From owner-chemistry@ccl.net Tue Aug 5 10:37:01 2008 From: "Oellien, F (Frank) frank.oellien*sp.intervet.com" To: CCL Subject: CCL: 4. German Conference on Chemoinformatics - Final Call for Papers Message-Id: <-37488-080805103345-3010-KFqFRi/OvzRpJUdgUsMRBw*server.ccl.net> X-Original-From: "Oellien, F (Frank)" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 5 Aug 2008 16:33:28 +0200 MIME-Version: 1.0 Sent to CCL by: "Oellien, F (Frank)" [frank.oellien() sp.intervet.com] !!! FINAL CALL FOR PAPERS !!! 4th German Conference on Chemoinformatics Hotel 'Der Achtermann', Goslar, Germany 9 - 11 November 2008 DEADLINE FOR SUBMISSION: August 10, 2008 Dear Colleagues, The CIC division of the German Chemical Society announces the 4. German = Conference on Chemoinformatics (http://www.gdch.de/gcc2008) to be held = in Goslar, Germany, November 9 - 11, 2008. We are inviting the submission of abstracts for talks and posters in the = following plenary sessions: * Chemoinformatics and Drug Development * Chemical Information * Molecular Modelling * Computational Material Science and Nanotechnology and other highlights in the field of Computational Chemistry. We encourage the submission of papers on both applications and case = studies as well as on method development and algorithmic work.=20 Visit the conference website at www.gdch.de/gcc2008 for more = information, including a link to the online abstract submission = interface, a more detailed, downloadable PDF version of the 1. circular = as well as additional information. The final deadline for the submission of posters and oral contributions = is August 10, 2008. Last minute posters can also be submitted until = October 28, 2008. The deadline for scholarships is August 20, 2008. Invited Speakers are: J=FCrgen Bajorath, University of Bonn, D Michael Berthold, University of Konstanz , D=20 Marcus Elstner, University of Braunschweig, D=20 Robert Glen, Cambridge University, UK=20 Kurt Varmuza, Technical University of Vienna, A=20 Brian Vickery, Chemistry Central, London, UK Because of the strong increase of the number of attendees during the = last two conferences, we have to impose a limit for the number of = conference participants this year (200 max). So please register early. = The online registration is now open = (http://www.gdch.de/vas/tagungen/tg/5327/anmeld__e.htm). http://www.gdch.de/vas/tagungen/tg/circular1.pdf I hope to see you in Goslar. Frank Oellien, Conference Chairman ################################################## Mit freundlichen Gr=FC=DFen / With kind regards =20 Dr. Frank Oellien BioChemInformatics Scientist Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany =20 E-Mail: frank.oellien*_*sp.intervet.com Phone: +49 (6130) 948 365 Fax: +49 (6130) 948 517 Home http://www.intervet.com =20 Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 = Gesch=E4ftsf=FChrer: Dr. Peter Schmid =20 -------------------------------------- This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- please immediately and permanently delete. -------------------------------------- From owner-chemistry@ccl.net Tue Aug 5 11:24:01 2008 From: "Simon Halstead shalstead . hit.edu.cn" To: CCL Subject: CCL: Ab initio on bridged rings Message-Id: <-37489-080805032936-17103-beJZc+Pasg1+Vp2shwhUaQ/a\server.ccl.net> X-Original-From: "Simon Halstead" Date: Tue, 5 Aug 2008 03:29:33 -0400 Sent to CCL by: "Simon Halstead" [shalstead:hit.edu.cn] Dear all, I am trying to optimize some bridged (1-4) cyclohexane rings. I initially optimized them using sempiempirical methods. These calculations converged very rapidly. However, I then tried to optimize the resulting structures at a higher level of theory. These high level calculations have failed to converge, despite being run for a large number of steps. I have tried HF, MP2 and B3LYP with a variety of basis sets but nothing appears to converge. Visualizing the outputs of the failed calculations shows no problems with the structure. Does anyone have any experience with structures like this or can anyone give me a suggestion of how best to optimize bridged rings? I am using GAMESS if this makes any differnce. Thanks for your help, Simon Halstead From owner-chemistry@ccl.net Tue Aug 5 11:58:00 2008 From: "Diego Gomez darkego21(~)yahoo.com" To: CCL Subject: CCL:G: Frequencies calculation mistake!! Message-Id: <-37490-080805115313-13785-fgmcqWsJBX3C35vqwQRwUA:_:server.ccl.net> X-Original-From: "Diego Gomez" Date: Tue, 5 Aug 2008 11:53:09 -0400 Sent to CCL by: "Diego Gomez" [darkego21%yahoo.com] Hello dear colleagues. Im doing a frequency calculation with Gaussian03. The structure contain V, O, Si, Al and H atoms; only one or two V atoms. the simple route section in the imput file that I have used is: # ub3lyp/lanl2dz freq test and I have got the following mistake: Differentiating once with respect to electric field. with respect to dipole field. Differentiating once with respect to nuclear coordinates. FoFCou: FMM=T IPFlag= 0 FMFlag= 100000 FMFlg1= 8193 NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T. Symmetry not used in FoFCou. FMM levels: 10 Number of levels for PrismC: 9 After all major allocation allocation failure: iend,mxcore= 1347663 1228066 Error termination via Lnk1e in C:\G03W\l1002.exe at Thu Jul 31 19:44:09 2008. Job cpu time: 2 days 5 hours 6 minutes 27.0 seconds. File lengths (MBytes): RWF= 859 Int= 0 D2E= 0 Chk= 6 Scr= 1 If anyone know a possible way to adjust my problem, I would be very grateful with him or her... Thanks in advance. Diego Armando Gmez H. From owner-chemistry@ccl.net Tue Aug 5 14:57:00 2008 From: "John McKelvey jmmckel!^!gmail.com" To: CCL Subject: CCL: Ab initio on bridged rings Message-Id: <-37491-080805140751-13844-b5jV6HPwIGkbk8FWemJGzw%%server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_66800_10476889.1217958088617" Date: Tue, 5 Aug 2008 13:41:28 -0400 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel,+,gmail.com] ------=_Part_66800_10476889.1217958088617 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Simon, Could you be more specific about what does not converge, the SCF or geometry optimizations?. If the SCF fails to converge, then a geometry optimization will likely fail also. If the issue is thae SCF will the SCF converge at the HF level with a simple basis such as STO-3G or 3-21? Do the HOMO and LUMO orbitals swap around during the SCF? Does level shifting help? Regards, John McKelvey On Tue, Aug 5, 2008 at 3:29 AM, Simon Halstead shalstead . hit.edu.cn < owner-chemistry**ccl.net> wrote: > > Sent to CCL by: "Simon Halstead" [shalstead:hit.edu.cn] > > Dear all, > > I am trying to optimize some bridged (1-4) cyclohexane rings. I initially > optimized them using sempiempirical methods. These calculations converged > very rapidly. However, I then tried to optimize the resulting structures at > a higher level of theory. These high level calculations have failed to > converge, despite being run for a large number of steps. I have tried HF, > MP2 and B3LYP with a variety of basis sets but nothing appears to converge. > Visualizing the outputs of the failed calculations shows no problems with > the structure. > Does anyone have any experience with structures like this or can anyone > give me a suggestion of how best to optimize bridged rings? > I am using GAMESS if this makes any differnce. > > Thanks for your help, > > Simon Halstead> > > ------=_Part_66800_10476889.1217958088617 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Simon,

Could you be more specific about what does not converge, the SCF or geometry optimizations?.  If the SCF fails to converge, then a geometry optimization will likely fail also.

If the issue is thae SCF will the SCF converge at the HF level with a simple basis such as STO-3G or 3-21?   Do the HOMO and LUMO orbitals swap around during the SCF?  Does level shifting help? 

Regards,

John McKelvey



On Tue, Aug 5, 2008 at 3:29 AM, Simon Halstead shalstead . hit.edu.cn <owner-chemistry**ccl.net> wrote:

Sent to CCL by: "Simon  Halstead" [shalstead:hit.edu.cn]

Dear all,

I am trying to optimize some bridged (1-4) cyclohexane rings. I initially optimized them using sempiempirical methods. These calculations converged very rapidly. However, I then tried to optimize the resulting structures at a higher level of theory. These high level calculations have failed to converge, despite being run for a large number of steps. I have tried HF, MP2 and B3LYP with a variety of basis sets but nothing appears to converge. Visualizing the outputs of the failed calculations shows no problems with the structure.
Does anyone have any experience with structures like this or can anyone give me a suggestion of how best to optimize bridged rings?
I am using GAMESS if this makes any differnce.

Thanks for your help,

Simon Halstead



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------=_Part_66800_10476889.1217958088617-- From owner-chemistry@ccl.net Tue Aug 5 16:23:00 2008 From: "Wayne Steinmetz WES04747_._pomona.edu" To: CCL Subject: CCL: Ab initio on bridged rings Message-Id: <-37492-080805143414-30256-HMXrxJ2fZMORFvJNPL+Uyw:-:server.ccl.net> X-Original-From: "Wayne Steinmetz" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Tue, 5 Aug 2008 11:33:56 -0700 MIME-Version: 1.0 Sent to CCL by: "Wayne Steinmetz" [WES04747:+:pomona.edu] You are having problems with convergence so your system shows sensitivity to structural details. I recommend that you first generate a structure using molecular mechanics and a good Class II force field, e.g. the Merck Molecular Force Field or Allinger's MM3. Sometimes, intuition in initially drawing the structure leads one astray. For example, when I drew the structure of calixarene, I started with a structure quite far in energy from the global minimum. Hence, after you have minimized your initial structure, you might also want to search conformational space. Spartan uses a Monte Carlo algorithm which usually works. In difficult cases such as calixarene, I have used distance geometry to get out of a trap. You can rely on the results of molecular mechanics if you use a Class II force field. Once you have located the global minimum, then proceed to Hartree Fock and then a more advanced method such as DFT with Becke's B3LYP functional or Truhlar's M06 functional. If the convergence falters, you might tweak a portion of this structure. This trick often helps getting out of a rut. Wayne E. Steinmetz Professor Emeritus of Chemistry USFS Volunteer Chemistry Department Pomona College 645 North College Avenue Claremont, California 91711-6338 USA phone: 1-909-621-8447 FAX: 1-909-607-7726 Email: wsteinmetz- -pomona.edu WWW: pages.pomona.edu/~wsteinmetz =20 -----Original Message----- > From: owner-chemistry- -ccl.net [mailto:owner-chemistry- -ccl.net]=20 Sent: Tuesday, August 05, 2008 12:30 AM To: Wayne Steinmetz Subject: CCL: Ab initio on bridged rings Sent to CCL by: "Simon Halstead" [shalstead:hit.edu.cn] Dear all, I am trying to optimize some bridged (1-4) cyclohexane rings. I initially optimized them using sempiempirical methods. These calculations converged very rapidly. However, I then tried to optimize the resulting structures at a higher level of theory. These high level calculations have failed to converge, despite being run for a large number of steps. I have tried HF, MP2 and B3LYP with a variety of basis sets but nothing appears to converge. Visualizing the outputs of the failed calculations shows no problems with the structure. Does anyone have any experience with structures like this or can anyone give me a suggestion of how best to optimize bridged rings? I am using GAMESS if this makes any differnce. Thanks for your help, Simon Halstead -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt------------------------------------------------------------- This message has been scanned by Postini anti-virus software. =0D From owner-chemistry@ccl.net Tue Aug 5 22:09:01 2008 From: "Hugo Villar hugo- -altoris.com" To: CCL Subject: CCL: Family/Functional Group Identification From 2D/3D mol file Message-Id: <-37493-080805220716-25322-85SrheIaI6XdYE4GVF//aA^server.ccl.net> X-Original-From: "Hugo Villar" Date: Tue, 5 Aug 2008 22:07:12 -0400 Sent to CCL by: "Hugo Villar" [hugo_-_altoris.com] Dear YangSoo, You may also want to try SARvision (www.chemapps.com) that let's you group your molecules according to chemotypes and then you can use their folders feature to remove particular chemical classes. There is a free demo that lasts about a month which should be enough for most of what you want to test. Good Luck, Hugo > "Forlani Roberto roberto.forlani/./nikemresearch.com" wrote: > > Sent to CCL by: "Forlani Roberto" [roberto.forlani]-[nikemresearch.com] > =20 > > > -----Original Message----- > > From: owner-chemistry^-^ccl.net [mailto:owner-chemistry^-^ccl.net]=20 > > Sent: Tuesday, July 29, 2008 2:11 PM > > To: Forlani Roberto > > Subject: CCL: Family/Functional Group Identification From=20 > > 2D/3D mol file > >=20 > >=20 > > Sent to CCL by: "Yangsoo Kim" [vsmember[#]gmail.com] Dear All, > >=20 > > I'm looking for a program that can automatically determine=20 > > the family and/or functional group of molecule from a kind of=20 > > a 2D or 3D molfile. The groups I want to identify are the=20 > > followings (total of 31 groups): > > (1)n-alkane, (2)iso-alkne, (3)cyclo-alkane, (4)n-alkene,=20 > > (5)iso-alkene, (6)aromatics, (7)alcohol, (8)ketone,=20 > > (9)aldehyde, (10)acetic acid, (11) ether, (12)ester,=20 > > (13)hydroperoxide, (14)peroxide, (15)formic acid, (16) amide,=20 > > (17)amine, (18)imines, (19)azo, (20)cyanate, (21)isocynate,=20 > > (22) nitrate, (23)nitrile, (24)nitrite, (25)nitro,=20 > > (26)pyridine, (27)pyrrole, (28)sulfide, (29)sulfoxide,=20 > > (30)thiol, (31)thiophene > >=20 > > I found checkmol=20 > > (http://merian.pch.univie.ac.at/~nhaider/cheminf/cmmm.html) > > so far, but some groups are missing in this software. > >=20 > > Any information related to this matter will greatly be appreciated. > >=20 > > Many thanks in advance, > >=20 > > YangSoo Kim. > > > Dear YangSoo, > > I think you can search and/or filter your molecular files by > corresponding functional groups SMARTS. > For your information Open Babel offers this functionality > http://openbabel.org/wiki/SMARTS > > Hope this helps. > > Regards, > Roberto > >