameters for oligonucleotides? Or how do AutoDock 3.0 do that? Best regards. ----- From the pain come the dream From the dream come the vision From the vision come the people And from the people come the power From this power come the change PG in "US" ________________________________________________________________________________ Ramon Kleber da 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 Thu Jul 15 22:18:11 1999 Received: from neon.chem.ucla.edu (neon.chem.ucla.edu [128.97.35.251]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA09863 for ; Thu, 15 Jul 1999 22:18:10 -0400 Received: from localhost (kuwata@localhost) by neon.chem.ucla.edu (8.8.0/8.8.0) with SMTP id TAA08869 for ; Thu, 15 Jul 1999 19:18:02 -0700 (PDT) X-Authentication-Warning: neon.chem.ucla.edu: kuwata owned process doing -bs Date: Thu, 15 Jul 1999 19:18:02 -0700 (PDT) From: Keith Kuwata To: chemistry@server.ccl.net Subject: CASMP2(10,10) Problems and Answers Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi CCLers, I apologize for the huge (2 month) delay in summarizing answers. _________________________________________________________________ Here was my original problem: I have converged CASSCF(10,10)/6-31G(d,p) wave functions (95 basis function total). I have been unable to obtain single-point MP2 corrections (using the keyword MP2=full) with either Gaussian 94 or Gaussian 98. G94 has failed on both an SP2 cluster and the NCSA HP Exemplar If I use the keyword iop(4/43=1), the job crashes before the CAS begins with the error message "OPERATION ON FILE OUT OF RANGE" If I omit this keyword, the job crashes with a "Segmentation Fault" right after the route information prints. This happens even when 4 GB of RAM are allotted. With G98 on the Exeplar, CASSCF(10,10) runs successfully with the battery of additional keywords posted by Wolfgang Roth last month: casscf(10,10,nofulldiag) iop(5/6=8) iop(4/46=1,5/39=000001) iop(5/16=1) Upon adding the keyword mp2=full, G98 at least doesn't crash (unlike G94). However, in the MP2 routine, all the configurations are skipped and there is zero MP2 correction to the CASSCF energy. I know that CASPT2 is arguably better, and I am pursuing those calculations as well. But it would be very useful to have CASMP2 (10,10) energies for comparison. If anyone knows how to get this to run on either G94 or G98, that'd be great. ______________________________________________________________ Here's what solved the problem: 1) The insight that I was running out of scratch disk space: Your input deck looks fine and the job runs if you reduce the active space so I think it must be a size problem. Does the job run without the 'mp2=full' option? The MP2 will need a lot of memory (actually I'd be surprised if it runs in G94 at all), whereas the CASSCF needs a lot of disk space but not so much memory. My guess is that the scratch files were probably not written properly as the job ran out of disk space. The only machine I ran my CAS(10,10) jobs on was NCSA which had a lot of disk space. Do you have access to a machine with a lot of disk space? The CAS should certainly run providing it has enough disk space - I don't think there is a problem with the code or your input deck. The MP2 I suspect is much too large to run with G94 - perhaps it will run with G98. Sarah Wilsey _________________________________________________________________ 2) And that CASMP2 even on G98 can run out of disk space easily: Gaussian evaluates MP2 corrections only for configurations having coefficients (in localized orbital basis) higher that a selected threshold. The problem in your case appears because all configurations have coefficients lower than the threshold. "Dr. Paolo Celani" _______________________________________________________________ 3) The fix for the problem, also from Dr. Celani: A IOP in GAUSSIAN is set with the syntax IOP( link_number / option_number = option_value ) link_number = 5 in your case because you want to set an option of l510 option_number = 52 this is the specific option you want to set option_value = 0,1,2, .... any integer number The threshold is set by default to 0.01 (option_value=0) which means that only configurations having CI coefficients >= 0.01 (in absolute value) will be considered for the successive correlation calculation. If you want to set a threshold to 0.001, you must add a card like iop(5/52=1000) For a threshold equal to 0.0025, the card is iop(5/52=400). In general (as said by the formula), the threshold for coefficients will be set to a value equal to the inverse of the value of the option 52 or it is set to 0.01 if option_value=0. Keep in mind that you might get different answers using different cutoffs. "Dr. Paolo Celani" _______________________________________________________________ Of course, this trick is never mentioned in the Gaussian documentation. Nor did I get any hint from Gaussian in my e-mail communication with them. In that vein, I received this comment: > P.S. [Needless to say], Gaussian has failed to respond to my three > requests for help. > We see this too often on CCL. I do not mind people asking for help, but the point is they should be getting help from Gaussian. They don't, so they turn to CCL, get the answer, and Gaussian is off the hook. Perhaps Jan and all the responders should collect a fee from Gaussian for doing their work for them? Or maybe users should abandon Gaussian and go with competitors who provide some real customer support. Other opinions, suggestions welcome. Jaime Martell _______________________________________________________________ The article in this week's (12 July 1999) C&E News provides further insights into Gaussian, Inc. Thanks much to everyone who responded, Keith Kuwata