From chemistry-request@server.ccl.net Thu Nov 21 07:50:22 2002 Received: from netra.ksu.edu.sa ([212.138.39.67]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gALCoL718452 for ; Thu, 21 Nov 2002 07:50:21 -0500 Received: from sun1.ksu.edu.sa (sun1.ksu.edu.sa [212.138.39.3]) by netra.ksu.edu.sa (8.9.0/8.9.0) with ESMTP id QAA20079 for ; Thu, 21 Nov 2002 16:16:17 -1700 (Mideast/Riyadh) Received: from adelelazhary ([10.0.21.133]) by sun1.ksu.edu.sa (8.9.0/8.7.3) with SMTP id PAA24897 for ; Thu, 21 Nov 2002 15:42:52 -0300 (GMT) Message-ID: <000c01c2915d$12715b00$8515000a@ksu.edu.sa> From: "Adel El-Azhary" To: Subject: Conformational search, Alchemy 2000 vs MM3 Date: Thu, 21 Nov 2002 15:54:04 +0300 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0009_01C29176.378C3860" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 This is a multi-part message in MIME format. ------=_NextPart_000_0009_01C29176.378C3860 Content-Type: text/plain; charset="windows-1256" Content-Transfer-Encoding: quoted-printable Deae CCL users: I am doing conformational search using the Alchemy 2000 program. It = looks that my molecule has a large ring of 18 atoms and the number of = possible conformations is quite large and taking a quite lot of effort. = This is because I create say 200 conformations and then do MM3 geometry = optimization on each manually and then examine each output. I have to = repeat this step for about a 100 time. I was thinking that the MM3(2000) = program running on unix might be more firiendly. Does anyone has a = suggestion or a similar experience.=20 Best regards, Adel El-Azhary ------=_NextPart_000_0009_01C29176.378C3860 Content-Type: text/html; charset="windows-1256" Content-Transfer-Encoding: quoted-printable

Deae CCL users:

I am doing conformational search using = the Alchemy=20 2000 program. It looks that my molecule has a large ring of 18 atoms and = the=20 number of possible conformations is quite large and taking a quite lot = of=20 effort. This is because I create say 200 conformations and then do MM3 = geometry=20 optimization on each manually and then examine each output. I have to = repeat=20 this step for about a 100 time. I was = thinking=20 that the MM3(2000) program running on unix might be more firiendly. Does = anyone=20 has a suggestion or a similar experience.

Best regards,

Adel = El-Azhary

------=_NextPart_000_0009_01C29176.378C3860-- From chemistry-request@server.ccl.net Thu Nov 21 07:56:25 2002 Received: from prserv.net ([32.97.166.34]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gALCuO718956 for ; Thu, 21 Nov 2002 07:56:24 -0500 Received: from attglobal.net (slip-12-64-48-7.mis.prserv.net[12.64.48.7]) by prserv.net (out4) with SMTP id <2002112112562220404uv4ioe>; Thu, 21 Nov 2002 12:56:23 +0000 Message-ID: <3DDC9222.1754970F@attglobal.net> Date: Thu, 21 Nov 2002 07:58:26 +0000 From: jmmckel@attglobal.net Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: John Bushnell CC: Connie Chang , chemistry@ccl.net Subject: Re: CCL:Gaussian98W and charged molecules (again) References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Thought, If the stable structure has symmetry, try turning off symmetry in the SCF for the frequency calculation. Am surprised to learn that Gaussian does frequency calculations only with PM3. I thought that IOP(4/20=M) allows choices between all the options found in MOPAC. John McKelvey John Bushnell wrote: > Hi, > > I think your problem now is that Gaussian only does > numerical frequency calculations with PM3 (according to > the manual we have). So Gaussian needs to do a whole slew > of SCF's to get frequencies. I have had difficult cases > where getting convergence was hard, but became impossible > at some point as Gaussian perturbs the structure and > redoes the SCF for a frequency calculation. This is > particularly bad for cases where the minimum has symmetry, > but the perturbed species do not. Fortunately, Gaussian > now can do analytical frequencies for DFT. I would be > surprised if adding SCF=qc did not help unless for some > reason this was not supported for PM3. But you never know. > > - John > > On Wed, 20 Nov 2002, Connie Chang wrote: > > > Hi -- > > > > I'm sorry to bother everyone again... But I have another question about > > Gaussian... > > > > I was finally able to get Gaussian to geometrically optimize my charged > > (-1) molecule with the following Route specification: > > > > # PM3 SCF=vshift=500 SCF=(Maxcyc=1200) Opt > > > > However, when I ran the job again and added the Freq keyword, although > > the geometry optimized, the SCF energy calculation in the Freq part of > > the job oscillates again until the job terminates with a > > UNABLE TO ACHIEVE SELF-CONSISTENCE error. Why does this happen? If I > > have the following route specification > > > > #PM3 SCF=vshift=500 SCG=(Maxcyc=1200) Opt Freq Test > > > > Does Gaussian know to use my prior specifications for finding the SCF > > (i.e. the Vshift and the increased MaxCyc) or does it use it but still > > fail? > > > > Does anyone have any suggestions? > > > > And thanks again for all your previous suggestions! > > > > Connie > > > > > > > > > > > > > > > > -= 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 Thu Nov 21 08:01:28 2002 Received: from mel-rto4.wanadoo.fr ([193.252.19.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gALD1S719763 for ; Thu, 21 Nov 2002 08:01:28 -0500 Received: from mel-rta9.wanadoo.fr (193.252.19.69) by mel-rto4.wanadoo.fr (6.5.007) id 3DDA133F001B0165 for chemistry@server.ccl.net; Thu, 21 Nov 2002 14:01:26 +0100 Received: from mail-web9 (193.252.19.75) by mel-rta9.wanadoo.fr (6.5.007) id 3DD3EB76003BEDB2 for chemistry@server.ccl.net; Thu, 21 Nov 2002 14:01:26 +0100 Message-ID: <3DD3EB76003BEDB2@mel-rta9.wanadoo.fr> (added by postmaster@wanadoo.fr) Received: from '' by www.wanadoo.fr with HTTP; Date: Thu, 21 Nov 2002 14:01:26 +0100 (MET) From: "Thomas HENRY" To: Subject: Autodock 3.0.5 Torsions 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 gALD1S719766 Dear CCL members, I try to use more torsions than 32 in Autodock3. I have changed MAX_TORS in constants.h, but the program returns to me : "ligand does not fit within grid, while in this orientation ! Trying a new, random-generated rigid body rotation" And the program can't stop, i must kill it. I am hoping someone could tell me what I am doing wrong. Thank you for your help. thomas HENRY University of Lille1 FRANCE henryt@wanadoo.fr From chemistry-request@server.ccl.net Thu Nov 21 04:42:32 2002 Received: from southwark.inpharmatica.co.uk ([195.102.24.12]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAL9gV714349 for ; Thu, 21 Nov 2002 04:42:31 -0500 Received: from inpharmatica.co.uk (localhost [127.0.0.1]) by southwark.inpharmatica.co.uk (SGI-8.9.3/8.9.3) with ESMTP id JAA53158; Thu, 21 Nov 2002 09:42:18 GMT Sender: mbrandl@southwark.inpharmatica.co.uk Message-ID: <3DDCAA7A.57FCD5DB@inpharmatica.co.uk> Date: Thu, 21 Nov 2002 09:42:18 +0000 From: Maria Brandl X-Mailer: Mozilla 4.76C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: olivier walker CC: chemistry@ccl.net Subject: Re: CCL:Ramachadran plot for the 20 amino acids References: <5.1.1.6.0.20021120134715.00aa8900@imap.wam.umd.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Olivier, you can use http://www.imb-jena.de/IMAGE_AA.html and find links to http://alpha2.bmc.uu.se/gerard/rama/ramarev.html#S8 and http://alpha2.bmc.uu.se/gerard/rama/ramarev.html#S10 for amino acid-specific Ramachandran plots in gif and ps formats. The program "procheck" (http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html) also gives you that sort of information. Best regards, Maria Brandl > Hi all, > > This question is not entirely related to computational chemistry but I need > it to move forward in my program. > Does anyone know where I can find Ramachadran plot for each of the 20 > amino-acid (or the allowed phi and psi angles to rotate around N---Calpha----C) > > I found it for some of them in Fasman's book "prediction of protein > structure and the principles of protein conformation" but I would like to > know if this kind of information exists for all amino acid. (book, review > or web site) > > Thanks in advance > > Olivier > > ************************************************** > Olivier WALKER > Department of Chemistry and Biochemistry > University of Maryland > College Park, MD 20742 > ************************************************** > E-mail : oliwalk@wam.umd.edu > ************************************************** > > -= 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 Thu Nov 21 02:42:45 2002 Received: from anchor-post-33.mail.demon.net ([194.217.242.91]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAL7gi711978 for ; Thu, 21 Nov 2002 02:42:44 -0500 Received: from ursus.demon.co.uk ([158.152.126.154] helo=ursus.cam.ac.uk) by anchor-post-33.mail.demon.net with esmtp (Exim 3.35 #1) id 18Elyz-000Fba-0X; Thu, 21 Nov 2002 07:42:42 +0000 Message-Id: <5.1.1.6.0.20021121072035.04ac2e98@hermes.cam.ac.uk> X-Sender: pm286@hermes.cam.ac.uk X-Mailer: QUALCOMM Windows Eudora Version 5.1.1 Date: Thu, 21 Nov 2002 07:39:45 +0000 To: Computational Chemistry List From: Peter Murray-Rust Subject: Re: CCL:Release of CML2.0 (Chemical Markup Language) ... Cc: Alk Dransfeld In-Reply-To: References: <5.1.1.6.0.20021118202510.029a1808@hermes.cam.ac.uk> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed At 11:00 20/11/2002 +0100, Alk Dransfeld wrote: >Dear Computational Chemists (CCs), > >The main aspect of storing results in archives and/or >dictionaries, whether CML based or not, is for CCs to >be able to REtrieve instead of REcalculate. Therefore, >an effective mechanism to find things in CML is essential. XML per se provides an extremely effective retrieval mechanism based on the XPath formalism and the XML Query language. It is possible to query and retrieve at the level of granularity that is provided in the markup language. This generic approach works well when the concepts are all interpretable by XML technology such as XPath. Thus //molecule[count(atomArray/atom[@elementType='O'])>2] will retrieve all molecules with 3 or more oxygen atoms in the document (wherever they occur). This is remarkably powerful for a generic language. >On Tue, 19 Nov 2002 09:59:10, Peter Murray-Rust wrote: >>... >>Several other modules are under active development >>- Computational Chemistry Markup Language (CCML) ... >>- CMLReaction. CML already supports reactions ... >>- CMLQuery. This is being built on the emerging XML Query language >>... > >Why wait for an "emerging XML Query language" >when the Xpath mechanism is already developed under surveillance >of W3C and is already supported in various toolkits (for instance >the PERL module XML::XPath from http://xml.sergeant.org/xpath.xml) ? Several working drafts of XML Query were released this week and are worth reading. Basically XPath is only part of the query mechanism - among the issues addressed are what objects are returned (pointers?, copies?) and context. However the main work is in synthesizing the various current methods of querying (many of which are in Closed software systems and so the semantics are not always easy to determine precisely). Essentially CML Query will have a representation independent of the target programming system and can translate into the local query language as appropriate. This is not easy, but we are making good progress with a program-independent CCML and the experience there will be useful for CML Query. >Is Xpath ( http://www.w3.org/TR/xpath ) >inappropriate to deal with CML? Beyond what I have described, yes. It is not easy to (say) retrieve a carbon atom with trigonal planar coordination using XSLT alone. This is a derived concept and requires domain specific queries. >Is this because the addressability >in CML is poor? The addressability is fine grained (atoms, bonds and electrons can have individual IDs and be precisely addressed), but some of the chemical concepts related to queries are (deliberately) not present in CML. CML represents what a substance IS, whereas CML Query introduces more generic concepts (coordination, hybridisation, rings, geometry, etc.) >I think CCs community should follow this weeks CLRC meeting >in United Kingdom to see where+how they go and look for >data. We shall publish our documentation shortly afterwards. Some is already present on http://www.xml-cml.org P. From chemistry-request@server.ccl.net Thu Nov 21 10:08:29 2002 Received: from postoffice2.mail.cornell.edu ([132.236.56.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gALF8T724137 for ; Thu, 21 Nov 2002 10:08:29 -0500 Received: from pobox.com (arginine.chem.cornell.edu [128.253.86.74]) by postoffice2.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id KAA06514; Thu, 21 Nov 2002 10:08:26 -0500 (EST) Message-ID: <3DDCF6EA.8A06299E@pobox.com> Date: Thu, 21 Nov 2002 10:08:26 -0500 From: Eric Bennett X-Mailer: Mozilla 4.75 [en] (X11; U; OSF1 V5.1 alpha) X-Accept-Language: en MIME-Version: 1.0 To: olivier walker , chemistry@ccl.net Subject: Re: CCL:Ramachadran plot for the 20 amino acids References: <5.1.1.6.0.20021120134715.00aa8900@imap.wam.umd.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit olivier walker wrote: > > Hi all, > > This question is not entirely related to computational chemistry but I need > it to move forward in my program. > Does anyone know where I can find Ramachadran plot for each of the 20 > amino-acid (or the allowed phi and psi angles to rotate around N---Calpha----C) The program PROCHECK, which is part of the CCP4 program suite, produces Ramachandran plots for each amino acid type when you run it on a protein structure. The plots it makes have a background color that varies according to how appropriate the phi and psi angles are for that particular amino acid. It just gives the colors rather than actual numerical ranges. Here's the reference for the program... maybe it can point you to the source of the information they used to color their plots and give you more detailed information: Roman A Laskowski, Malcolm W MacArthur, David S Moss and Janet M Thornton, J. App. Cryst. 26 283 (1993) The CCP4 package is here: http://www.ccp4.ac.uk/main.html -- Eric Bennett ( ericb@pobox.com ; http://www.pobox.com/~ericb ) We've been doubling sales every 18 months. However, when you start > from zero, it takes a long while. - Stephen Yeo, marketing director for Wyse From chemistry-request@server.ccl.net Thu Nov 21 09:48:46 2002 Received: from sccrmhc01.attbi.com ([204.127.202.61]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gALEmk709331 for ; Thu, 21 Nov 2002 09:48:46 -0500 Received: from daveg.cachesoftware.com ([12.224.252.136]) by sccrmhc01.attbi.com (InterMail vM.4.01.03.27 201-229-121-127-20010626) with ESMTP id <20021121144845.OMVG3664.sccrmhc01.attbi.com@daveg.cachesoftware.com>; Thu, 21 Nov 2002 14:48:45 +0000 Message-Id: <5.2.0.9.0.20021121062750.0356d530@mail.cachesoftware.com> X-Sender: X-Mailer: QUALCOMM Windows Eudora Version 5.2.0.9 Date: Thu, 21 Nov 2002 06:48:08 -0800 To: omar Deeb From: David Gallagher Subject: Computer methods in chemistry Cc: chemistry@ccl.net In-Reply-To: <20021120034918.92524.qmail@web12304.mail.yahoo.com> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_42126634==.ALT" --=====================_42126634==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Hi Omar, There is an instructors book that integrates computational methods into Organic, Inorganic, Physical and General chemistry and it comes complete with protocols, student pre-lab and post-lab exercises, and instructor's notes. "Teaching with CAChe" is written by James Currie and Crispin Wong of Pacific University and the PDF version is available for free download from http://www.cachesoftware.com/teaching/ . Educators can request a hard copy for review from kbriggs@cachesoftware.com. David Gallagher, Fujitsu. At 07:49 PM 11/19/2002 -0800, omar Deeb wrote: >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 --=====================_42126634==.ALT Content-Type: text/html; charset="us-ascii" Hi Omar,

There is an instructors book that integrates computational methods into Organic, Inorganic, Physical and General chemistry and it comes complete with protocols, student pre-lab and post-lab exercises, and instructor's notes. "Teaching with CAChe" is written by James Currie and Crispin Wong of Pacific University and the PDF version is available for free download from http://www.cachesoftware.com/teaching/ . Educators can request a hard copy for review from kbriggs@cachesoftware.com.

David Gallagher, Fujitsu.

At 07:49 PM 11/19/2002 -0800, omar Deeb wrote:

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

--=====================_42126634==.ALT-- From chemistry-request@server.ccl.net Thu Nov 21 12:09:47 2002 Received: from ntsmtp01.usc.edu ([128.125.179.129]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gALH9k713562 for ; Thu, 21 Nov 2002 12:09:47 -0500 Received: by NTSMTP01 with Internet Mail Service (5.5.2653.19) id ; Thu, 21 Nov 2002 09:09:46 -0800 Message-ID: From: "Pandey, Jaya" To: "'chemistry@ccl.net'" Subject: Drug Discovery Date: Thu, 21 Nov 2002 09:09:39 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain Dear All, Please suggest me a freeware or a download to undersatnd the principles of Drug Disocvery and designing small molecules for drug testing, Thanks Jaya