From chemistry-request@server.ccl.net Wed Nov 1 01:27:05 2000 Received: from dns2.seanet.com (dns2.seanet.com [199.181.164.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA28400 for ; Wed, 1 Nov 2000 01:27:05 -0500 Received: from biggeek (dialup-63.214.12.53.Seattle1.Level3.net [63.214.12.53]) by dns2.seanet.com (8.9.3/8.9.0) with SMTP id WAA02960; Tue, 31 Oct 2000 22:26:13 -0800 (PST) Message-ID: <008d01c043cc$c350dda0$01808080@biggeek> From: "Mark A. Thompson" To: chemistry@server.ccl.net Cc: Subject: ArgusLab 2.0: beta2 released Date: Tue, 31 Oct 2000 22:27:00 -0800 ArgusLab 2.0 beta2 is available for download. http://www.seanet.com/~mthompson/ArgusLab Changes from beta1 include: -------------------------------- 1. different install program: fixed a lot of complaints. 2. 800x600 pixel support for those who did not have the higher screen resolutions. 3. minor bug fixes. 4. more fragments added to fragment library. ArgusLab is a molecular modeling program for Microsoft Windows operating systems. Overview of 2.0 features: ----------------------------- 1. Interactive 3D Molecule Builder with: Interactive 3D manipulator Fragment Library Beautify Geometry Automatically Add/Hide/Delete Hydrogens Cut & Paste Supports Multiple-Level Undo/Redo. Multiple Rendering Styles for Atoms and Bonds Geometry Monitors 2. Calculation Types Single-Point Energies Optimize Geometries Electronic Excitation Spectra Self Consistent Reaction Field (SCRF) Solvent Model for Electronic Spectra 3. Molecular Mechanics Universal Force Field (UFF) for the entire periodic table 4. Quantum Mechanics Extended Huckel for entire periodic table MNDO, AM1, and PM3 semi-empirical Hamiltonians INDO1/s semi-empirical Hamiltonian Restricted and Unrestricted Hartree-Fock SCF 5. File Types: supports XYZ, PDB, and ArgusLab XML file formats. 6. HTML Help 7. No size limitations for molecules or calculations other than = available system resources 8. Multi-threaded architecture allows multiple molecules opened = simultaneously and running calculations 9. Runs on Windows 95/98, Windows NT 4.0, Windows 2000 From chemistry-request@server.ccl.net Wed Nov 1 08:23:28 2000 Received: from compchem.dfh.dk (compchem.dfh.dk [130.225.225.51]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA30966 for ; Wed, 1 Nov 2000 08:23:26 -0500 Received: (from jeremy@localhost) by compchem.dfh.dk (SGI-8.9.3/8.9.3) id OAA47995 for chemistry@ccl.net; Wed, 1 Nov 2000 14:21:16 +0100 (MET) Date: Wed, 1 Nov 2000 14:21:16 +0100 From: Jeremy Greenwood To: chemistry@ccl.net Subject: Re: Gaussian: recalculating thermochem Message-ID: <20001101142116.B1279887@compchem.dfh.dk> References: <20001026190754.A1254620@compchem.dfh.dk> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 1.0i In-Reply-To: <20001026190754.A1254620@compchem.dfh.dk>; from jeremy@compchem.dfh.dk on Thu, Oct 26, 2000 at 07:07:54PM +0200 QUESTION > Gaussian allows the rapid recalculation of thermochemical data > (e.g. with new scaling factor, temp., pressure) from the checkpoint > file after a frequency job using freq=readfc > However, if the checkpoint file is missing, it gets more tricky. > We would like to recalculate the thermochemistry without having > to resort to re-running the frequency job. > A checkpoint file can be created by a single point calculation. > The force constants are listed in the archive, and can be read in > using opt=fccards, or by editing the formatted checkpoint file by > hand and unformatting, but this doesn't seem sufficient to > convince Gaussian to perform freq=readfc. > One could use the information in the output file to recalculate > the thermochemistry from first principles, but this is a little > laborious. It would be nice to have an automated procedure. > Does someone have a good way to do this? ANSWER using Gaussian, for the cost of a cheap frequency job and a single point calculation: 1) Run a frequency job at HF/sto-3g using the geometry optimised at the higher level 2) Format the checkpoint file using formchk 3) Replace the force constants in the checkpoint file with those >from the archive of the output file. Handy extraction script from Per-Ola Norrby: ftp://compchem.dfh.dk:/pub/QueueScripts/po_getForce 4) Unformat the new checkpoint file with unfchk 5) Run a single point calculation using the checkpoint file, specifying geom=check guess=read, and maybe scf=sleazy 6) Run a freq=(readisotopes,readfc) job to recalculate the thermochem (Thanks to Joseph Ochterski, help@gaussian.com for help with this) ALTERNATIVE at virtually no cost Frank Jensen (frj@dou.dk) kindly supplied a short Fortan program to directly calculate ZPE, and vibrational contributions to H and S from a list of the frequencies, temperature and scale factor; from these the desired quantities can be found. Cheers, Jeremy ---------------------------------------------------------------------- Jeremy Greenwood jeremy.greenwood@i.am Department of Medicinal Chemistry ph +45 35306117 Royal Danish School of Pharmacy fx +45 35306040 Universitetsparken 2, DK-2100 Copenhagen, Denmark ---------------------------------------------------------------------- I am busy just now again on electro-magnetism, and think I have got hold of a good thing, but can't say. It may be a weed instead of a fish that, after all my labor, I may at last pull up. -Michael Faraday ---------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Nov 1 12:47:03 2000 Received: from post2.inre.asu.edu (post2.inre.asu.edu [129.219.110.73]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA32198 for ; Wed, 1 Nov 2000 12:47:02 -0500 From: Benjamin.Moritz@asu.edu Received: from conversion.post2.inre.asu.edu by asu.edu (PMDF V6.0-24 #47347) id <0G3C00H01WBAMZ@asu.edu> for chemistry@ccl.net; Wed, 01 Nov 2000 10:23:34 -0700 (MST) Received: from general2.asu.edu (general2.asu.edu [129.219.10.242]) by asu.edu (PMDF V6.0-24 #47347) with ESMTP id <0G3C00GP7WBAHQ@asu.edu> for chemistry@ccl.net; Wed, 01 Nov 2000 10:23:34 -0700 (MST) Received: from localhost (localhost [127.0.0.1]) by general2.asu.edu (8.9.3/8.9.3) with ESMTP id KAA03628 for ; Wed, 01 Nov 2000 10:23:33 -0700 (MST) Date: Wed, 01 Nov 2000 10:23:33 -0700 (MST) Subject: Transition Metals for G98 X-Sender: bmoritz@general2.asu.edu To: chemistry@ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII I was wondering if anyone has had trouble running transition metals in G98. I'm trying to run calculations with Hg but my error message keeps stating that the basis set won't work because the atomic number is out of range. Is there any way to correct for this? Thanks. Benjamin J. Moritz Chemical & Materials Engineering Arizona State University Mailto:bmoritz@asu.edu From chemistry-request@server.ccl.net Wed Nov 1 12:46:24 2000 Received: from uucphost.mcs.net (Kitten2.mcs.com [192.160.127.90]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA32186 for ; Wed, 1 Nov 2000 12:46:22 -0500 Received: from becky (P24-Chi-Dial-3.pool.mcs.net [205.253.224.152]) by uucphost.mcs.net (8.9.3/8.9.3) with SMTP id LAA89722; Wed, 1 Nov 2000 11:46:02 -0600 (CST) (envelope-from rone@mcs.net) Message-ID: <001b01c044f4$adabf290$98e0fdcd@becky> From: "Rebecca Rone" To: "Zhenyu Lu" , References: <003901c0435e$a5a4c640$8da90398@chem.duke.edu> Subject: Re: CCL:molecular mechanic paramters for neutralized residues Date: Thu, 2 Nov 2000 11:44:33 -0600 Dear Zshenyu, If you are using CHARMm from MSI the neutral residue should be available. You need to check the documentation and rename the resudues you want to neutralize in order to get the neutral form. By carefully about modeling things this way. Make certain that your structure truly supports the neutral form. If it is on the surface and you wish to avoid the extra overhead of using explicit water molecules or counterions you are probably OK, but if you wish to neutralize residues in the binding site be certain it is justified. In either case if you see major refolding of the protein you may have a problem. ----- Original Message ----- From: Zhenyu Lu To: chemistry@ccl.net Sent: Tuesday, October 31, 2000 11:18 AM Subject: CCL:molecular mechanic paramters for neutralized residues Dear CCL folks: I am trying QM/MM calculations on a enzyme. We are interested in the electrostatic role of the enzyme enviroment. Instead of using counter ions, we just neutralized most Lys, Arg, Glu, Asp redsidues to see what will happen. I am using Tinker program, and the paramter files (Amber, Charmm,etc) don't accomordate these neutralized residues. My quetion is : Where or is there some way that I can obtain the parameters for the neutralized Lys, Arg, Glu, Asp residues? Help on how to simulate the true system, using counter ions, protonation state exploration,etc. is also appreciated. Thanks in advance! Best, Zhenyu Lu Duke University From chemistry-request@server.ccl.net Wed Nov 1 14:16:37 2000 Received: from cheetah.it.wsu.edu (root@cheetah.it.wsu.edu [134.121.1.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA00015 for ; Wed, 1 Nov 2000 14:16:37 -0500 Received: from ucis (ucis.chem.wsu.edu [134.121.41.180]) by cheetah.it.wsu.edu (8.9.3/8.9.3) with SMTP id LAA30714; Wed, 1 Nov 2000 11:16:38 -0800 (PST) Message-ID: <001d01c04438$401b4440$b4297986@chem.wsu.edu> From: "Phillip D. Matz" To: , References: Subject: Re: CCL:Transition Metals for G98 Date: Wed, 1 Nov 2000 11:16:34 -0800 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 5.00.3018.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.3018.1300 Hi Benjamin! For Hg (and most transition metals) you will need to use a basis set modified with an electrostatic core potential (ECP) which basically removes the core electrons from the atom and replaces them with an empirical potential. G98 comes with the LANL2DZ basis and ECP built-in. If you want to use this basis then set your input like the following: #P RHF/GEN Pseudo=read comments... charge multiplicity molecular specifications C N 0 6-31+G(d') **** Hg 0 LANL2DZ **** Hg 0 LANL2DZ The important parts are the Gen and Pseudo=read - this tells gaussian to look at the end of the input file for the basis set (which can be different for each atom) and the ECP. In the example above I used carbon and nitrogen, you would put the element symbol for whatever atoms are in your molecule there. Let me know if this works for you! Respectfully, Phillip Matz matz@wsunix.wsu.edu ----- Original Message ----- From: To: Sent: Wednesday, November 01, 2000 9:23 AM Subject: CCL:Transition Metals for G98 > I was wondering if anyone has had trouble running transition metals in > G98. I'm trying to run calculations with Hg but my error message keeps > stating that the basis set won't work because the atomic number is out of > range. Is there any way to correct for this? Thanks. > > Benjamin J. Moritz > Chemical & Materials Engineering > Arizona State University > Mailto:bmoritz@asu.edu > > > -= 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 Nov 1 15:11:44 2000 Received: from lambda.inrs.uquebec.ca (lambda.inrs.uquebec.ca [207.162.3.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA00385 for ; Wed, 1 Nov 2000 15:11:43 -0500 Received: from iaf.uquebec.ca ([198.168.44.64]) by lambda.inrs.uquebec.ca (Netscape Messaging Server 3.62) with ESMTP id 380 for ; Wed, 1 Nov 2000 15:07:31 -0500 Message-ID: <3A0079F1.52B3260B@iaf.uquebec.ca> Date: Wed, 01 Nov 2000 15:15:46 -0500 From: "Jianhui Wu" X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: template, NMR or X-ray Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, everyone, I have a general question regarding homology modelling. I would like to build a protein model for docking study. This protein have two close homology proteins (A and B) with their structures solved: A from X-ray and B from NMR. I wonder which template I should use? or perhaps I should use two of them at the same time? What kind of template will produce better protein model if we try to judge the model by the docking result as well as the biological experimental result. It seems that NMR structure will be more in accord with what is going on in solution. Can we say that model built by template from NMR will give a better result in docking study? Let`s assume the docking method and biological assay method are reasonable here. Any help will be grateful appreciated. Yours Sincerely, Jianhui Wu email: JianHui_Wu@IAF.Uquebec.ca