From chemistry-request@server.ccl.net Mon Nov 18 08:46:42 2002 Received: from mail.jadeinc.com ([209.57.24.15]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAIDkfu22835 for ; Mon, 18 Nov 2002 08:46:41 -0500 Received: from igor.jadeinc.com [209.57.24.188] by mail.jadeinc.com with ESMTP (SMTPD32-6.06) id AED07BD10108; Mon, 18 Nov 2002 08:44:48 -0500 Message-Id: <5.2.0.9.2.20021118084429.009ff540@mail.jadeinc.com> X-Sender: smolnar@mail.jadeinc.com X-Mailer: QUALCOMM Windows Eudora Version 5.2.0.9 Date: Mon, 18 Nov 2002 08:47:12 -0500 To: Chemistry@ccl.net From: "Stephen P. Molnar, Ph.D." Subject: Which Program Has Wider Usage Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed I am preparing some instructional material for use in a computational science curriculum and should like to solicit answers to the question of which package has the most usage - Gaussian or Hyperchem. Thanks in advance Stephen P. Molnar, Ph.D. Life is a fuzzy set Consultant Multivariant and stochastic Material Science/Project Management/Modeling http://web.jadeinc.com/FoundationChem From chemistry-request@server.ccl.net Mon Nov 18 20:57:22 2002 Received: from rm-rstar.sfu.ca ([142.58.120.21]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAJ1vMu07238 for ; Mon, 18 Nov 2002 20:57:22 -0500 Received: from fraser.sfu.ca (johnsont@fraser.sfu.ca [142.58.101.25]) by rm-rstar.sfu.ca (8.12.5/8.12.5/SFU-5.0H) with ESMTP id gAJ1vEsK013992; Mon, 18 Nov 2002 17:57:15 -0800 (PST) Received: from localhost (johnsont@localhost) by fraser.sfu.ca (8.9.2/8.9.2/SFU-5.0C) with ESMTP id RAA28151; Mon, 18 Nov 2002 17:57:14 -0800 (PST) X-Authentication-Warning: fraser.sfu.ca: johnsont owned process doing -bs Date: Mon, 18 Nov 2002 17:57:14 -0800 (PST) From: Margaret Johnson To: William Wei cc: CCLers Subject: Re: CCL:Homology modeling software? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi William, You can add gaps in Composer simply by changing the boundaries of the SCRs and the gap penalty -- perhaps you could try decreasing the gap penalty. Best regards, Maggie Margaret A. Johnson Department of Chemistry Simon Fraser University 8888 University Dr. Burnaby, B.C. Canada V5A 1S6 Tel: (604) 291-5650 Fax: (604) 291-3765 From chemistry-request@server.ccl.net Mon Nov 18 20:00:39 2002 Received: from mxout2.cac.washington.edu ([140.142.33.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAJ10du06595 for ; Mon, 18 Nov 2002 20:00:39 -0500 Received: from mailscan-out3.cac.washington.edu (mailscan-out3.cac.washington.edu [140.142.32.170]) by mxout2.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW02.11) with SMTP id gAJ10NEC031797 for ; Mon, 18 Nov 2002 17:00:27 -0800 Received: FROM smtp.washington.edu BY mailscan-out3.cac.washington.edu ; Mon Nov 18 17:00:23 2002 -0800 Received: from donald ([128.95.128.116]) by smtp.washington.edu (8.12.1+UW01.12/8.12.1+UW02.11) with SMTP id gAJ10Muk005932 for ; Mon, 18 Nov 2002 17:00:22 -0800 Message-ID: <009801c28f66$826812d0$74805f80@donald> From: "Carsten Detering" To: Subject: sybyl vs insightII Date: Tue, 19 Nov 2002 01:56:34 +0100 Organization: University of Washington MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0095_01C28F6E.E3BFFD60" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0095_01C28F6E.E3BFFD60 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi folks, for quite a while now, I am pondering about the folling: why is it that = most of the modellers use Sybyl rather than InsightII? In most = publications, people say in the methods section (or elsewhere) that they = used Sybyl. I was told once that InsightII was more powerful, once you = get to know it, but since I have never used Sybyl, I cannot really = compare. Maybe some of you could point out the advantages/disadvantages that you = encountered when using either of the two programs. Thanks in advance for any helpful comments. Cheers, Carsten=20 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ Carsten Detering, Ph.D. University of Washington Seattle, WA 98195 Phone 206-543-5081 Fax 206-685-8665 email detering@u.washington.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~ ------=_NextPart_000_0095_01C28F6E.E3BFFD60 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi folks,
 
for quite a while now, I am pondering about the folling: why is it = that=20 most of the modellers use Sybyl rather than InsightII? In most = publications,=20 people say in the methods section (or elsewhere) that they used Sybyl. I = was=20 told once that InsightII was more powerful, once you get to know it, but = since I=20 have never used Sybyl, I cannot really compare.
Maybe some of you could point out the advantages/disadvantages=20 that you encountered when using either of the = two programs.
Thanks in advance for any helpful comments.
 
Cheers, Carsten 
 
~~~~~~~~~~~~~~~~~~~~~~~~~~~
Carsten Detering, = Ph.D.
University of=20 Washington
Seattle, WA 98195
Phone 206-543-5081
Fax=20 206-685-8665
email detering@u.washington.edu~~~~~~~~~~~~~~~~~~~~~~~~~~~
------=_NextPart_000_0095_01C28F6E.E3BFFD60-- From chemistry-request@server.ccl.net Mon Nov 18 14:35:03 2002 Received: from aleph.net.uniovi.es ([156.35.11.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAIJZ1u00816 for ; Mon, 18 Nov 2002 14:35:01 -0500 Received: from CONVERSION-DAEMON.aleph.net.uniovi.es by aleph.net.uniovi.es (PMDF V6.1 #39514) id <01KP0YLCY4GG00KMKW@aleph.net.uniovi.es> for chemistry@ccl.net; Mon, 18 Nov 2002 20:34:50 +0100 (MET) Received: from pcc135.quimica.uniovi.es (ercina.si.uniovi.es [156.35.14.3]) by aleph.net.uniovi.es (PMDF V6.1 #39514) with SMTP id <01KP0YL91HZK00KI3G@aleph.net.uniovi.es> for chemistry@ccl.net; Mon, 18 Nov 2002 20:34:45 +0100 (MET) Date: Mon, 18 Nov 2002 20:34:44 +0000 (MET-1METDST) From: hvg@correo.uniovi.es Subject: To: chemistry@ccl.net Message-id: <01KP0YL91ZVM00KI3G@aleph.net.uniovi.es> X-Mailer: Endymion MailMan Standard Edition v3.0.17 Content-transfer-encoding: 7BIT Dear CCl users, I'm trying to calculate BSSE correction on van der Waals complexes with heavy atoms. The problem arises when I'm using the keyword `massage' in gaussian 98. The program does not read the pseudopotential. My input is: # MP2/Gen Pseudo=read guess(core) massage Title 0 1 Molecule specification Atoms from the second period 0 6-31G(d,p) **** Heavy atom 0 basis set **** Heavy atom 0 pseudopotential 1 NUC 0.0 .. am I doing something wrong? Thanks in advance. hvg From chemistry-request@server.ccl.net Mon Nov 18 09:30:49 2002 Received: from alchemy.chem.utoronto.ca ([142.150.224.224]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAIEUmu23942 for ; Mon, 18 Nov 2002 09:30:49 -0500 Received: from localhost (cmatta@localhost) by alchemy.chem.utoronto.ca (8.11.6/8.11.6) with ESMTP id gAIEUkD01382; Mon, 18 Nov 2002 09:30:46 -0500 Date: Mon, 18 Nov 2002 09:30:46 -0500 (EST) From: "Cherif F. Matta" X-X-Sender: cmatta@alchemy To: Szilveszter Juhos cc: Computational Chemistry List Subject: Re: CCL:PDB H atom name convention Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8BIT Dear Dr. Juhos We have recently faced the same problem to present some of our results regarding the geometries of the genetically-encoded amino acids. In view of the lack of specific IUPAC rules (to my knowledge) for the labeling of H atoms in the amino acids, we proposed a set of rule to label them uniquely based on their geometric location with respect to their neighbours. You will find this set of rules in the Appendix to our following paper: Matta CF, Bader RFW. Atoms-in-molecules study of the genetically-encoded amino acids. II. Computational study of molecular geometries. Proteins: Struct. Funct. Genet. 2002;48:519-538. Hope this be of help. All the best. Cherif ----------------------------------------- Chérif F. Matta, Ph. D. Theoretical/Computational Chemist, Polanyi Research Group, Lash Miller Chemical Laboratories, Chemistry Department, University of Toronto, 80 St. George Street (Room 261), Toronto, Ontario, Canada M5S 1A1. .......................................... Telephone: (416) 978 - 3625 Cellular: (416) 996 - 2444 Fax: (416) 978 - 7580 Web Site: http://chem.utoronto.ca/~cmatta/ ------------------------------------------ From chemistry-request@server.ccl.net Mon Nov 18 11:36:25 2002 Received: from travelers.mail.cornell.edu ([132.236.56.13]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAIGaOu28117 for ; Mon, 18 Nov 2002 11:36:24 -0500 Received: from travelers.mail.cornell.edu (travelers.mail.cornell.edu [132.236.56.13]) by travelers.mail.cornell.edu (8.9.3/8.9.3) with SMTP id LAA17974 for ; Mon, 18 Nov 2002 11:36:18 -0500 (EST) Date: Mon, 18 Nov 2002 11:36:17 -0500 (EST) From: jdg9@cornell.edu X-Sender: jdg9@travelers.mail.cornell.edu To: chemistry@ccl.net Subject: CCL: Qmol and PrestoPlot Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII There are new versions of both Qmol (a molecular viewer for windows) and PrestoPlot (a graphing/plotting program for windows) available for download from the Shalloway Lab at Cornell University: http://www.mbg.cornell.edu/shalloway/shalloway.html Here are the improvements: Qmol: (1) Import multiple structures in a pdb file as a molecular trajectory (for animation) (2) Read multiple structures/trajectories. Each structure can be rendered and adjusted independently. (3) Calculate the RMSD between two structures. (4) Align two molecules by rigid-body translation and rotation. (5) Measurement, hydrogen bond determination and RMSD calculation can all be performed in "real" time (i.e. move a molecule and watch dependant values change). (6) Numerous bug fixes! PrestoPlot: (1) Import and export audio data in the WAVE format. (2) Numerous bug fixes. While I am no longer at Cornell, I will support these programs in my spare time. Bug reports and questions may be sent to jdg9@cornell.edu. Regards, Jason Gans, PhD From chemistry-request@server.ccl.net Mon Nov 18 09:17:13 2002 Received: from exchange.neokimia.com ([132.210.158.207]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAIEHDu23526 for ; Mon, 18 Nov 2002 09:17:13 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 content-class: urn:content-classes:message Subject: RE: PDB H atom name convention MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 18 Nov 2002 09:15:53 -0500 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: PDB H atom name convention Thread-Index: AcKO9RhpC/vbixK/TuijeDm4Uf97BgAGBqsg From: "Axel Mathieu" To: "Szilveszter Juhos" , "CCL" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id gAIEHEu23527 You might find what you need here : http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html A mirror site of the protein data bank ... Axel -----Original Message----- From: Szilveszter Juhos [mailto:szilva@ribotargets.com] Sent: 18 novembre, 2002 06:05 To: Computational Chemistry List Subject: CCL:PDB H atom name convention Dear CCL, I could not find a definitive guide how the hydrogens in PDB files should be called. There is an advisory with some IUPAC->PDB hints at http://www.rcsb.org/pdb/lists/pdb-l/199907/msg00013.html , but I hope there is a concise on-line version somewhere since this list does not include nucleic acid residues I need. The article they are referring to J.L.Markley, et al., "Recommendations for the Presentation of NMR Structures of Proteins and Nucleic Acids," Pure & Appl. Chem., 70 (1998): 117-142 is still a recommendation or an accepted standard? If you know an URL (or an article) that serves as the standard, please let me know. Thanks: Szilva -= 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 From chemistry-request@server.ccl.net Tue Nov 19 05:49:45 2002 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAJAniu18519 for ; Tue, 19 Nov 2002 05:49:44 -0500 Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 18E5sq-0006TR-00 for chemistry@ccl.net; Tue, 19 Nov 2002 10:45:32 +0000 Date: Tue, 19 Nov 2002 10:45:32 +0000 (GMT) From: Szilveszter Juhos To: Computational Chemistry List Subject: Re: CCL:PDB H atom name convention In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, Thank you for all the replies on H names, apparently for nucleic acids (and likely for amino acids as well) the guideline is still the IUPAC paper that can be found here: http://www.bmrb.wisc.edu/home/iupac.pdf Cheers: Szilva From chemistry-request@server.ccl.net Tue Nov 19 05:02:08 2002 Received: from anchor-post-35.mail.demon.net ([194.217.242.85]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAJA28u17509 for ; Tue, 19 Nov 2002 05:02:08 -0500 Received: from ursus.demon.co.uk ([158.152.126.154] helo=ursus.cam.ac.uk) by anchor-post-35.mail.demon.net with esmtp (Exim 3.36 #2) id 18E5Cm-0007m6-0U for chemistry@ccl.net; Tue, 19 Nov 2002 10:02:05 +0000 Message-Id: <5.1.1.6.0.20021118202510.029a1808@hermes.cam.ac.uk> X-Sender: pm286@hermes.cam.ac.uk X-Mailer: QUALCOMM Windows Eudora Version 5.1.1 Date: Tue, 19 Nov 2002 09:59:10 +0000 To: Computational Chemistry List From: Peter Murray-Rust Subject: Release of CML2.0 (Chemical Markup Language) and Schema In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed The CML (Chemical Markup Language) DTD which has been in use for 3 years has now been upgraded to conform to the W3C [1] specification for Schemas. All specifications and software are OpenSource/OpenData. The basic chemical concepts of CML are not significantly changed and Version 1 will continue to be usable. There are several advantages to Schemas: - the syntax of CML documents is considerably simpler and less verbose (e.g. the "builtin" attribute is no longer necessary) - there is much stronger datatyping; elements can be validated against the Periodic tables and floats, integers etc are fully supported - they support XML namespaces so designs can be modular - modern XML software concentrates on Schemas rather than DTDs This has allowed us to create a modular design with the following components: - CMLCore which is reused by other modules - STMML [2] which supports numeric data, scalars, arrays, matrices, dictionaries, metadata and experimental procedures. (CML also interoperates with major W3C languages such as XHTML, MathML and SVG [3]. With these complete chemical documents (such as publications) can be created, queried, processed and rendered. Several other modules are under active development - Computational Chemistry Markup Language (CCML) whose first phase is being presented to a CLRC [4] meeting of early adopters from UK eScience projects this week. CCML will be run as an Open community activity to develop XML support for all aspects of Computational chemistry. We shall announce details of the mailing list very shortly. - CMLReaction. CML already supports reactions and this functionality is being refactored and expanded into a separate module. - CMLQuery. This is being built on the emerging XML Query language CML modularity relies heavily on the creation of dictionaries and we are part of the IUPAC XML Dictionary project. The CML and STMML Schemas can be found as XML, XHTML and PDF[*] at http://www.xml-cml.org and will also be posted in the repository at http://cml.sourceforge.net shortly. The distribution contains many examples of CML and STMML which have been validated against the Schema with 3 independent toolkits [5]. Several OpenSource projects have early implementations of CML2 including OpenBabel, BKChem, and JUMBO. Peter Murray-Rust Henry Rzepa [1] World Wide Web Consortium [2] Scientific Technical Medical Markup Language [3] Scalable Vector Graphics [4] Central Laboratory of the Research Councils (UK) [*] all specifications are autogenerated by XML technology.from the original schema document. [5] Apache/Xerces, MSIE MSXML4, IBM Schema validator. From chemistry-request@server.ccl.net Tue Nov 19 06:18:15 2002 Received: from GWIA.HSC.WVU.EDU ([157.182.105.18]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAJBIEu18693 for ; Tue, 19 Nov 2002 06:18:14 -0500 Received: from HSC-DOM5-MTA by GWIA.HSC.WVU.EDU with Novell_GroupWise; Tue, 19 Nov 2002 06:18:10 -0500 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.2 Date: Tue, 19 Nov 2002 06:17:54 -0500 From: "Peter Gannett" To: , Subject: Re: CCL:sybyl vs insightII Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id gAJBIFu18694 Carsten: I am not sure that your statement is true as I really have little idea which is used more. We use both. The people looking at DNA tend to use Sybyl and the Protein people use InsightII. But, that is more a result of what their mentors were accustom too. I also think you will find that many publications use Amber, Charmm, or Macromolecule However, from a money point of view, the initial cost of the software is greater for Insight (though this depends some on the modules your purchase) and a license for Sybyl is much less than for Insight (depending on the level of service, by 33-66%) and people who publish tend to come from an academic setting. Personally, I prefer to use Amber. Amber does not have a 'graphical user interface' (ignoring xleap) but there are enough freeware or very low cost programs available to help you with analysis (eg vmd, moilview, curves, dials and windows, etc) that this is not a big problem. In addition, Amber takes advantage of a multi-processor environment and it scales reasonable well. And, if you are going to do anything out of the ordinary, in our experience, it has been easier to accomplish with Amber. I also think that people have to understand what they are doing to a far greater extent with Amber, etc. which, in the long run, is a good thing. Finally, I've found Tech service from Insight/Sybyl to be less than helpful with all but the most rudimentary problems. The Amber_reflector, on the other hand, has answered nearly all of my questions, etc. Pete Gannett >>> "Carsten Detering" 11/18/02 07:56PM >>> Hi folks, for quite a while now, I am pondering about the folling: why is it that most of the modellers use Sybyl rather than InsightII? In most publications, people say in the methods section (or elsewhere) that they used Sybyl. I was told once that InsightII was more powerful, once you get to know it, but since I have never used Sybyl, I cannot really compare. Maybe some of you could point out the advantages/disadvantages that you encountered when using either of the two programs. Thanks in advance for any helpful comments. Cheers, Carsten ~~~~~~~~~~~~~~~~~~~~~~~~~~~ Carsten Detering, Ph.D. University of Washington Seattle, WA 98195 Phone 206-543-5081 Fax 206-685-8665 email detering@u.washington.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Tue Nov 19 03:24:01 2002 Received: from euroscreen.be ([212.224.144.180]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAJ8O0u15035 for ; Tue, 19 Nov 2002 03:24:00 -0500 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C28FA5.55E0D42E" Subject: RE: sybyl vs insightII X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 Date: Tue, 19 Nov 2002 09:26:19 +0100 Message-ID: <5198ADA420721246BC35BFA666E24F1619B01A@euromail.euroscreen.be> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: sybyl vs insightII Thread-Index: AcKPo7HJR3MOooDvT+OE0UXWk8rzegAABOKA From: =?iso-8859-1?Q?Fr=E9d=E9ric_Ooms?= To: "Carsten Detering" , This is a multi-part message in MIME format. ------_=_NextPart_001_01C28FA5.55E0D42E Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Carsten, I had the chance to work with the 2 softwares during my Ph.D. and my = post-doc and to my point of view both softwares are complementary: Sybyl is really powerfull for the molecular modelling of small = molecules. You can also perform CoMFA studies which is not possible with = InsightII. Most of the docking tools use sybyl file format as input and = output. Another big advantage is that Sybyl will be available on Linux = in Q1 2003 so if you don't have a lot of money you should be able to run = Sybyl on a good Linux-PC. InsightII is more powerfull for the molecular modelling of the proteins = (homology modelling). Nevertheless it seems that things are changing and = I heard that improvment will be done in Sybyl to work more easily with = proteins. Finally Accelerys provide a tool (Catalyst) which is really = interesting for the development of pharmacophores and to perform = pharmacophoric searches. To summarize if you want to work especially with small molecules I would = suggest Sybyl but if you are working only on proteins and you are not = at all interested by the molecular modelling of small molecules then I = would suggest InsightII. Best regards Fred =20 -----Original Message----- From: Carsten Detering [mailto:detering@u.washington.edu]=20 Sent: Tuesday, November 19, 2002 1:57 AM To: chemistry@ccl.net Subject: CCL:sybyl vs insightII Hi folks, =20 for quite a while now, I am pondering about the folling: why is it that = most of the modellers use Sybyl rather than InsightII? In most = publications, people say in the methods section (or elsewhere) that they = used Sybyl. I was told once that InsightII was more powerful, once you = get to know it, but since I have never used Sybyl, I cannot really = compare. Maybe some of you could point out the advantages/disadvantages that you = encountered when using either of the two programs. Thanks in advance for any helpful comments. =20 Cheers, Carsten=20 =20 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ Carsten Detering, Ph.D. University of Washington Seattle, WA 98195 Phone 206-543-5081 Fax 206-685-8665 email detering@u.washington.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~ ------_=_NextPart_001_01C28FA5.55E0D42E Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Message
Dear=20 Carsten,
I had=20 the chance to work with the 2 softwares during my Ph.D. and my post-doc = and to=20 my point of view both softwares are complementary:
Sybyl=20 is really powerfull for the molecular modelling of small molecules. You = can also=20 perform CoMFA studies which is not possible with InsightII. Most of the = docking=20 tools use sybyl file format as input and output. Another big advantage = is that=20 Sybyl will be available on Linux in Q1 2003 so if you don't have a lot = of money=20 you should be able to run Sybyl on a good Linux-PC.
InsightII = is more=20 powerfull for the molecular modelling of the proteins (homology = modelling).=20 Nevertheless it seems that things are changing and I heard that = improvment will=20 be done in Sybyl to work more easily with proteins. Finally Accelerys = provide a=20 tool (Catalyst) which is really interesting for the development of=20 pharmacophores and to perform pharmacophoric=20 searches.
To=20 summarize if you want to work especially with small molecules I would = suggest=20 Sybyl but if you are working only on proteins and you  are not at = all=20 interested by the molecular modelling of small molecules then I would = suggest=20 InsightII.
Best=20 regards
Fred
 
 -----Original = Message-----
From:=20 Carsten Detering [mailto:detering@u.washington.edu]
Sent: = Tuesday,=20 November 19, 2002 1:57 AM
To: = chemistry@ccl.net
Subject:=20 CCL:sybyl vs insightII

Hi folks,
 
for quite a while now, I am pondering about the folling: why is = it that=20 most of the modellers use Sybyl rather than InsightII? In most = publications,=20 people say in the methods section (or elsewhere) that they used Sybyl. = I was=20 told once that InsightII was more powerful, once you get to know it, = but since=20 I have never used Sybyl, I cannot really compare.
Maybe some of you could point out the advantages/disadvantages=20 that you encountered when using either of the = two programs.
Thanks in advance for any helpful comments.
 
Cheers, Carsten 
 
~~~~~~~~~~~~~~~~~~~~~~~~~~~
Carsten Detering, = Ph.D.
University of=20 Washington
Seattle, WA 98195
Phone 206-543-5081
Fax=20 206-685-8665
email detering@u.washington.edu~~~~~~~~~~~~~~~~~~~~~~~~~~~
=00 ------_=_NextPart_001_01C28FA5.55E0D42E-- From chemistry-request@server.ccl.net Tue Nov 19 03:22:55 2002 Received: from alpha1.ebi.ac.uk ([193.62.196.122]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAJ8Msu14994 for ; Tue, 19 Nov 2002 03:22:54 -0500 Received: from goyder.ebi.ac.uk (goyder.ebi.ac.uk [193.62.199.57]) by alpha1.ebi.ac.uk (8.9.3/8.9.3) with ESMTP id IAA79529; Tue, 19 Nov 2002 08:22:15 GMT Date: Tue, 19 Nov 2002 08:22:14 +0000 (GMT) From: Kim Henrick To: "Cherif F. Matta" cc: Szilveszter Juhos , Computational Chemistry List Subject: Re: CCL:PDB H atom name convention In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id gAJ8Mtu14995 Re conventions for H atoms names etc and prochirality If you follow links from http://www.chem.qmw.ac.uk/iupac/ you will find the rules for H-atom names and pro-chirality, including details on amino acid naming (http://www.chem.qmw.ac.uk/iupac/misc/ppep1.html ) The BMRB http://www.bmrb.wisc.edu/ The IUPAC recommendations are published in J. L. Markley, Y. Arata, A. Bax, C. W. Hilbers, R. Kaptein, B. D. Sykes, P. E. Wright, and K. Wuethrich, "Recommendations for the Presentation of NMR Structures of Proteins and Nucleic Acids", Pure & Appl. Chem. 70, 117-142 (1998). in particular see http://www.bmrb.wisc.edu/ref_info/atom_nom.tbl and links from http://www.bmrb.wisc.edu/referenc/aa_chem.html kim On Mon, 18 Nov 2002, Cherif F. Matta wrote: > > Dear Dr. Juhos > > We have recently faced the same problem to present some of our results > regarding the geometries of the genetically-encoded amino acids. > In view of the lack of specific IUPAC rules (to my knowledge) for the > labeling of H atoms in the amino acids, we proposed a set of rule to > label them uniquely based on their geometric location with respect to > their neighbours. You will find this set of rules in the Appendix to > our following paper: > > Matta CF, Bader RFW. Atoms-in-molecules study of the genetically-encoded > amino acids. II. Computational study of molecular geometries. Proteins: > Struct. Funct. Genet. 2002;48:519-538. > > Hope this be of help. > > All the best. > > Cherif > > ----------------------------------------- > Chérif F. Matta, Ph. D. > Theoretical/Computational Chemist, > Polanyi Research Group, > Lash Miller Chemical Laboratories, > Chemistry Department, > University of Toronto, > 80 St. George Street (Room 261), > Toronto, Ontario, Canada M5S 1A1. > .......................................... > Telephone: (416) 978 - 3625 > Cellular: (416) 996 - 2444 > Fax: (416) 978 - 7580 > Web Site: http://chem.utoronto.ca/~cmatta/ > ------------------------------------------ > > > > > -= 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 > > > > > > Kim HENRICK henrick@ebi.ac.uk ::telephone: +44 (0) 1223 494629 From chemistry-request@server.ccl.net Tue Nov 19 11:31:50 2002 Received: from dedalus.lcc.ufmg.br ([150.164.65.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAJGVnu26592 for ; Tue, 19 Nov 2002 11:31:49 -0500 Received: from localhost (noronha@localhost) by dedalus.lcc.ufmg.br (8.9.3/8.9.3) with ESMTP id OAA37082 for ; Tue, 19 Nov 2002 14:31:38 -0200 Date: Tue, 19 Nov 2002 14:31:38 -0200 (BDB) From: antonio luiz oliveira de noronha X-X-Sender: noronha@dedalus To: chemistry@ccl.net Subject: GAMESS compilation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Sorry for this question but something is bothering me for some time. I have a RedHat 7.3 with GCC version 2.96 20000731 (Red Hat Linux 7.3 2.96-112). And even following, step by step, the GAMESS compilation manual ( readme.unix ), I can't compile the program. I receiving a message like this ======================== blas ============================== Tue Nov 19 14:14:17 BRST 2002 g77 -c -O2 -malign-double -fautomatic -Wno-globals -fno-globals blas.f g77: blas.f: No such file or directory g77: No input files unset echo mv: cannot stat `blas.o': No such file or directory For almost all steps. I tried compile it, after generating the actvte.x with several commands, and none of then worked ( they generate the actvte.x executable but it didn't seem to work). I tried g77 -o actvte.x actvte.f, f77 -o actvte.x actvte.f, gcc -o actvte.x actvte.f, and the one indicated for linux f2c actvte.f gcc -o actvte.x actvte.c -lf2c -lm ( wich didn't work at all even to generate the actvte.x, looks like I don have f2c installed ) How can I fiz this problem? Thank you for the patience From chemistry-request@server.ccl.net Tue Nov 19 13:00:58 2002 Received: from sandmail01.sd.accelrys.com ([209.120.169.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAJI0vu28954 for ; Tue, 19 Nov 2002 13:00:57 -0500 To: chemistry@ccl.net Cc: elizabethc@accelrys.com Subject: Accelrys Customer Training Workshops in January MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.9a January 7, 2002 Message-ID: From: jnauss@accelrys.com Date: Tue, 19 Nov 2002 10:00:56 -0800 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 11/19/2002 10:00:58 AM, Serialize complete at 11/19/2002 10:00:58 AM Content-Type: text/plain; charset="us-ascii" Accelrys Inc. will be holding the following training workshops at locations in the US and Europe during January 2003. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. Costs are $600 per day for commercial, $450 per day for government and $330 per day for academic. Macromolecular Modeling: Introduction to Life Science Modeling with InsightII 7th-8th January in San Diego, CA Structure-Based Drug Design with InsightII 9th-10th January in San Diego, CA Desktop Visualization and Communication with DS ViewerPro 21st January in San Diego, CA Introduction to Discovery Studio Modeling 22nd-23rd January in San Diego, CA For course details and registration see: http://www.accelrys.com/training/macro/schedule.html Rational Drug Design: DS MedChem Explorer 20th January in Cambridge, UK Introduction to Cerius2 for Life Sciences 21st-22nd January in Cambridge, UK Pharmacophore Generation with Catalyst 23rd-24th January in Cambridge, UK For course details and registration see: http://www.accelrys.com/training/rdd/schedule.html -- Jeffrey L. Nauss, Ph.D. Manager, Discovery Studio Training Accelrys Inc. 9685 Scranton Road San Diego, CA 92121-3752 Phone: 858-799-5555 Fax: 858-799-5100 E-mail: jnauss@accelrys.com http://www.accelrys.com/training From chemistry-request@server.ccl.net Tue Nov 19 09:40:13 2002 Received: from exchange.neokimia.com ([132.210.158.207]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAJEeDu23879 for ; Tue, 19 Nov 2002 09:40:13 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 content-class: urn:content-classes:message Subject: RE: sybyl vs insightII MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C28FD9.6061E9E0" Date: Tue, 19 Nov 2002 09:38:50 -0500 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: sybyl vs insightII Thread-Index: AcKPnsbo00wr6IkwQ6GfnN29zofpygANa1Dg From: "Axel Mathieu" To: "Carsten Detering" , This is a multi-part message in MIME format. ------_=_NextPart_001_01C28FD9.6061E9E0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello Carsten, =20 Unfortunately, I have not worked with Sybyl long enough to really = understand its advantages. On the other hand, I have used InsightII and = AMBER much during the past 2 years. I agree with Fred that Insight II is = powerful for homology modeling and that Sybyl is very good for small = moleules. The downside of Amber is of course that it uses command lines, = not an interactive GUI. Still, I obtained very good models from Amber = and InsightII (protein models that is!) and acceptable models in Sybyl = (small molecules). The problem with Sybly is that its conformational = searches for macrocyclic molecules still remains to be improved. When I = finished my studies and started my new job, my first objective was to = choose a modeling software (for small molecules) for which we would be = able to make protein models for rational design down the line. We were = looking for a cost effective software that would not require buying = expensive computers (I was setting up the Molecular Modeling department = for a new Biotech). Looking around, I came about MOE (Molecular = Operating Environment) from the Chemical Computing Group (CCG Inc.) = based in Montreal, QC. What is really interesting about MOE is that = there is only one price for the entire package (it is not modular) and = the price is VERY reasonable. Moreover, MOE runs on everything but MACS = for the moment!!!!! So not only can you run it on a PC for cheap, you = can also run it in windows if you cannot afford to hire a Linux = administrator (check out = http://www.bio-itworld.com/archive/071102/linux.html for a review about = cost effectiveness of using Linux). There will obviously be some loss in = computational power but it may be worth it ... =20 Anyhow, MOE can perform everything from small molecule modeling to large = proteins, docking, flexible alignments, etc. The only thing they are = missing at the moment is a particular section to handle NMR data. It is = very user friendly and can be very easy on the point and click side to = get what you want (maybe just a littlle too easy sometimes!). I don't = understand why MOE doesn't make it in these CCL archives because I know = a several large pharmas that use it and love it, along with academic = researches and undergraduate programs using it to teach molecular = modeling techniques. With respect to price, performace, and flexibility = of use, I (would like to) believe MOE will start taking a large segment = of the industry. Moreoever, their supprt is extensive and rapid. Take a = look at http://www.chemcomp.com for more details. The only disadvantage = of MOE is that they haven't been around for a very long time and = sometimes lack the vision of a molecular modeler, but they are keen to = learn. MOE was developped by programmers, not molecular modelers so you = can modify the entire MOE environment with a bit of programming skills. = Moreover, I find interesting tools that were developed by CCG for model = analyses (tools that I did not have the chance to discover in other = programs if they exist). Needless to say, I'm convinced that MOE is a = serious competitor to the other more traditional programs. On the other = hand, I'll say the same thinig to you as a molecular modelre at = Pharmacia told me: "... not one program can perform everything you need = which is why you need them all ;o)" . MOE on the other hand, comes close = to completeness in my opinion ... I haven't had to get other programs = yet (I've had it for 9 months). =20 Axel=20 =20 -----Original Message----- From: Carsten Detering [mailto:detering@u.washington.edu]=20 Sent: 18 novembre, 2002 19:57 To: chemistry@ccl.net Subject: CCL:sybyl vs insightII Hi folks, =20 for quite a while now, I am pondering about the folling: why is it that = most of the modellers use Sybyl rather than InsightII? In most = publications, people say in the methods section (or elsewhere) that they = used Sybyl. I was told once that InsightII was more powerful, once you = get to know it, but since I have never used Sybyl, I cannot really = compare. Maybe some of you could point out the advantages/disadvantages that you = encountered when using either of the two programs. Thanks in advance for any helpful comments. =20 Cheers, Carsten=20 =20 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ Carsten Detering, Ph.D. University of Washington Seattle, WA 98195 Phone 206-543-5081 Fax 206-685-8665 email detering@u.washington.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~ ------_=_NextPart_001_01C28FD9.6061E9E0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Message
Hello=20 Carsten,
 
Unfortunately, I have not worked with Sybyl = long enough=20 to really understand its advantages. On the other hand, I have used = InsightII=20 and AMBER much during the past 2 years. I agree with Fred that = Insight II=20 is powerful for homology modeling and that Sybyl is very good for small=20 moleules. The downside of Amber is of course that it uses command lines, = not an=20 interactive GUI. Still, I obtained very good models from Amber=20 and InsightII (protein models that is!) and acceptable models in = Sybyl=20 (small molecules). The problem with Sybly is that its conformational = searches=20 for macrocyclic molecules still remains to be improved. When I finished = my=20 studies and started my new job, my first objective was to choose a = modeling=20 software (for small molecules) for which we would be able to make = protein models=20 for rational design down the line. We were looking for a cost effective = software=20 that would not require buying expensive computers (I was setting up the=20 Molecular Modeling department for a new Biotech). Looking around, I came = about=20 MOE (Molecular Operating Environment) from the Chemical Computing Group = (CCG=20 Inc.) based in Montreal, QC. What is really interesting about MOE is = that there=20 is only one price for the entire package (it is not modular) and the = price is=20 VERY reasonable. Moreover, MOE runs on everything but MACS for the = moment!!!!!=20 So not only can you run it on a PC for cheap, you can also run it in = windows if=20 you cannot afford to hire a Linux administrator (check out http://www.= bio-itworld.com/archive/071102/linux.html for=20 a review about cost effectiveness of using Linux). There will obviously = be some=20 loss in computational power but it may be worth it = ...
 
Anyhow, MOE can perform everything from small = molecule=20 modeling to large proteins, docking, flexible alignments, etc. The only = thing=20 they are missing at the moment is a particular section to handle NMR = data. It is=20 very user friendly and can be very easy on the point and click side to = get what=20 you want (maybe just a littlle too easy sometimes!). I don't = understand why=20 MOE doesn't make it in these CCL archives because I know a several large = pharmas=20 that use it and love it, along with academic researches and = undergraduate=20 programs using it to teach molecular modeling techniques. With respect = to price,=20 performace, and flexibility of use, I (would like to) believe MOE will = start=20 taking a large segment of the industry. Moreoever, their supprt is = extensive and=20 rapid. Take a look at http://www.chemcomp.com for = more=20 details. The only disadvantage of MOE is that they haven't been around = for a=20 very long time and sometimes lack the vision of a molecular modeler, but = they=20 are keen to learn. MOE was developped by programmers, not molecular = modelers so=20 you can modify the entire MOE environment with a bit of programming=20 skills. Moreover, I find interesting tools that were developed by = CCG for=20 model analyses (tools that I did not have the chance to discover in = other=20 programs if they exist). Needless to say, I'm convinced that MOE is a = serious=20 competitor to the other more traditional programs. On the other hand, = I'll say=20 the same thinig to you as a molecular modelre at Pharmacia told me: "... = not one=20 program can perform everything you need which is why you need them all = ;o)" .=20 MOE on the other hand, comes close to completeness in my opinion ... I = haven't=20 had to get other programs yet (I've had it for 9 = months).
 
Axel
 
-----Original Message-----
From: Carsten Detering=20 [mailto:detering@u.washington.edu]
Sent: 18 novembre, 2002=20 19:57
To: chemistry@ccl.net
Subject: CCL:sybyl vs=20 insightII

Hi folks,
 
for quite a while now, I am pondering about the folling: why is it = that=20 most of the modellers use Sybyl rather than InsightII? In most = publications,=20 people say in the methods section (or elsewhere) that they used Sybyl. I = was=20 told once that InsightII was more powerful, once you get to know it, but = since I=20 have never used Sybyl, I cannot really compare.
Maybe some of you could point out the advantages/disadvantages=20 that you encountered when using either of the = two programs.
Thanks in advance for any helpful comments.
 
Cheers, Carsten 
 
~~~~~~~~~~~~~~~~~~~~~~~~~~~
Carsten Detering, = Ph.D.
University of=20 Washington
Seattle, WA 98195
Phone 206-543-5081
Fax=20 206-685-8665
email detering@u.washington.edu~~~~~~~~~~~~~~~~~~~~~~~~~~~
------_=_NextPart_001_01C28FD9.6061E9E0-- From chemistry-request@server.ccl.net Tue Nov 19 20:44:48 2002 Received: from yakko.cimav.edu.mx ([148.223.46.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAK1ilu06257 for ; Tue, 19 Nov 2002 20:44:47 -0500 Received: from LAQUICOM02 (mild.cimav.edu.mx [148.223.46.1]) by yakko.cimav.edu.mx (8.11.6/8.11.2) with SMTP id gAK2Ydi16305; Tue, 19 Nov 2002 19:34:39 -0700 Message-ID: <006901c2902e$6c864770$fc02000a@LAQUICOM02> From: "Dr. Daniel Glossman-Mitnik" To: , , , Subject: g98 for Linux + LINDA problem Date: Tue, 19 Nov 2002 18:47:34 -0600 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0066_01C28FFC.1FB94000" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 Disposition-Notification-To: "Dr. Daniel Glossman-Mitnik" X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0066_01C28FFC.1FB94000 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear netters: I have the following problem trying to make G98 run in paralell with LINDA: I have built a LINUX Clusters with four nodes. I have compiled G98 with Portland Compiler on Red Hat 7.2 (kernel 2.4.7.10) and it runs smoothly. I purchased Linda. It is Rev. 5.0. Linux binary. It came as a=20 .rpm file, so I tried to open with no luck. The rpm file says that it is for RH 5.1 to 6.0. Suspecting that I have received an older version, I went to the SCA web page and I downloaded the latest trial version available. I tried to rpm this file but with no luck again. The file is labelled as for RH 7.1. Thus, my questions are: * Is there anybody who has built a Linux Cluster with RH 7.2 and been lucky running G98 with Linda ? * Is there any problem with RH 7.2 for paralell computations and should I install RH 7.1 ? * Why the rpm file can't be open with rpm in order to install LINDA? Any suggestions will be appreciated. Thanks in advance Dr. Daniel = Glossman-Mitnik *************************************************************************= *** Dr. Daniel Glossman-Mitnik Centro de Investigacion en Materiales Avanzados (CIMAV) LAQUICOM - Laboratorio de Quimica Computacional Miguel de Cervantes 120 - Complejo Industrial Chihuahua Chihuahua, Chih. 31109 - Mexico Phone: (52) 614 4391151 FAX: (52) 614 4391112 E-mail: daniel.glossman@cimav.edu.mx glossman@hotmail.com dglossman@yahoo.com *************************************************************************= *** ------=_NextPart_000_0066_01C28FFC.1FB94000 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
 
Dear netters:
 
I have the following problem trying to = make G98 run=20 in paralell
with LINDA:
 
I have built a LINUX Clusters with four = nodes.=20 I have compiled
G98 with Portland Compiler on Red Hat = 7.2 (kernel=20 2.4.7.10)
and it runs smoothly.
 
I purchased Linda. It is Rev. 5.0. = Linux binary. It=20 came as a
.rpm file, so I tried to open with no = luck. The rpm=20 file says that
it is for RH 5.1 to 6.0. Suspecting = that I have=20 received an older
version, I went to the SCA web page and = I=20 downloaded the latest
trial version available. I tried to rpm = this file=20 but with no luck
again. The file is labelled as for RH=20 7.1.
 
Thus, my questions are:
 
* Is there anybody who has built a = Linux Cluster=20 with RH 7.2
and been lucky running G98 with Linda=20 ?
 
* Is there any problem with RH 7.2 for = paralell=20 computations
 and should I install RH 7.1 = ?
 
* Why the rpm file can't be open with = rpm in order=20 to install LINDA?
 
 
 
Any suggestions will be = appreciated.
 
 
Thanks in advance
 
          &nbs= p;            = ;            =             &= nbsp;  =20 Dr. Daniel Glossman-Mitnik
 
 
 
****************************************************************= ************
Dr.=20 Daniel Glossman-Mitnik
Centro de Investigacion en Materiales = Avanzados=20 (CIMAV)
LAQUICOM - Laboratorio de Quimica Computacional
Miguel de=20 Cervantes 120 - Complejo Industrial Chihuahua
Chihuahua, Chih. 31109 = -=20 Mexico
Phone: (52) 614 4391151      FAX: = (52) 614=20 4391112
E-mail: daniel.glossman@cimav.edu.mx=
           = ;=20 glossman@hotmail.com
 &n= bsp;         =20 dglossman@yahoo.com
**********= ******************************************************************=
------=_NextPart_000_0066_01C28FFC.1FB94000-- From chemistry-request@server.ccl.net Tue Nov 19 17:13:30 2002 Received: from mail2.cc.duq.edu ([165.190.121.190]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAJMDUu01778 for ; Tue, 19 Nov 2002 17:13:30 -0500 Received: from woodstock.cr.duq.edu (woodstock.cr.duq.edu [165.190.1.35]) by mail2.cc.duq.edu (8.11.6/8.10.1) with SMTP id gAJMDPj07636 for ; Tue, 19 Nov 2002 17:13:30 -0500 (EST) Received: (from ritchie [165.190.51.63]) by woodstock.cr.duq.edu (NAVGW 2.5.2.11) with SMTP id M2002111917132516459 for ; Tue, 19 Nov 2002 17:13:25 -0500 Message-ID: <00d601c29018$e11f87b0$3f33bea5@ritchie> From: "Pranav Dalal" To: Subject: sugar - oxazoline parameters Date: Tue, 19 Nov 2002 17:13:24 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_00D3_01C28FEE.F83B27D0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_00D3_01C28FEE.F83B27D0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, I am looking for forcefield parameters for oxazoline. I would = appreciate if somebody could point me in the right direction. Thank you Pranav ------=_NextPart_000_00D3_01C28FEE.F83B27D0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi,
I am looking for forcefield parameters = for=20 oxazoline.  I would appreciate if somebody could point me in the = right=20 direction.
 
Thank you
Pranav
------=_NextPart_000_00D3_01C28FEE.F83B27D0-- From chemistry-request@server.ccl.net Tue Nov 19 14:22:30 2002 Received: from wrzx35.rz.uni-wuerzburg.de ([132.187.3.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAJJMUu31186 for ; Tue, 19 Nov 2002 14:22:30 -0500 Received: from wrzx34.rz.uni-wuerzburg.de (wrzx34.rz.uni-wuerzburg.de [132.187.3.34]) by wrzx35.rz.uni-wuerzburg.de (8.8.8/8.8.8/uniwue-MM-1.05) with ESMTP id UAA06792 for ; Tue, 19 Nov 2002 20:22:25 +0100 (MET) Received: from localhost (localhost [127.0.0.1]) by virusscan.rz.uni-wuerzburg.de (Postfix) with ESMTP id 812DBD0F for ; Tue, 19 Nov 2002 20:22:25 +0100 (CET) Received: from wrzx37.rz.uni-wuerzburg.de (wrzx37.rz.uni-wuerzburg.de [132.187.3.37]) by wrzx34.rz.uni-wuerzburg.de (Postfix) with ESMTP id 62FB6BA7 for ; Tue, 19 Nov 2002 20:22:25 +0100 (CET) Received: from wocx51.chemie.uni-wuerzburg.de (wocx51.chemie.uni-wuerzburg.de [132.187.64.51]) by wrzx37.rz.uni-wuerzburg.de (Postfix) with ESMTP id 4A0B8A10F for ; Tue, 19 Nov 2002 20:22:25 +0100 (CET) Received: from chemie.uni-wuerzburg.de (wocd73.chemie.uni-wuerzburg.de [132.187.64.173]) by wocx51.chemie.uni-wuerzburg.de (SGI-8.9.3/8.9.3/uniwue-M-1.0) with ESMTP id UAA88567 for ; Tue, 19 Nov 2002 20:22:25 +0100 (MEZ) Message-ID: <3DDA9084.4179033A@chemie.uni-wuerzburg.de> Date: Tue, 19 Nov 2002 20:27:00 +0100 From: Bernd Engels X-Mailer: Mozilla 4.78 [de] (Windows NT 5.0; U) X-Accept-Language: de MIME-Version: 1.0 To: ccl Subject: vibrational CD Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Virus-Scanned: by AMaViS snapshot-20020422 Dear all, some experimentalist got interested in the computation of vibrational CD. Do anyone know, which programm package includes this property? Bernd -- Prof. Dr. Bernd Engels Institut für Organische Chemie Bayerische Julius-Maximilians-Universität Würzburg Am Hubland D- 97074 Würzburg Tel.: ++49 (0)931 - 888 - 5394 Fax: ++49 (0)931 - 888 - 4606 e-mail: bernd@chemie.uni-wuerzburg.de From chemistry-request@server.ccl.net Tue Nov 19 22:49:22 2002 Received: from web12304.mail.yahoo.com ([216.136.173.102]) by server.ccl.net (8.11.6/8.11.0) with SMTP id gAK3nMu08663 for ; Tue, 19 Nov 2002 22:49:22 -0500 Message-ID: <20021120034918.92524.qmail@web12304.mail.yahoo.com> Received: from [212.25.107.100] by web12304.mail.yahoo.com via HTTP; Tue, 19 Nov 2002 19:49:18 PST Date: Tue, 19 Nov 2002 19:49:18 -0800 (PST) From: omar Deeb Subject: computer methods in chemistry To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-744235245-1037764158=:91636" --0-744235245-1037764158=:91636 Content-Type: text/plain; charset=us-ascii Dear ccl users, We are interested in giving our undergraduate students a new course titled "computer methods in chemistry" or "chemistry and computer". In this course , we want the students to use the computer in all the fields of chemistry. It is not exactly a computational chemistry or molecular modeling course rather than using computers in chemistry and the molecular moldeling will be one of the experiments . The course will be one lecture a week plus one lab. (3 credit hours) Any suggestions. Thanks in advance Dr. Omar Deeb Alquds University --------------------------------- Do you Yahoo!? Yahoo! Web Hosting - Let the expert host your site --0-744235245-1037764158=:91636 Content-Type: text/html; charset=us-ascii

Dear ccl users,

We are interested in giving our undergraduate students a new course titled "computer methods in chemistry" or "chemistry and computer". In this course , we want the students to use the computer in all the fields of chemistry.

It is not exactly a computational chemistry or molecular modeling course rather than using computers in chemistry and the molecular moldeling will be one of the experiments .

The course will be one lecture a week plus one lab. (3 credit hours)

Any suggestions.

Thanks in advance

Dr. Omar Deeb

Alquds University


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