From spoel@xray.bmc.uu.se Tue May 5 03:28:57 1998 Received: from hermes.bmc.uu.se for spoel@xray.bmc.uu.se by www.ccl.net (8.8.3/950822.1) id DAA14313; Tue, 5 May 1998 03:20:55 -0400 (EDT) Received: from alpha2.bmc.uu.se ([130.238.37.65]) by hermes.bmc.uu.se (post.office MTA v2.0 0813 ID# 0-17733) with SMTP id AAA25917 for ; Tue, 5 May 1998 09:18:59 +0200 Received: from munch.bmc.uu.se by alpha2.bmc.uu.se; (5.65v3.2/1.1.8.2/30Jan97-1111AM) id AA16855; Tue, 5 May 1998 09:20:48 +0200 Date: Tue, 5 May 1998 09:20:47 +0200 (MET DST) From: David van der Spoel X-Sender: spoel@munch To: CHEMISTRY@www.ccl.net Subject: LJ Params for Fe2+/Fe3+ Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, I am looking for LJ parameters for an Fe2+/Fe3+ ion for use in MD simulations. Our force field is GROMOS, but that has only parameters for Heme irons (with LJ params 0.0). We have an enzyme with a non-covalently bound Fe2+/Fe3+ ion, without LJ the iron would just jump on one of the ligands. Groeten, David. ________________________________________________________________________ Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From wibke@theochem.uni-duesseldorf.de Tue May 5 04:28:57 1998 Received: from lithium.theochem.uni-duesseldorf.de for wibke@theochem.uni-duesseldorf.de by www.ccl.net (8.8.3/950822.1) id DAA14356; Tue, 5 May 1998 03:31:58 -0400 (EDT) Received: (from wibke@localhost) by lithium.theochem.uni-duesseldorf.de (8.8.8/8.8.8) id RAA00944; Mon, 4 May 1998 17:52:43 +0200 (MET DST) Date: Mon, 4 May 1998 17:52:43 +0200 (MET DST) From: Wibke Sudholt Message-Id: <199805041552.RAA00944@lithium.theochem.uni-duesseldorf.de> Subject: normal coordinate displacements Cc: wibke@theochem.uni-duesseldorf.de To: chemistry@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-MD5: ZUsxGUuYueXx88meCaPeUA== Dear CCLers, I'm searching for a program that can do the following: Transform cartesian normal coordinate displacements into internal symmetry coordinates, and generate with them (stepwise and iteratively) a new displaced geometry for each vibration. This should be not as disturbed as if one would directly add cartesian normal coordinates to the minimum geometry which only holds for infinitisimal displacements. I know that a program named BALGA (in conjunction with some help programs) can do this. But our version seems only to handle small systems, and I need a program that works with more than 20 atoms. Has anybody written or knows of such a program? Preferably, it should directly read in cartesian normal coordinates from quantum chemistry packages like GAUSSIAN, GAMESS, ... Any hints are welcome! Thank you very much in advance Dipl.-Chem. Wibke Sudholt Institute of Theoretical Chemistry Heinrich-Heine-University Duesseldorf, Germany wibke@theochem.uni-duesseldorf.de From bernd@rs5.thch.uni-bonn.de Tue May 5 10:29:02 1998 Received: from rs5.thch.uni-bonn.de for bernd@rs5.thch.uni-bonn.de by www.ccl.net (8.8.3/950822.1) id KAA15607; Tue, 5 May 1998 10:00:50 -0400 (EDT) Received: (from bernd@localhost) by rs5.thch.uni-bonn.de (8.8.8/8.8.5) id QAA13544 for chemistry@www.ccl.net; Tue, 5 May 1998 16:00:52 +0200 From: Bernd Engels Message-Id: <199805051400.QAA13544@rs5.thch.uni-bonn.de> Subject: averaged orbitals in Gaussian To: chemistry@www.ccl.net (Computational Chemistry List) Date: Tue, 5 May 1998 16:00:51 +0200 (MES) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit dear netters I have a question how the orbitals of O2 (oxygen molecule) are made in the Gaussian. The program gives out pig, piu, sigg and sigu orbitals, i.e. it uses the correct symmetry D(infinity)h. However, it also gives the highest abelian subgroup D2h. So I guess, it computes everything in D2h, but treats the pix and the piy components in an averaged manner. However, I would like to know it exactly. Thanks in advance Bernd Engels Inst. fuer Theor. Chemie Uni Bonn Germany From Sandra.Wauters@rug.ac.be Mon May 4 03:51 EDT 1998 Received: from mserv.rug.ac.be for Sandra.Wauters@rug.ac.be by www.ccl.net (8.8.3/950822.1) id DAA07208; Mon, 4 May 1998 03:51:07 -0400 (EDT) Received: from elptrs5.rug.ac.be by mserv.rug.ac.be with SMTP id AA26959 (5.67b/IDA-1.5 for ); Mon, 4 May 1998 09:50:50 +0200 Received: by elptrs5.rug.ac.be (AIX 4.1/UCB 5.64/4.03) id AA19872; Mon, 4 May 1998 09:50:03 +0200 Date: Mon, 4 May 1998 09:50:03 +0200 From: Sandra.Wauters@rug.ac.be (Sandra Wauters) Message-Id: <9805040750.AA19872@elptrs5.rug.ac.be> To: chemistry-request@www.ccl.net Subject: Problem with imaginary frequency in path calculation with MORATE Mime-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Md5: QAzxQSht2JPoJpzueYFREQ== Content-Type: text/plain; charset=US-ASCII Hi there, We are dealing here again with a little problem. We are trying to run a MORATE7.8.1 job. During the path calculation an imaginary frequency is encountered which is not located in the saddle point. This imaginary frequency is probably due to little vibrations during the VTST path calculation and is quite small (about 30). Whenever such an imaginary frequency is encountered, the program sets the vibration partition function equal to 10E10. This causes the rate to be a lot higher. Does the fact that this happens, change anything to the position of the dividing surface in the VTST calculation ? Does anyone know if the factor 10E10 can be put equal to 1 and if not, can we just divide the rate by the factor 10E10 without introducing large errors ? With kind regards, Sandra Wauters PhD student Laboratorium voor Petrochemische Techniek Universiteit Gent Krijgslaan 281, S5 9000 Gent From che5jwc@titan.vcu.edu Tue May 5 13:29:02 1998 Received: from titan.vcu.edu for che5jwc@titan.vcu.edu by www.ccl.net (8.8.3/950822.1) id MAA17394; Tue, 5 May 1998 12:29:17 -0400 (EDT) Received: from localhost (che5jwc@localhost) by titan.vcu.edu (8.8.8/8.8.8) with SMTP id MAA52676 for ; Tue, 5 May 1998 12:29:32 -0400 Date: Tue, 5 May 1998 12:29:31 -0400 (EDT) From: "John W. Cox" To: chemistry@www.ccl.net Subject: CCL: ? ester using AMBER ? (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > I'm interested in modeling DNA adducts with compounds that have ester > ligands using the AMBER parameter set in Insight/Discover. I am familiar > with adding atom types and parameter values to AMBER, but have run across > a problem in the attempt to model esters (there are insufficient values > for the OS atom type and its environment). Are these parameters available? > I appreciate the help. > Regards, > John Cox > Virginia Commonwealth University > che5jwc@titan.vcu.edu From kynn@panix.com Tue May 5 13:38:01 1998 Received: from panix3.panix.com for kynn@panix.com by www.ccl.net (8.8.3/950822.1) id MAA17450; Tue, 5 May 1998 12:34:25 -0400 (EDT) Received: (from kynn@localhost) by panix3.panix.com (8.8.5/8.8.8/PanixU1.4) id MAA22728; Tue, 5 May 1998 12:34:17 -0400 (EDT) Date: Tue, 5 May 1998 12:34:17 -0400 (EDT) Message-Id: <199805051634.MAA22728@panix3.panix.com> From: "Kynn O. Jones" To: chemistry@www.ccl.net Subject: ISO smallest proteins Hello. I'd like to find out what are the smallest known proteins in the following categories: 1. all alpha 1.i helix bundle 2. all beta 3. no secondary structure (helix or b-sheet) My interest is not limited to naturally-occurring or biologically active proteins; artificially generated proteins as well as protein fragments, as long as they fold independently, have a stable, well-defined (and published!), tertiary structure, are also OK. Does anybody know how to go about finding out what I'm looking for? (I've searched for recent papers on the matter, but the topic of size records in proteins doesn't seem terribly popular.) I'd appreciate suggestions; I'll post a summary. Regards, kynn@panix.com