From owner-chemistry@ccl.net Tue Jan 8 00:46:01 2008 From: "Bob Snyder noordwijkerhout*comcast.net" To: CCL Subject: CCL: Second Call for Papers: 8th International Conf. on Chemical Structures Message-Id: <-35996-080108004237-1298-qeYIX9VRTuRenK4mELML8g|-|server.ccl.net> X-Original-From: "Bob Snyder" Date: Tue, 8 Jan 2008 00:42:33 -0500 Sent to CCL by: "Bob Snyder" [noordwijkerhout\a/comcast.net] This is the second "Call for Papers" for the 8th International Conference on Chemical Structures (ICCS). Please note that abstracts can now be submitted at the conference web site at http://www.int-conf-chem-structures.org/. The deadline for the submission of abstracts is 15 February 2008. The conference is now open for attendee registration at the same addreess. The deadline to take advantage of the early registration discount is 25 March 2008. We hope to see you in Noordwijkerhout. Bob Snyder, ICCS Program Chair Markus Wagener, ICCS Vice Chair ------------------------------------------------------------------ C A L L F O R P A P E R S 8th International Conference on Chemical Structures NH Leeuwenhorst Conference Hotel, Noordwijkerhout, The Netherlands 1 - 5 June 2008 Visit the conference website at www.int-conf-chem-structures.org for more information. Joint Organizers: o Division of Chemical Information of the American Chemical Society (CINF) o Chemical Structure Association Trust (CSA Trust) o Division of Chemical Information and Computer Science of the Chemical Society of Japan (CSJ) o Chemistry-Information-Computer Division of the Society of German Chemists (GDCh) o Royal Netherlands Chemical Society (KNCV) o Chemical Information Group of the Royal Society of Chemistry (RSC) o Swiss Chemical Society (SCS) The 8th International Conference on Chemical Structures is seeking presentations of novel research and emerging technologies for the following plenary sessions: o Cheminformatics > molecular similarity and diversity > library analysis and profiling > chemical information visualization > representation and searching of conformationally flexible compounds o Structure-Activity and Structure-Property Prediction > data fusion, consensus modeling and multi-property optimization > prediction of ADME/Tox properties > industrialized and large-scale QSAR/QSPR model building o Structure-Based Drug Design and Virtual Screening > protein flexibility in docking > improved chemical models and scoring functions > integration of virtual and high-throughput screening o Analysis of Large Data Sets > data mining of HTS data > analysis of large chemistry spaces > machine learning o Informatics for Bridging Between Chemistry and Biology > integrative discovery informatics > virtual pharmacology > target family based approaches to drug discovery o Virtual Chemistry > structure- and ligand-based de-novo design > synthesis planning and design > mining electronic lab journals > reaction networks, reaction databases and reaction retrieval We encourage the submission of papers on both applications and case studies as well as on method development and algorithmic work. The final program will be a balance of these two aspects. Posters can be submitted for any of the above and related areas, but we also welcome contributions in any aspect of the computer handling of chemical structure information, such as: o representation and manipulation of organic and inorganic compounds, biomacromolecules and polymers o new algorithms for searching and managing chemical structures and reactions o 3D databases and pharmacophore modeling o (automatic) structure elucidation o combinatorial chemistry, diversity analysis o web technology and its effect on chemical information o electronic publishing o searching/dealing with patent spaces o MM or QM/MM simulations o practical free energy calculations o material sciences The conference will feature a new product review session for commercial presentations. Visit the conference website at www.int-conf-chem-structures.org for more information, including details on procedures for online abstract submission and conference registration. The deadline for the submission of abstracts is 15 February 2008. We hope to see you in Noordwijkerhout. Bob Snyder, ICCS Program Chair Markus Wagener, ICCS Vice Chair From owner-chemistry@ccl.net Tue Jan 8 10:01:00 2008 From: "Kowalczyk, Marta MKowalczyk++gc.cuny.edu" To: CCL Subject: CCL:G: optimization problem, g03 Message-Id: <-35997-080107183453-14404-TEXtMUhB7lpQDeisQ9yW0A() server.ccl.net> X-Original-From: "Kowalczyk, Marta" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C85181.5814F512" Date: Mon, 7 Jan 2008 18:02:15 -0500 MIME-Version: 1.0 Sent to CCL by: "Kowalczyk, Marta" [MKowalczyk,,gc.cuny.edu] This is a multi-part message in MIME format. ------_=_NextPart_001_01C85181.5814F512 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello, I do optimizations(in G03) for squaramide diphen molecues with nitro = substitution in ortho, meta, para position. I use TD DFT method with = b3lyp functional (and unrestricted formalism for ions). Base 6-31g(d,p) = has been used. But with 631g+(d,p) base calculations stop via the = l502.exe. ----------------------------------------- Convergence failure -- run terminated. Error termination via Lnk1e in /opt/g03/l502.exe ----------------------------------------------------- This problems is present only for molecule with para-substitution(both = neutral and ionic ground state). Keywords such as Fopt=3Dtight, Fopt=3Dverytight or change from lower to = higher multiplicity doesn't help. Using option symmetry(PG=3DC2v) = doesn't help neither.=20 What should I do? Best regards, Marta Kowalczyk Phd student, CUNY New York ------_=_NextPart_001_01C85181.5814F512 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable optimization problem, g03

Hello,
I do optimizations(in G03) for squaramide diphen molecues with nitro = substitution in ortho, meta, para position. I use TD DFT method with = b3lyp functional (and  unrestricted formalism for ions). Base = 6-31g(d,p) has been used. But with 631g+(d,p) base calculations stop via = the l502.exe.
-----------------------------------------
Convergence failure -- run terminated.
 Error termination via Lnk1e in /opt/g03/l502.exe
-----------------------------------------------------
This problems is present only for molecule with para-substitution(both = neutral and ionic ground state).
Keywords  such as Fopt=3Dtight, Fopt=3Dverytight or change from = lower to higher multiplicity doesn't help. Using option = symmetry(PG=3DC2v) doesn't help neither.
What should I do?

Best regards,
Marta Kowalczyk
Phd student, CUNY
New York

------_=_NextPart_001_01C85181.5814F512-- From owner-chemistry@ccl.net Tue Jan 8 12:20:00 2008 From: "Soren Eustis soreneustis=gmail.com" To: CCL Subject: CCL:G: optimization problem, g03 Message-Id: <-35998-080108121334-7283-7+/FsjijJ+2kxAHZs6YdbA++server.ccl.net> X-Original-From: "Soren Eustis" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_0039_01C851E7.F91CD250" Date: Tue, 8 Jan 2008 11:16:53 -0500 MIME-Version: 1.0 Sent to CCL by: "Soren Eustis" [soreneustis _ gmail.com] This is a multipart message in MIME format. ------=_NextPart_000_0039_01C851E7.F91CD250 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit It seems as if there is either an SCF or optimization convergence failure try: SCF=(maxcycle=256,xqc) OPT=maxcycle=300 Soren Eustis > From: owner-chemistry- -ccl.net [mailto:owner-chemistry- -ccl.net] Sent: Monday, January 07, 2008 6:02 PM To: Eustis, Soren Subject: CCL:G: optimization problem, g03 Hello, I do optimizations(in G03) for squaramide diphen molecues with nitro substitution in ortho, meta, para position. I use TD DFT method with b3lyp functional (and unrestricted formalism for ions). Base 6-31g(d,p) has been used. But with 631g+(d,p) base calculations stop via the l502.exe. ----------------------------------------- Convergence failure -- run terminated. Error termination via Lnk1e in /opt/g03/l502.exe ----------------------------------------------------- This problems is present only for molecule with para-substitution(both neutral and ionic ground state). Keywords such as Fopt=tight, Fopt=verytight or change from lower to higher multiplicity doesn't help. Using option symmetry(PG=C2v) doesn't help neither. What should I do? Best regards, Marta Kowalczyk Phd student, CUNY New York ------=_NextPart_000_0039_01C851E7.F91CD250 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable optimization problem, g03

It seems as if there is either an SCF or optimization convergence failure try:

 

SCF=3D(maxcycle=3D256,xqc)

OPT=3Dmaxcycle=3D300

 

Soren Eustis

 

 

From:= owner-chemistry- -ccl.net [mailto:owner-chemistry- -ccl.net]
Sent: Monday, January 07, 2008 6:02 PM
To: Eustis, Soren
Subject: CCL:G: optimization problem, g03

 

Hello,
I do optimizations(in G03) for squaramide diphen molecues with nitro substitution in ortho, meta, para position. I use TD DFT method with = b3lyp functional (and  unrestricted formalism for ions). Base 6-31g(d,p) = has been used. But with 631g+(d,p) base calculations stop via the = l502.exe.
-----------------------------------------
Convergence failure -- run terminated.
 Error termination via Lnk1e in /opt/g03/l502.exe
-----------------------------------------------------
This problems is present only for molecule with para-substitution(both = neutral and ionic ground state).
Keywords  such as Fopt=3Dtight, Fopt=3Dverytight or change from = lower to higher multiplicity doesn't help. Using option symmetry(PG=3DC2v) = doesn't help neither.
What should I do?

Best regards,
Marta Kowalczyk
Phd student, CUNY
New York

------=_NextPart_000_0039_01C851E7.F91CD250-- From owner-chemistry@ccl.net Tue Jan 8 14:51:00 2008 From: "Sebastian Rohrer s.rohrer(a)tu-bs.de" To: CCL Subject: CCL: Ligand Based Virtual Screening Success Stories Message-Id: <-35999-080108123649-14786-2aeQb10ZPiTJxXKXmUXz1g__server.ccl.net> X-Original-From: Sebastian Rohrer Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 08 Jan 2008 18:06:27 +0100 MIME-Version: 1.0 Sent to CCL by: Sebastian Rohrer [s.rohrer[-]tu-bs.de] Hi all, I am compiling a few slides for our students about ligand based VS. Can anybody point me to some references where ligand based virtual screening actually succeeded in a prospective manner (i.e. finding new drugs)? Thanks a lot, Sebastian -- Sebastian Rohrer AK Baumann - Molecular Modelling Group Institute of Pharmaceutical Chemistry Braunschweig University of Technology Beethovenstr. 55 38106 Braunschweig Germany Phone: +49-531-3912797 From owner-chemistry@ccl.net Tue Jan 8 15:26:00 2008 From: "diana tscheschmedjiewa did_wal#abv.bg" To: CCL Subject: CCL:G: about transition state Message-Id: <-36000-080107083921-2769-B6qfyJHBBAmDIgtAc5MlQg*server.ccl.net> X-Original-From: diana tscheschmedjiewa Content-Type: multipart/alternative; boundary="----=_Part_4048_1453151901.1199710080486" Date: Mon, 7 Jan 2008 14:48:00 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: diana tscheschmedjiewa [did_wal(_)abv.bg] ------=_Part_4048_1453151901.1199710080486 Content-Type: text/plain; charset="windows-1251" Content-Transfer-Encoding: quoted-printable Hi there, my suggestion is first to optimise the transition state structure at HF lev= el of theory and after that using that structure as an initial guess to mak= e the optimization at DFT level using opt(ts,noeigentest...). hope it will = work i would be happy if you let me know the result. best wishes diana >-------- =CE=F0=E8=E3=E8=ED=E0=EB=ED=EE =EF=E8=F1=EC=EE -------- >=CE=F2: "nand kishor gour gour_nand()rediffmail.com" =20 >=CE=F2=ED=EE=F1=ED=EE: CCL:G: about transition state >=C4=EE: "Valentinova, Did " =20 >=C8=E7=EF=F0=E0=F2=E5=ED=EE =ED=E0: =D1=FA=E1=EE=F2=E0, 2008, =DF=ED=F3= =E0=F0=E8 5 12:35:03 EET >---------------------------------- > > >Sent to CCL by: "nand kishor gour" [gour_nand-.-rediffmail.com] >how does open chain(1,2,4,5-hexatetraene)cyclizes to ( fulvene) going thr= ough transition state using gaussian view. >i have always fail to find transition structure between them i m performi= ng my calculation DFT(B3LYP)6-31g(d) and opt=3Dno eigentest and nosymm but = link is always died. > > > >-=3D This is automatically added to each message by the mailing script = =3D-> >Subscribe/Unsubscribe:=20> >Job: http://www.ccl.net/jobs=20> > > ------=_Part_4048_1453151901.1199710080486 Content-Type: text/html; charset="windows-1251" Content-Transfer-Encoding: quoted-printable Hi there,
my suggestion is first to optimise the transition state struct= ure at HF level of theory and after that using that structure as an initial= guess to make the optimization at DFT level using opt(ts,noeigentest...). = hope it will work
i would be happy if you let me know the result.
bes= t wishes
diana



>-------- =CE=F0=E8=E3=E8=ED=E0=EB=ED= =EE =EF=E8=F1=EC=EE --------
>=CE=F2: "nand kishor gour gour_nand()= rediffmail.com"
>=CE=F2=ED=EE=F1=ED=EE: CC= L:G: about transition state
>=C4=EE: "Valentinova, Did "
>=C8=E7=EF=F0=E0=F2=E5=ED=EE =ED=E0: =D1=FA=E1=EE=F2= =E0, 2008, =DF=ED=F3=E0=F0=E8 5 12:35:03 EET
>----------------------= ------------
>
>
>Sent to CCL by: "nand kishor gour" [= gour_nand-.-rediffmail.com]
>how does open chain(1,2,4,5-hexatetraen= e)cyclizes to ( fulvene) going through transition state using gaussian view= .
>i have always fail to find transition structure between them i m = performing my calculation DFT(B3LYP)6-31g(d) and opt=3Dno eigentest and nos= ymm but link is always died.
>
>
>
>-=3D This i= s automatically added to each message by the mailing script =3D-
>To= recover the email address of the author of the message, please change
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> ------=_Part_4048_1453151901.1199710080486-- From owner-chemistry@ccl.net Tue Jan 8 16:00:01 2008 From: "Rajarshi Guha rguha-x-indiana.edu" To: CCL Subject: CCL: 1st Call for Papers: "Chemical Systems Biology: Integrating Chemistry and Biology for Network Models" at the Fall ACS Conference Message-Id: <-36001-080108154405-2649-DgO5EvwhqLcQx0gI6Pa8xw|server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Tue, 8 Jan 2008 15:43:55 -0500 Mime-Version: 1.0 (Apple Message framework v753) Sent to CCL by: Rajarshi Guha [rguha|a|indiana.edu] Chemical Systems Biology: Integrating Chemistry and Biology for Network Models 236th ACS National Meeting Philadelphia, August 17-21, 2008 CINF Division ---------------------------------- Dear Colleagues, Josef Scheiber and I are organizing a symposium focusing on the use of biological networks and their models for the purposes of drug discovery. Traditionally, such models have been applied to large scale biological systems such as protein-protein interaction networks. Recently, there has been increased interest in the study of these networks to gain a global understanding of biological systems and the impact of small molecules to them in the context of drug discovery. As a result, it has become important that such models integrate small molecules with the usual biological systems. By leveraging the power of established cheminformatics methods along with the network models we get closer to the goal of "chemical systems biology", the full integration of chemical and biological data in the development of better in silico-methods for drug discovery. We invite you to submit contributions that address various computational aspects of this approach including, but not limited to: network construction, integration of multiple data sources in network models, drug repurposing, target identification, polypharmacology, incorporation of chemical structure/similarity into network models, bridging chemical structure and biological structure based network models. Case studies where computational network models have provided experimental insight are also welcome. We would also like to point out that sponsorship opportunities are available. Please use the on-line abstract submission system (OASYS) for submitting your abstract (http://oasys.acs.org/oasys.htm). OASYS will be accepting abstracts between 28th January and 24th March, 2008. Please contact Josef or myself if you have any questions. Thanks, Josef Scheiber Rajarshi Guha Novartis Indiana University josef.scheiber]|[novartis.com rguha]|[indiana.edu Ph: +1-617-871-3697 Ph: +1-814-404-5449 ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Heisenberg may have slept here... From owner-chemistry@ccl.net Tue Jan 8 17:55:00 2008 From: "Green Power powergreen * gmail.com" To: CCL Subject: CCL:G: Timing of One SCF Iteration cycle Message-Id: <-36002-080108170932-19201-6hgIRLTauDmQzBOHDi/flQ,server.ccl.net> X-Original-From: "Green Power" Content-Type: multipart/alternative; boundary="----=_Part_17412_30726346.1199826621681" Date: Tue, 8 Jan 2008 16:10:21 -0500 MIME-Version: 1.0 Sent to CCL by: "Green Power" [powergreen]-[gmail.com] ------=_Part_17412_30726346.1199826621681 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear All, Anybody can tell me how to check the time for one SCF iteration cycle using Gaussian. Thank you in advance. Best Tian ------=_Part_17412_30726346.1199826621681 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear All,

Anybody can tell me how to check the time for one SCF iteration cycle using Gaussian.
Thank you in advance.

Best

Tian
------=_Part_17412_30726346.1199826621681-- From owner-chemistry@ccl.net Tue Jan 8 19:01:00 2008 From: "Jozsef Csontos jozsefcsontos(0)creighton.edu" To: CCL Subject: CCL:G: Timing of One SCF Iteration cycle Message-Id: <-36003-080108185841-16938-z38te6PgSimckAwtuRMc5w\a/server.ccl.net> X-Original-From: Jozsef Csontos Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 08 Jan 2008 17:58:30 -0600 Mime-Version: 1.0 Sent to CCL by: Jozsef Csontos [jozsefcsontos_-_creighton.edu] Hi, put "SCF=(MaxCycle=1)" in the route section then "grep -i 'leave link 502' yourlogfile" gives you the cpu information in seconds. You can calculate the average time for one scf cycle, too (if you don't use the maxcycle keyword). 1, "grep -i 'leave link 502' yourlogfile" gives the total time 2, "grep -i 'scf done'" gives the number of cycles Hope it helps, Jozsef On Tue, 2008-01-08 at 16:10 -0500, Green Power powergreen * gmail.com wrote: > Dear All, > > Anybody can tell me how to check the time for one SCF iteration cycle > using Gaussian. > Thank you in advance. > > Best > > Tian -- Jozsef Csontos, Ph.D. (jozsefcsontos_at_creighton_dot_edu) Department of Biomedical Sciences Creighton University, Omaha, NE From owner-chemistry@ccl.net Tue Jan 8 22:07:00 2008 From: "Renxiao Wang wangrx::mail.sioc.ac.cn" To: CCL Subject: CCL: Release note of I-interpret v.1 Message-Id: <-36004-080108202243-26215-52gVL7VscTzArpZ7vH4KCw:-:server.ccl.net> X-Original-From: "Renxiao Wang" Date: Tue, 8 Jan 2008 20:22:39 -0500 Sent to CCL by: "Renxiao Wang" [wangrx . mail.sioc.ac.cn] Dear CCLers, We announce the release of the I-interpret program. This program interprets the chemical structure of a given organic molecule based on its essential structural information, including element identities and three-dimensional coordinates of its component atoms (J. Chem. Inf. Model. 2007, 47, 1379-1385). As demonstrated in our recent tests, I-interpret has achieved a very high success rate in interpreting diverse organic structures. It thus may serve as a handy tool for database processing, format conversion as well as other preparation tasks in molecular modeling. The current release (v.1) of I-interpret accepts three popular formats as inputs and outputs, including SDF, Mol2, and PDB. On-line testing of this program is provided to all users at http://www.sioc-ccbg.ac.cn/software/I-interpret/. I-interpret is available for free to download for academic and governmental users. We provide pre-compiled executable codes for UNIX/LINUX and Windows platforms. You may follow the instructions on the above web page to go through the registration process. A special board for I-interpret has been created at our discussion form at http://www.sioc-ccbg.ac.cn/forum/. Current members of our discussion forum may download the I-interpret program with your registration. We would love to get any feedback from you! Best regards, Renxiao Wang, Ph.D. Professor Shanghai Institute of Organic Chemistry China, P.R.