From chemistry-request@server.ccl.net Wed Jan 22 07:29:15 2003 Received: from sims.csuohio.edu ([137.148.5.58]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0MCTFe18919 for ; Wed, 22 Jan 2003 07:29:15 -0500 Received: from csuohio.edu (titanium.asic.csuohio.edu [137.148.208.32]) by sims.csuohio.edu (Sun Internet Mail Server sims.4.0.1999.09.28.17.31.p2) with ESMTP id <0H9400FO182S17@sims.csuohio.edu> for chemistry@ccl.net; Wed, 22 Jan 2003 07:30:28 -0500 (EST) Date: Wed, 22 Jan 2003 07:29:13 -0500 From: Valentin Gogonea Subject: CHelpG charges on Fe-PPIX To: chemistry@ccl.net Cc: gmx-users Message-id: <1D7ED9FA-2E05-11D7-8DAA-003065CDB448@csuohio.edu> MIME-version: 1.0 X-Mailer: Apple Mail (2.551) Content-type: text/plain; format=flowed; charset=US-ASCII Content-transfer-encoding: 7BIT Dear CCLers and GMX users, A couple of months ago I asked a question about what van der Waals radius should be used for Fe(2+) to obtain CHelpG charges (to be used with OPLS parameters). I got few replies and consequently, following the suggestions from the list I tried few exploratory calculations on Fe(2+)-porphyrin IX (without axial ligands). I am listing here the results obtained for different van der Waals radii in the range of 1.00-2.00A: CHelpG charges for Fe(2+)-PPIX Total Charge=0, Multip=5 Radius-Fe(A) Charge(au) 1.0 4.226756 1.2 3.069658 1.5 0.943646 1.7 -0.342193 2.0 -1.644652 Mulliken charge is 0.318069 Radius for C,N,O is 1.50A and for H 1.45A (Breneman model as implemented in Gaussian98) There is a large variability in the charges and I am wondering how to get a value which is acceptable. Further MD simulations will clearly depend on the charge values. I used UHF/LanL2DZ basis set on Fe and STO-3G for the atoms in the porphyrin ring. I would really appreciate any suggestions on how to proceed in order to get acceptable charges for Fe. Thank you, Valentin Gogonea Cleveland State University Cleveland, Ohio, USA From chemistry-request@server.ccl.net Wed Jan 22 09:11:14 2003 Received: from mailer.gwdg.de ([134.76.10.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0MEBDe21774 for ; Wed, 22 Jan 2003 09:11:13 -0500 Received: from [134.76.211.99] (helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 3.33 #13) id 18bLaz-0006BS-00 for chemistry@ccl.net; Wed, 22 Jan 2003 15:11:13 +0100 Message-ID: <3E2EA67E.7050302@mpi-bpc.mpg.de> Date: Wed, 22 Jan 2003 15:11:10 +0100 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en, ro MIME-Version: 1.0 To: CCL Subject: Delphi question Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear CClers, I have a question about DELPHI. I am submiting a job and I get the following error when reading the file that contain radii: maximum # of radius records exceeded increase nrmax Could somebody explain what is this and how can I get rid of it? Thanks a lot in advance, -- Vlad Cojocaru Max Planck Institute for Biophysical Chemistry Department: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1327 e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de home tel: ++49-551-9963204 From chemistry-request@server.ccl.net Wed Jan 22 05:17:16 2003 Received: from scsx01.sc.ehu.es ([158.227.150.40]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0MAHFe15825 for ; Wed, 22 Jan 2003 05:17:16 -0500 Received: from sq.ehu.es (scuc02.sc.ehu.es [158.227.101.50]) by scsx01.sc.ehu.es (8.9.3/8.9.1) with ESMTP id LAA22246 for ; Wed, 22 Jan 2003 11:17:12 +0100 (MET) Message-ID: <3E2E6FA5.4060103@sq.ehu.es> Date: Wed, 22 Jan 2003 11:17:09 +0100 From: Txema Mercero User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry@ccl.net Subject: "Theoretical Biochemistry Symposium" Announcement Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear colleagues, We are pleased to announce the "Theoretical Biochemistry Symposium" which will be held on march 5-7, 2003 in Donostia. Theoretical modeling has evolved to a very important tool in biochemistry and biophysics, and ranges from elementary modeling to classical MD simulations or sophisticated quantum chemical treatments. Theoretical biochemists have over the years successfully addressed a wide variety of topics such as enzymatic reactions, drug design, DNA structure and function, biomimetics, and of course the recent applications in the area of bioinformatics. The aim of the present symposium is however to not only present explicit results from modeling studies, but also to allow for presentations of methodology, and we hope for a stimulating symposium with plentiful discussions and exchange of knowledge and ideas in the broad and fascinating field of Theoretical Biochemistry. The symposium will take place at the conference room of the Donostia International Physics Center (DIPC), which is located just across the road of the Chemistry Department Building on Campus. Please refer to the meals link on the main page of the Symposium for a map. The maximum number of participants will be 40 people. The organizers are planning to publish the proceedings of the Symposium as a special dedicated issue of a journal of the field. Instructions for the authors will be announced as soon as possible. Please check this web page regularly (http://www.sc.ehu.es/powgep99/dcytp/teoricos/Biophys/i_main.html) The list of invited speakers that have already confirmed their participation can be found in the following link: http://www.sc.ehu.es/powgep99/dcytp/teoricos/Biophys/STB.html Donostia (San Sebastian in Spanish) is located in Northern Spain very close to the France South border and it is surrounded by three airports. The closest is the airport of San Sebastian, which is 10 Km East. The Biarritz airport in France, is also close to San Sebastian at approximately 40 Km North. However, the major airport is at Bilbao, approximately at 100 Km West from San Sebastian. Transportation from Bilbao airport to San Sebastian is fluent by bus. They run from Bilbao downtown every 30 minutes. San Sebastian can also be conveniently reached by car, and traffic in the city is easy. Accommodation is not expected to suppose any trouble for the participants, who are refereed to the main page of the web site of the Symposium for more information about this point. Please make your choice and drop us an e-mail message ( ugalde@sq.ehu.es) so we can do the reservation for you. Finally, may I ask you to distribute this message to all of your colleagues that might be interested in the Conference. The organizing committee is pleased to thank you in advance for you help in the dissemination of this announcement. Please do not hesitate to contact us if you need further information. We look forward to your reply. Leif A. Eriksson (leifaxel@xray.bmc.uu.se) Jesus M. Ugalde (ugalde@sq.ehu.es) From chemistry-request@server.ccl.net Wed Jan 22 01:27:00 2003 Received: from hisar.cc.boun.edu.tr ([193.140.192.229]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0M6Que29025 for ; Wed, 22 Jan 2003 01:26:58 -0500 Received: by hisar.cc.boun.edu.tr (Postfix, from userid 4210) id A679D1391; Wed, 22 Jan 2003 08:26:46 +0200 (EET) Received: from localhost (localhost [127.0.0.1]) by hisar.cc.boun.edu.tr (Postfix) with ESMTP id 7ADE8FE3 for ; Wed, 22 Jan 2003 08:26:46 +0200 (EET) Date: Wed, 22 Jan 2003 08:26:46 +0200 (EET) From: "Alimet S. Ozen" X-Sender: ozensem@hisar.cc.boun.edu.tr To: chemistry@ccl.net Subject: Fukui functions at the semi-empirical level.. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, Does it make sense to calculate the Fukui functions at the semi-empirical level or using the electron density calculated with DFT(B3LYP/6-31+G* for example) over the semi-empirical geometries? Or would you rather prefer an optimization even with a minimal basis set and at a lower level of theory like HF for the electron density? This question is on the behalf of a friend : they have modeled their big system semi-empirically and their concern with fukuis is of consistency... (i am ,however, not an expert with semi-empirical models..) Thanks in advance Best Regards Alimet "Real value:is not the one whose presence fills an empty space but the one whose absence creats one" Ozdemir Asaf ozensem@boun.edu.tr alimetsema@yahoo.com http://www.geocities.com/alchemistrial From chemistry-request@server.ccl.net Wed Jan 22 06:21:52 2003 Received: from alpha.cerm.unifi.it ([150.217.146.11]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h0MBLge17250 for ; Wed, 22 Jan 2003 06:21:51 -0500 Received: (qmail 9604 invoked by uid 204); 22 Jan 2003 11:00:45 -0000 Received: from unknown (HELO cerm.unifi.it) (127.0.0.1) by localhost with SMTP; 22 Jan 2003 11:00:44 -0000 Received: from 150.217.145.160 (SquirrelMail authenticated user sbaglia) by alpha.cerm.unifi.it with HTTP; Wed, 22 Jan 2003 12:00:44 +0100 (CET) Message-ID: <1588.150.217.145.160.1043233244.squirrel@alpha.cerm.unifi.it> Date: Wed, 22 Jan 2003 12:00:44 +0100 (CET) Subject: Another Autodock Question From: "Robert Sbaglia" To: X-Priority: 3 Importance: Normal X-Mailer: SquirrelMail (version 1.2.10) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Virus-Scanned: by AMaViS perl-11 Hi all, I'm starting out using Autodock but would like to use it to run large numbers of molecules, which I have in mol2 form. I notice Autotors uses "deftors" to produce a pdbq file which Autodock can use, however using deftors is a bit tedious when I want to dock 100 (or more) molecules and I want to have maximum flexibility in each compound anyway. Is there any program which will produce automatically a pdbq file from a mol2 with all allowed rotations? Finally, does anyone have any other tips for using Autodock to virtually screen large numbers of compounds? Many thanks, Rob Sbaglia. -------------------------------------------------- Robert Sbaglia CERM Polo Scientifico Universita' degli Studi di Firenze 50019 Sesto Fiorentino (Florence) Italy PH: +39 055 457 4241 FAX: +39 055 457 4271 From chemistry-request@server.ccl.net Wed Jan 22 03:52:15 2003 Received: from web20418.mail.yahoo.com ([66.163.169.94]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h0M8qFe01281 for ; Wed, 22 Jan 2003 03:52:15 -0500 Message-ID: <20030122085214.12908.qmail@web20418.mail.yahoo.com> Received: from [202.185.66.42] by web20406.mail.yahoo.com via HTTP; Wed, 22 Jan 2003 00:52:14 PST Date: Wed, 22 Jan 2003 00:52:14 -0800 (PST) From: Juraina Jamil Subject: On AutoDock To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear all, While running AutoDock I got this warning message that the population has converged.. what does it mean? Regards, Juraina __________________________________________________ Do you Yahoo!? Yahoo! Mail Plus - Powerful. Affordable. Sign up now. http://mailplus.yahoo.com From chemistry-request@server.ccl.net Wed Jan 22 10:42:03 2003 Received: from salmon.maths.tcd.ie ([134.226.81.11]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h0MFg2e25179 for ; Wed, 22 Jan 2003 10:42:02 -0500 Received: from gosset.maths.tcd.ie by salmon.maths.tcd.ie with SMTP id ; 22 Jan 2003 15:42:01 +0000 (GMT) Date: Wed, 22 Jan 2003 15:42:01 +0000 (GMT) From: Gemma Kinsella To: Gemma Kinsella cc: chemistry@ccl.net Subject: CCL: Amber electrostatic potential in GULP Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, I was wondering if anyone had experience in using GULP. I have successfully added, bond, angle, dihedral, improper Amber potential parameters and Lennard-Jones interactions, for some drug molecules, but fail with replicating the Amber electrostatic part of the potential with GULP, ie. I need to include 1,4 electrostatic interactions. I am a little confused with the molmec, molq, molecule options in gulp, I would have thought the correct option would be to use molmec (coulomb subtract when 1,2 1,3 bonded), and ensure box size and charges were the same in both. However the outputed electrostatic energy values for GULP and AMBER7 are very different. Is there other ways to change electrostatic parameters in gulp, or alternatively what do I need to change in Amber7? Many thanks, Gemma From chemistry-request@server.ccl.net Wed Jan 22 10:00:17 2003 Received: from sandmail01.sd.accelrys.com ([209.120.169.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0MF0Ge23758 for ; Wed, 22 Jan 2003 10:00:17 -0500 To: Vlad Cojocaru Cc: CCL Subject: Re: CCL:Delphi question MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.9a January 7, 2002 Message-ID: From: "Ken Butenhof" Date: Wed, 22 Jan 2003 10:00:13 -0500 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 01/22/2003 07:00:17 AM, Serialize complete at 01/22/2003 07:00:17 AM Content-Type: multipart/alternative; boundary="=_alternative 005242D985256CB6_=" This is a multipart message in MIME format. --=_alternative 005242D985256CB6_= Content-Type: text/plain; charset="us-ascii" Hello Vlad, A assume you are using Delphi 2 or at least one of the academic Delphi programs. These versions do indeed have a hard-coded limit on the number of entries in the .siz file. Three options come to mind: 1) use a more generic descriptions of the radii (they are not specific for each atom name anyway ...) 2) recompile Delphi to increase the limit or 3) build a pdb format file with the radii and charge in the last two columns, create dummy .siz and .crg files (need headers only) , and read in the pdb file. Note, the pdb file must begin with the following two header lines (line 1 and line 2) HEADER DELPHI PDB HEADER FORMAT = 1 _______________________________________________ Kenneth Butenhof phone: 800 756-4674 Principal Scientist email: kenb@accelrys.com Accelrys Inc. web: www.accelrys.com Vlad Cojocaru Sent by: "Computational Chemistry List" 01/22/2003 09:11 AM To: CCL cc: Subject: CCL:Delphi question Dear CClers, I have a question about DELPHI. I am submiting a job and I get the following error when reading the file that contain radii: maximum # of radius records exceeded increase nrmax Could somebody explain what is this and how can I get rid of it? Thanks a lot in advance, -- Vlad Cojocaru Max Planck Institute for Biophysical Chemistry Department: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1327 e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de home tel: ++49-551-9963204 -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net --=_alternative 005242D985256CB6_= Content-Type: text/html; charset="us-ascii"
Hello Vlad,

A assume you are using Delphi 2 or at least one of the academic Delphi programs.   These versions do indeed have a hard-coded limit on the number of entries in the .siz file.  Three options come to mind:

1) use a more generic descriptions of the radii (they are not specific for each atom name anyway ...)
2) recompile Delphi to increase the limit
or
3) build a pdb format file with the radii and charge in the last two columns,  create dummy .siz and .crg files (need headers only) , and read in the pdb file.  Note, the pdb file must begin with the following two header lines (line 1 and line 2)
HEADER DELPHI PDB
HEADER FORMAT = 1
 
_______________________________________________
Kenneth Butenhof          phone:  800 756-4674
Principal Scientist           email:    kenb@accelrys.com
Accelrys Inc.                   web:     www.accelrys.com


Vlad Cojocaru <Vlad.Cojocaru@mpi-bpc.mpg.de>
Sent by: "Computational Chemistry List" <chemistry-request@ccl.net>

01/22/2003 09:11 AM

       
        To:        CCL <chemistry@ccl.net>
        cc:        
        Subject:        CCL:Delphi question



Dear CClers,
  I have a question about DELPHI.
  I am submiting a job and I get the following error when reading the
file that contain radii:

 maximum # of radius records exceeded
 increase nrmax

Could somebody explain what is this and how can I get rid of it?
Thanks a lot in advance,

--
Vlad Cojocaru
Max Planck Institute for Biophysical Chemistry
Department: 060
Am Fassberg 11, 37077 Goettingen, Germany
tel: ++49-551-201.1327
e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de
home tel: ++49-551-9963204  




-= This is automatically added to each message by mailing script =-
CHEMISTRY@ccl.net -- To Everybody  | CHEMISTRY-REQUEST@ccl.net -- To Admins
Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | Jan: jkl@ccl.net

--=_alternative 005242D985256CB6_=-- From chemistry-request@server.ccl.net Wed Jan 22 15:26:08 2003 Received: from relay.unizar.es ([155.210.11.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0MKQ7e00711 for ; Wed, 22 Jan 2003 15:26:08 -0500 Received: from there ([155.210.93.83]) by relay.unizar.es (8.12.6/8.12.3) with SMTP id h0MKP6fD019319 for ; Wed, 22 Jan 2003 21:25:06 +0100 Message-Id: <200301222025.h0MKP6fD019319@relay.unizar.es> Content-Type: text/plain; charset="iso-8859-1" From: Santiago Cuesta <405137@docto.unizar.es> Reply-To: 405137@docto.unizar.es Organization: Ciencias To: chemistry@ccl.net Subject: patching heme (cytochrome c) charmm Date: Wed, 22 Jan 2003 21:24:03 +0100 X-Mailer: KMail [version 1.3.2] MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Virus-Scanned: TAMIZ + Sophos en unizar.es Hi !!!! Does anybody know how to make a patch in order to link heme group to cysteine in cytochrome c ??? (in charmm academic version). I mean something similar to GENERATE HEME PATCH PHEM PROT 93 HEME 1 used to link heme (Fe) with a histidine. I have checked top_all27... file and there are no cysteine patch. I would be very grateful if you could solve my problem. thanks in advance Yours sincerely Santiago Cuesta ------------------------------------- Santiago Cuesta Lopez PhD Student University of Zaragoza (Spain) Dep. Física de la Materia Condensada. Dep.Teoria y simulacion de Sistemas Complejos (ICMA-CSIC) e-mail: 405137@docto.unizar.es From chemistry-request@server.ccl.net Wed Jan 22 13:25:22 2003 Received: from mailbox.engr.sc.edu ([129.252.21.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0MIPMe29726 for ; Wed, 22 Jan 2003 13:25:22 -0500 Received: by mailbox.engr.sc.edu with Internet Mail Service (5.5.2656.59) id ; Wed, 22 Jan 2003 13:25:21 -0500 Message-ID: From: "CONG, WEIJIAN " To: "'CHEMISTRY@ccl.net'" Subject: request information on Genetic Algorithms source code and applica tions Date: Wed, 22 Jan 2003 13:25:12 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2656.59) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C2C243.9A224610" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C2C243.9A224610 Content-Type: text/plain Dear CCL: My name is mike cong from University of South Carolina. I have started doing research on how to implement Genetic Algorithms. I would like to ask for some source codes on genetic algorithms used for chemistry problems. I need these codes of the programs so I could have a better understanding of how the theorem is implemented. The applications you could help me find don't have to be limited to chemistry problems, any other applications or webpage links will also be useful for me too. I thank you so much for your help. I greatly appreciate it. Weijian Mike Cong Department of Electrical Engineering University of South Carolina Columbia, SC 29208 Phone: 803-777-0967 E-mail: cong@engr.sc.edu ------_=_NextPart_001_01C2C243.9A224610 Content-Type: text/html Content-Transfer-Encoding: quoted-printable

Dear CCL:

 

My name is mike cong from = University of = South Carolina. I have started doing = research on how to implement Genetic Algorithms. I would like to ask for some = source codes on genetic algorithms used for chemistry problems. I need these codes = of the programs so I could have a better understanding of how the theorem is implemented. The applications you could help me find don't have to be limited to chemistry problems,  any other applications = or webpage links will also be useful for me too. I thank you so much for your = help. I greatly appreciate it.   

 

Weijian Mike Cong

Department of Electrical = Engineering

University of South = Carolina

Columbia, SC<= /font> 29208

Phone: 803-777-0967

E-mail: cong@engr.sc.edu

 

------_=_NextPart_001_01C2C243.9A224610-- From chemistry-request@server.ccl.net Wed Jan 22 19:18:18 2003 Received: from mrelay.inscc.utah.edu ([155.101.3.60]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0N0IHe07936 for ; Wed, 22 Jan 2003 19:18:18 -0500 Received: from mail.inscc.utah.edu (mail.inscc.utah.edu [155.101.3.59]) by mrelay.inscc.utah.edu (8.9.2/8.9.2) with ESMTP id RAA03635 for ; Wed, 22 Jan 2003 17:18:15 -0700 (MST) Received: from mercury.hec.utah.edu (tntpc2.hec.utah.edu [155.101.19.38]) by mail.inscc.utah.edu with ESMTP id RAA25668 for ; Wed, 22 Jan 2003 17:18:14 -0700 (MST) Message-ID: <3E2F34C5.3178CE75@mercury.hec.utah.edu> Date: Wed, 22 Jan 2003 17:18:13 -0700 From: Atchara Wijitkosoom X-Mailer: Mozilla 4.79 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: About missing residues Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit To whom it may concern, Does anybody know the program that be able to add some missing residues in protein? Thanks in advance. Yours, Atchara From chemistry-request@server.ccl.net Wed Jan 22 17:03:41 2003 Received: from nature.Berkeley.EDU ([128.32.175.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0MM3ee04460 for ; Wed, 22 Jan 2003 17:03:40 -0500 Received: from localhost (localhost [127.0.0.1]) by nature.Berkeley.EDU (Postfix) with ESMTP id 7BD7026126F for ; Wed, 22 Jan 2003 14:03:40 -0800 (PST) Received: from nature.Berkeley.EDU ([127.0.0.1]) by localhost (nature.Berkeley.EDU [127.0.0.1:10024]) (amavisd-new) with ESMTP id 15973-03 for ; Wed, 22 Jan 2003 14:03:39 -0800 (PST) Received: from nature.berkeley.edu (localhost [127.0.0.1]) by nature.Berkeley.EDU (Postfix) with SMTP id 37764261252 for ; Wed, 22 Jan 2003 14:03:39 -0800 (PST) Received: from 128.32.27.14 (SquirrelMail authenticated user moconnor) by nature.berkeley.edu with HTTP; Wed, 22 Jan 2003 14:03:39 -0800 (PST) Message-ID: <1331.128.32.27.14.1043273019.squirrel@nature.berkeley.edu> Date: Wed, 22 Jan 2003 14:03:39 -0800 (PST) Subject: Manganese and Iron oxides From: To: "computational chemistry" X-Priority: 3 Importance: Normal X-Mailer: SquirrelMail (version 1.2.10) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-new Dear CCL folks: Can anyone provide me with literature references for computational modelling of manganese and iron oxides? Also, and good articles on the merits of different ECPs for these elements? Thank-you and will summarize. Mary V. O'Connor, Ph.D. UC Berkeley (formerly Rutgers, New Jersey) From chemistry-request@server.ccl.net Wed Jan 22 17:13:56 2003 Received: from chem.skku.ac.kr ([203.252.48.78]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0MMDte04826 for ; Wed, 22 Jan 2003 17:13:55 -0500 Received: (from wkpark@localhost) by chem.skku.ac.kr (8.11.6/8.11.6) id h0MMDl703572 for chemistry@ccl.net; Thu, 23 Jan 2003 07:13:47 +0900 Date: Thu, 23 Jan 2003 07:13:47 +0900 From: Won Kyu Park To: chemistry@ccl.net Subject: [Announce] DisMol reborn Message-ID: <20030122221347.GA3392@chem.skku.ac.kr> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.3.28i This is a modified version of the DisMol The DisMol based on the NanoCad and the RasMol 2.6 http://www.openchem.org/dismol/DisMol.html == added features == * new rendering styles: wireframe, ball&stick, sticks, spacefill * hot-key * toggle between display styles * rotating * toggle atomic symbols * query molecular informations: distance, angle, torsional angle - imported feature from the RasMol 2.7.x == minor enhancements == * specular shading * local data(pdb) loading * embeding pdb files like a JME method * many clipping bugs are eliminated Source file also available at http://chem.skku.ac.kr/~wkpark/java/dismol/dismol_20021215.tar.gz Samples http://chem.skku.ac.kr/~wkpark/java/dismol/DisMol.html http://chem.skku.ac.kr/~wiki/moin.cgi/DisMol I hope that new DisMol will prove useful to somebody. Bug reports, etc. are welcome. Regards, Won-kyu Park