From owner-chemistry@ccl.net Tue Jun 14 07:31:01 2011 From: "Michel Petitjean petitjean.chiral() gmail.com" To: CCL Subject: CCL: sources for chemical dscriptors Message-Id: <-44889-110614043441-28345-70BBs2rRWWfr8XfrM1JYMw{:}server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 14 Jun 2011 10:34:31 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral(0)gmail.com] Dear Sajeev, In case you have not yet collected them, some 2D and 3D descriptors are available from my freeware page: http://petitjeanmichel.free.fr/itoweb.petitjean.html (references are cited in the associated documentations) In 2D, from the GRD freeware: - D : diameter of the molecular graph - R : radius of the molecular graph - I : graph shape index (D-R)/R (values in [0;1]) In 3D, from the ASV freeware: - S : van der Waals surface - V : van der Waals volume - G : sphericity index 36*pi*V*V/S*S*S In 3D, from the RADI freeware, all convex hull related parameters: - N : number of atoms of the hull - F : number of faces of the hull - E : number of edges of the hull - S : surface of the hull - V : volume of the hull - D : diameter of the hull - R : radius of the hull (i.e. radius of the smallest enclosing sphere) - NRe : number of R-extremal atoms            (i.e. number of atoms lying on the smallest sphere: 2 or 3 or 4) - Ic : geometrical convex shape index  (D-R)/R (values in [0;1]) - Is : surfacic convex shape index (sphericity of the hull) 4*pi*R*R/S*S - Iv : volumic convex shape index (sphericity of the hull) 4*pi*R*R*R/3*V - H : smallest size (defined by the closest pair of enclosing planes) In 3D, but depends also on the 2D connection table, from the QCM freeware: - CHI : degree of chirality of the rigid conformer (values in [0;1]) - DSI : degree of direct simmetry of the rigid conformer (values in [0;1]) - NA: number of automorphisms of the molecular graph         (in fact does not depend on 3D coordinates) - T : geometric inertia (atoms have unit masses) Apart CHI and DSI, it is likely that the other descriptors are described somewhere else. May I add that my experience is that, most complicated the descriptors are, less useful they appear to be at the occasion of QSAR analysis. E.g., the total number of atoms of the molecule is by far much more useful that many sophisticated descriptors which sometimes are even not rigorously defined in the softwares calculating them. In fact, my opinion is that we need descriptors because QSAR methods apply to "vectors" (i.e. tuples of values) and do not apply to basic chemical structures such as graphs or 3D sets. So, a huge of descriptors were created to overcome this lack of methods dealing directly with 2D or/and 3D chemical data. Best regards, Michel. Michel Petitjean MTi, INSERM UMR-S 973, University Paris 7, 35 rue Helene Brion, 75205 Paris Cedex 13, France. Phone: +331 5727 8434; Fax: +331 5727 8372 E-mail: petitjean.chiral ~ gmail.com (preferred), michel.petitjean ~ univ-paris-diderot.fr http://petitjeanmichel.free.fr/itoweb.petitjean.html 2011/6/12 sajeev r sajucheminformatics^^^gmail.com : > > Hello members, >                    I am in search of new chemical descriptor, could anyone > tell what are the different sources available ?.for eg. I have collected > some descriptors from various sources like physical chemistry,organic > chemistry, graph theory, quantum chemistry etc... > regards > -- > Sajeev R > Research Scholar > Cheminformatics Centre. > Malabar Christian College > Calicut-673001 > Kerala, India. > phone :09846041423 > email  :sajucheminformatics+/-gmail.com > From owner-chemistry@ccl.net Tue Jun 14 08:06:00 2011 From: "Marcel Brautzsch marcel.brautzsch^^student.uni-halle.de" To: CCL Subject: CCL: Calculating Solvated Molecule Excitation in Gaussian 09 Message-Id: <-44890-110614022603-27938-ycqO2wT5vcc0PZbs5dROOQ-$-server.ccl.net> X-Original-From: "Marcel Brautzsch" Date: Tue, 14 Jun 2011 02:26:02 -0400 Sent to CCL by: "Marcel Brautzsch" [marcel.brautzsch+/-student.uni-halle.de] A termination of the job file by 2 blank lines did the job, somehow. Thanks to everyone investigating in this problem. > "Marcel Brautzsch marcel.brautzsch#student.uni-halle.de" wrote: > > Sent to CCL by: "Marcel Brautzsch" [marcel.brautzsch : student.uni-halle.de] > Dear priyanka goud, > > There is a blank line in the end of the file, it was just cut off by this website. Any other suggestions out there? > > > "priyanka goud priyankagoud8{:}gmail.com" wrote: > > > > Sent to CCL by: priyanka goud [priyankagoud8]_[gmail.com] > > --90e6ba4fc1c01c807704a591b3cb > > Content-Type: text/plain; charset=ISO-8859-1 > > > > Dear Marcel Brautzsch, > > > > Just specify a one line blank > > space after the > > NonEq=Read and run again. > > > > --90e6ba4fc1c01c807704a591b3cb > > Content-Type: text/html; charset=ISO-8859-1 > > Content-Transfer-Encoding: base64 > > > > RGVhciBNYXJjZWwgoEJyYXV0enNjaCw8YnI+oKCgoKCgIDxicj6goKCgoKCgoKCgoKCgoKCgoKCg > > oKCgoKCgoKCgoKCgoKCgoKCgoKCgoKAgSnVzdCBzcGVjaWZ5IGEgb25lIGxpbmUgYmxhbmsgc3Bh > > Y2UgYWZ0ZXIgdGhlPGJyPk5vbkVxPVJlYWQgYW5kIHJ1biBhZ2Fpbi48YnI+PGJyPjxicj48YnI+ > > PGJyPgo= > > --90e6ba4fc1c01c807704a591b3cb-- > > > > > > From owner-chemistry@ccl.net Tue Jun 14 08:40:00 2011 From: "Peeter Burk peeter * chem.ut.ee" To: CCL Subject: CCL: ESOR 2011 reminder Message-Id: <-44891-110614073457-3149-yMrb+8NexAltLQVtnXpigA[]server.ccl.net> X-Original-From: "Peeter Burk" Date: Tue, 14 Jun 2011 07:34:55 -0400 Sent to CCL by: "Peeter Burk" [peeter*chem.ut.ee] Dear Colleagues, Please let me remind you that the deadlines for submission of abstracts and early bird registration for 13th European Symposium on Organic Reactivity in Tartu, Estonia, (ESOR, see http://esor13.baltictours.ee) are approaching. Please join us at Tartu for both work and enjoyment in September 2011 to explore a plethora of information on current research in physical organic chemistry and to network with fellow academics and industrial researchers. IMPORTANT DATES: Abstract submission: 20th July, 2011 Early-bird (students 100 Euro, academic participants 225 Euro) registration: 20th July, 2011 Conference 11-16 September, 2011 We apologize for possible cross-postings! Best regards, Peeter Burk, Conference Chair on behalf of ESOR XIII 2011 Organizing Committee From owner-chemistry@ccl.net Tue Jun 14 09:15:00 2011 From: "Dan Maftei dan.maftei : uaic.ro" To: CCL Subject: CCL:G: Calculating Solvated Molecule Excitation in Gaussian 09 Message-Id: <-44892-110614073103-30320-zZlk6rggq8dixYUQZRMiQg===server.ccl.net> X-Original-From: Dan Maftei Content-Type: multipart/mixed; boundary="------------050508020801000504030004" Date: Tue, 14 Jun 2011 14:30:20 +0300 MIME-Version: 1.0 Sent to CCL by: Dan Maftei [dan.maftei(~)uaic.ro] This is a multi-part message in MIME format. --------------050508020801000504030004 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit G09 manual says that StateSpecific is synonym with ExternalIteration (an external iteration is performed via the l124.exe or so). Try to replace StateSpecific with ExternalIteration in SCRF options of internal job. On 12.06.2011 18:44, Marcel Brautzsch marcel.brautzsch_-_student.uni-halle.de wrote: > Sent to CCL by: "Marcel Brautzsch" [marcel.brautzsch]^[student.uni-halle.de] > Dear CCL'ers, > I'm trying to calculate the emission and other excitet properties of 10287-53-3 following the guide provided in the SCRF Keyword Section of Gaussian 09 Website (http://www.gaussian.com/g_tech/g_ur/k_scrf.htm). > > The first two steps (Step 1: Ground state geometry optimization and frequencies; Step 2: Vertical excitation with linear response solvation) just using Water instead of Ethanol working fine. Step 3: State-specific solvation of the vertical excitation - Part II (Link1) quits with the following message: > > SC-PCM: Self-consistent PCM reaction field calculation. > Using the following non-standard input for PCM: > NonEq=Read > End of line while reading PCM input. > Error termination via Lnk1e in xxx/GAUSSIAN/g09/l124.exe at Sun Jun 12 17:02:49 2011. > Job cpu time: 0 days 0 hours 0 minutes 0.1 seconds. > File lengths (MBytes): RWF= 36 Int= 0 D2E= 0 Chk= 56 Scr= 4 > > This is the Jobfile: > > %mem=8GB > %nprocshared=8 > %chk=03-calc.chk > # B3LYP/6-31+G(d,p) SCRF=(Solvent=Water,Read) Geom=Check Guess=Read > > DMABE: prepare for state-specific non-eq solvation by saving the solvent reaction field from the ground state > > 0 1 > > NonEq=Write > > --link1-- > %chk=03-calc.chk > # B3LYP/6-31+G(d,p) TD(NStates=6,Root=1) SCRF=(Solvent=Water,StateSpecific,Read) Geom=Check Guess=Read > > DMABE: read non-eq solvation from ground state and compute energy of the first excited with the state-specific method > > 0 1 > > NonEq=Read > > > Any suggestions on how to solve this problem? > > Thanks in advance, > Marcel Brautzsch (marcel.brautzsch..student.uni-halle.de) > Martin-Luther University Halle-Wittenberg > Faculty of Natural Sciences II/Institute of Chemistry > Kurt-Mothes-Str 4 > D-06120 Halle> > -- Dan Maftei, Assistant Professor, Faculty of Chemistry/Department of Chemistry University Alexandru Ioan Cuza Iasi Bd. Carol 1, Nr. 11, 700506 Iasi, Romania Tel: +40 232 201307 E-mail(s): dan.maftei*chem.uaic.ro dan.maftei*uaic.ro --------------050508020801000504030004 Content-Type: application/pgp-keys; name="0xF59B8983.asc" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0xF59B8983.asc" -----BEGIN PGP PUBLIC KEY BLOCK----- Version: GnuPG v2.0.14 (GNU/Linux) mQGiBEjrO0wRBACQkJChhDxP3N+/d5o1B/6TCA54b9w+qbhDnW7GK/wZDunsmEKY XVsAcWt+O32NHVekEyOBYetR8wctmyWogIjn9YZznk/PkQzZhqL6bD4MirXbyBvP MiII7iF1T+Ou7tiv7UbmpwRYX2Wb02ey51i0qdq9WQ1E+XATmifzXGGFIwCg3u/O +oyu37f+7hm92q1Ls20AxrsD/jN2Fh7yjl0erV4Sy/USe+CS+lKWZDAMkCFj5wTe +SqTPWtN0GKfiWeXjgUBCdRCktVfOEHjo0bcpnYpm7BY7hnGbD7+ceO2dSvCFRf2 NWmWpDgW6+zLKhuoMpVYwYtkGD0v9as14MQJyDyZewonP5mPwN/aMBA12iPOifQ4 Pgw9A/4mvsmoTLnSPkoauLoU+mRKbGFGBNUeLUFfzxLxcOei5BrRg3nKLW9p+sUZ tVdMPbpWSAf88HambwFR6TOwmwrX0pbRo5gucWga6txESPP8cw2FA9CTpSn+CrIO iqPRr+g48yoMYiWGT4t2PalrEgof+yyE+75It5Io7ihUzix2jbQkRGFuIE1hZnRl 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/4jBYLsbUjYqkquosf7rIeWpgGKlduYRyWHogq8n2REvvZ9eW37zA7p9wCXRSiNv E5sGw5Krb86fl78gjSJj6Bbtk5rzI+qmwAloXMI+Sh+VDpxBMwxxRC6We65g8c64 wHsHI2QMrHWhVwT6KHG67YQ2bz72lUYraCLYJWMe4riDcqlOPXWEx7g7zNyFW3pS PFf1bSxAniKjuzHOqYcvW4R0mbgq0SU5k9YzGGdySMG/TlSL79Nt/PI0tjjJ3zVZ wZFRFOfPcPFYXzfViwtPzuyBggbXMhmISQQYEQIACQUCSOs7TAIbDAAKCRCuzeA+ 9ZuJg0zDAJ9yNfoMzjmmu6WA9/VB/CnoAELnnQCfZDR6d4z8OoXO/kJtY48tUFuF 4Y0= =Lm3B -----END PGP PUBLIC KEY BLOCK----- --------------050508020801000504030004-- From owner-chemistry@ccl.net Tue Jun 14 10:07:00 2011 From: "Dan Maftei dan.maftei~~uaic.ro" To: CCL Subject: CCL:G: Calculating Solvated Molecule Excitation in Gaussian 09 Message-Id: <-44893-110614073738-4394-W/BwuGD2N3j0tWThM3hSEg|-|server.ccl.net> X-Original-From: Dan Maftei Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 14 Jun 2011 14:37:21 +0300 MIME-Version: 1.0 Sent to CCL by: Dan Maftei [dan.maftei-.-uaic.ro] G09 manual says that StateSpecific is synonym with ExternalIteration (an external iteration is performed via the l124.exe or so). Try to replace StateSpecific with ExternalIteration in SCRF options of internal job. On 12.06.2011 18:44, Marcel Brautzsch marcel.brautzsch_-_student.uni-halle.de wrote: > Sent to CCL by: "Marcel Brautzsch" [marcel.brautzsch]^[student.uni-halle.de] > Dear CCL'ers, > I'm trying to calculate the emission and other excitet properties of 10287-53-3 following the guide provided in the SCRF Keyword Section of Gaussian 09 Website (http://www.gaussian.com/g_tech/g_ur/k_scrf.htm). > > The first two steps (Step 1: Ground state geometry optimization and frequencies; Step 2: Vertical excitation with linear response solvation) just using Water instead of Ethanol working fine. Step 3: State-specific solvation of the vertical excitation - Part II (Link1) quits with the following message: > > SC-PCM: Self-consistent PCM reaction field calculation. > Using the following non-standard input for PCM: > NonEq=Read > End of line while reading PCM input. > Error termination via Lnk1e in xxx/GAUSSIAN/g09/l124.exe at Sun Jun 12 17:02:49 2011. > Job cpu time: 0 days 0 hours 0 minutes 0.1 seconds. > File lengths (MBytes): RWF= 36 Int= 0 D2E= 0 Chk= 56 Scr= 4 > > This is the Jobfile: > > %mem=8GB > %nprocshared=8 > %chk=03-calc.chk > # B3LYP/6-31+G(d,p) SCRF=(Solvent=Water,Read) Geom=Check Guess=Read > > DMABE: prepare for state-specific non-eq solvation by saving the solvent reaction field from the ground state > > 0 1 > > NonEq=Write > > --link1-- > %chk=03-calc.chk > # B3LYP/6-31+G(d,p) TD(NStates=6,Root=1) SCRF=(Solvent=Water,StateSpecific,Read) Geom=Check Guess=Read > > DMABE: read non-eq solvation from ground state and compute energy of the first excited with the state-specific method > > 0 1 > > NonEq=Read > > > Any suggestions on how to solve this problem? > > Thanks in advance, > Marcel Brautzsch (marcel.brautzsch..student.uni-halle.de) > Martin-Luther University Halle-Wittenberg > Faculty of Natural Sciences II/Institute of Chemistry > Kurt-Mothes-Str 4 > D-06120 Halle> > -- Dan Maftei, Assistant Professor, Faculty of Chemistry/Department of Chemistry University Alexandru Ioan Cuza Iasi Bd. Carol 1, Nr. 11, 700506 Iasi, Romania Tel: +40 232 201307 E-mail(s): dan.maftei===chem.uaic.ro dan.maftei===uaic.ro From owner-chemistry@ccl.net Tue Jun 14 10:42:00 2011 From: "Eliac Brown Eliacbrown _ yahoo.com" To: CCL Subject: CCL: PDB Survey Message-Id: <-44894-110614100953-30989-fyMT4w71U7xq7a1V+GVFbA%x%server.ccl.net> X-Original-From: "Eliac Brown" Date: Tue, 14 Jun 2011 10:09:52 -0400 Sent to CCL by: "Eliac Brown" [Eliacbrown_+_yahoo.com] Dear CCL First of all, I am sorry if it is not the right place to post of question. I am looking for a certain types of proteins interact with the ligand via non covalent interaction. Is there any software/website can be used used for this job? The search should be base on the distance between the ligand atom type and the protein. I used isostar software, and looking for another one. Thanks in advance Eliac From owner-chemistry@ccl.net Tue Jun 14 15:00:00 2011 From: "Jing Kong jkong^q-chem.com" To: CCL Subject: CCL: Reminder: Workshop on Electronic Structure Calculations preceding WATOC 2011 Message-Id: <-44895-110614093705-4305-x1mrcGgHqeHGg+f2P3jrSA^_^server.ccl.net> X-Original-From: "Jing Kong" Content-Language: en-us Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 14 Jun 2011 09:36:55 -0400 MIME-Version: 1.0 Sent to CCL by: "Jing Kong" [jkong:-:q-chem.com] Dear Colleague, This is a reminder that Q-Chem will hold a workshop on electronic structure calculations. It will consist of seminars by several leading quantum chemists and a demonstration of new Q-Chem 4.0. The half-day workshop will take place in the afternoon on Saturday, July 16, the day before WATOC 2011 starts, in Santiago de Compostela, Spain at the site of the WATOC conference. We offer free six-month licenses of unlimited use of Q-Chem 4.0 for the workshop participants. The registration deadline is extended to June 30. Please visit the workshop webpage (http://www.q-chem.com/wsspa_hh.html) for registration and other details. Included below is the first announcement. I apologize if you receive multiple copies of this announcement. Happy Computing, Jing Kong, PhD CEO and Chief Scientist Q-Chem, Inc. The original message was as follows: Dear colleague: Q-Chem would like to invite you to a workshop of quantum chemistry in Santiago de Compostela, Spain in the afternoon of Saturday, July 16, 2011.  It is the day before WATOC 2011 starts. The workshop will highlight some of the features in the new Q-Chem 4.0 software package.  Q-Chem 4.0 contains significant new functionality, including: * TD-DFT analytic gradient and Hessian for excited-state structure optimization; * IRC searches for mapping complicated potential energy surfaces; * Range-separated and dispersion-corrected DFT functionals; * Faster algorithms for DFT, HF and coupled-cluster calculations; * More choices for excited-state, solvation and charge-transfer calculations; * Effective Fragment Potential and QM/MM for treating large systems; * Maximum Overlap Method for excited-state calculations of large systems; * Intracules for analysis of two-electron properties; * Shared-memory for multicore systems and implementations for GPUs; as well as many other areas. The workshop will consist of seminars and a demonstration of Q-Chem 4.0. Seminar speakers include Christian Ochsenfeld (Uni Muenchen), David Casanova (Uni Barcelona), Martin Head-Gordon (Uni California, Berkeley), Peter Gill (Australian National Uni) and Anna Krylov (Uni Southern California). The meeting will take place at the site of WATOC. The registration fee is $25 and covers coffee, tea and soft drinks. All workshop participants will receive a free six-month license for unlimited use of Q-Chem 4.0. Please register by June 16 on our website (www.q-chem.com/wsspa_regist.html). I apologize if you receive multiple copies of this announcement. Happy Computing, Jing Kong, PhD CEO and Chief Scientist Q-Chem, Inc.   From owner-chemistry@ccl.net Tue Jun 14 15:35:00 2011 From: "Oellien, F \(Frank\) frank.oellien],[sp.intervet.com" To: CCL Subject: CCL: GCC2011 - Call for Paper - 25th Anniversary of the CIC-Workshop Message-Id: <-44896-110614105123-459-SWcFSSR49bWxH1RBl09DYQ[#]server.ccl.net> X-Original-From: "Oellien, F \(Frank\)" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 14 Jun 2011 16:51:07 +0200 MIME-Version: 1.0 Sent to CCL by: "Oellien, F \(Frank\)" [frank.oellien\a/sp.intervet.com] CALL FOR PAPERS 7th German Conference on Chemoinformatics (GCC2011) Hotel 'Der Achtermann', Goslar, Germany 6 - 8 November 2011 Dear Colleagues, The CIC division of the German Chemical Society announces the 7. German Conference on Chemoinformatics (GCC2011)(http://www.gdch.de/gcc2011) to be held in Goslar, Germany, November 6 - 8, 2011. Seven years ago the international conference arised from the CIC workshops which have become popular as the 'Hochfilzen' workshops initiated by Johnny Gasteiger in the 1980s. With the 7. GCC we now can celebrate the 25th anniversary of the CIC workshops! We are inviting the submission of abstracts for talks, posters and free software contributions in the following plenary sessions: * Chemoinformatics and Drug Discovcery * Chemical Information, Patents, and Databases * Molecular Modelling * Computational Material Science and Nanotechnology In addition other highlights in the field of Computational Chemistry are also welcome. The deadline for the submissions of oral contributions is August 1, 2011. The submission deadline for posters and free software session contributions is September 1, 2011. Please visit our online submission form on http:/www.gdch.de/gcc2011 to submit your abstract. Invited Speakers this year are: * Johann Gasteiger, University of Erlangen/Molecular Networks, Erlangen, DE * Oliver Kohlbacher, University of Tübingen, DE * Eva Rauls, University of Paderborn, DE * Herbert Koeppen, Boehringer Ingelheim, Biberach, DE * Colin Batchlor, RCS, London, UK * Colin Groom, CCDC, Cambridge, UK * Xavier Barril, University of Barcelona, ES * Secret Guest Speaker from MIT! Visit the conference website at www.gdch.de/gcc2011 for more information or access directly the Call-for-Paper PDF http://www.gdch.de/vas/tagungen/tg/5227_einladung.pdf We have added some special events to the technical program (social event, MIT Speaker, Gala Dinener) to pay tribute to 25 years of meetings in the field of Computational Chemistry in Germany. Frank Oellien Chairman GDCh CIC Division Mit freundlichen Grüßen / With kind regards Dr. Frank Oellien BioChemInformatics Scientist Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: frank.oellien**sp.intervet.com Phone: +49 (6130) 948 365 Fax: +49 (6130) 948 517 Home http://www.intervet.com A subsidiary of Merck & Co., Inc., Whitehouse Station, NJ, USA Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Geschäftsführer: Dr. Peter Schmid Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. 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