From owner-chemistry@ccl.net Thu Jun 7 04:21:01 2012 From: "=?ISO-8859-1?Q?Gregorio_Garc=EDa_Moreno?= gjgarcia()ujaen.es" To: CCL Subject: CCL: Predict crystal structure Message-Id: <-47053-120607041912-28219-HKmCiUfuy7+mnAxPOfZzNg : server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Gregorio_Garc=EDa_Moreno?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 07 Jun 2012 10:18:54 +0200 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Gregorio_Garc=EDa_Moreno?= [gjgarcia]![ujaen.es] Hi all I have two compounds, A and B. For A, I know the experimental crystal structure (and therefore the symmetry of the crystal). However for B, I only now the molecular structure. If I know the molecular structure of B and it symmetry (the same symmetry that A, there are some way to predict the crystal structure of B? The aim is to obtain a crystal structure of B, I will use it a starting point for a optimization using PBC. Thanks Gregorio -- Gregorio García Moreno Department of Physical and Analytical Chemistry University of Jaén From owner-chemistry@ccl.net Thu Jun 7 04:55:00 2012 From: "Olasunkanmi Lukman Olawale walecomuk : yahoo.co.uk" To: CCL Subject: CCL: Cnh & Dnh molecules: planar or non-planar Message-Id: <-47054-120607043356-23058-cR15Ew3vlUy1Ij69p0eJug[a]server.ccl.net> X-Original-From: Olasunkanmi Lukman Olawale Content-Type: multipart/alternative; boundary="368313653-810512888-1339058028=:11952" Date: Thu, 7 Jun 2012 09:33:48 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Olasunkanmi Lukman Olawale [walecomuk _ yahoo.co.uk] --368313653-810512888-1339058028=:11952 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Does presence of a horizontal plane of symmetry in a molecule suggests that= it is PLANAR: e.g. Cnh and Dnh molecules? I had a molecule in which some a= toms are not in the same plane and yet it has a C2h point group. Should I s= ay it is a planar molecule even though some atoms are not in the same plane= ?=0AThank you in anticipation of your contributions.=0A=0AOlasunkanmi Lukma= n Olawale=0A________________________________=0ACurrent Address:=0ADepartmen= t of Chemistry,=0AObafemi Awolowo University,=0AIle-Ife, Osun State.=0ANige= ria.=0A=0A+234-0-80-52401564 Or +234-0-80-67161091=0A______________________= __________ --368313653-810512888-1339058028=:11952 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Does presence of= a horizontal plane of symmetry in a molecule suggests that it is PLANAR: e= .g. Cnh and Dnh molecules? I had a molecule in which some atoms are not in = the same plane and yet it has a C2h point group. Should I say it is a plana= r molecule even though some atoms are not in the same plane?
Thank you i= n anticipation of your contributions.
Olasunkanmi Lukman Olawale
Cur= rent Address:
Department of Chemistry,
Ile-Ife, = Osun State.
<= span style=3D"color: rgb(0, 0, 191); font-weight: bold;">Nigeria.
= +234-0-80-52401564 Or +234-0-80-6716109= 1
--368313653-810512888-1339058028=:11952-- From owner-chemistry@ccl.net Thu Jun 7 05:58:00 2012 From: "DJUKIC Jean-Pierre djukic/./unistra.fr" To: CCL Subject: CCL: Cnh & Dnh molecules: planar or non-planar Message-Id: <-47055-120607055105-3440-69R5uKodRoFFeUDvsZByfw]^[server.ccl.net> X-Original-From: DJUKIC Jean-Pierre Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Thu, 07 Jun 2012 11:50:40 +0200 MIME-Version: 1.0 Sent to CCL by: DJUKIC Jean-Pierre [djukic]_[unistra.fr] Dear Obafemi, It depends really on the context of your description and on its "destination". For example, it is common to state that some palladium complexes have a square-planar geometry, whereas it is obvious from there X-ray diffraction structure that they aren't so, strictly speaking; the "plane" made of the atoms of interest is kinda twisted. Strict symmetry analysis may indeed deliver a confusing result and an apparent paradox...Common sense would consider such cases of distorted Pd complexes as still "planar" eventhough distorted for some damn good real world reason.... Everything depends on the use you want to make of all these considerations and on the type of "public" before which you wanna present your analysis or on the time-length you want your calculation to last. Since combined electronic structure and non covalent interactions rule almost anything, in tricky cases (where it's not clear whether the distortion stems from environmental effects of the crystal lattice, or > from inherent structural effects within the molecule), I would not constrain the theoretical description of my system with symmetry constraints unless the case is so simple that such a constraint would not invalidate the overall analysis and conclusions...and make you save a lot of computer time ressource. Best regards, JPD Le 07/06/2012 10:33, Olasunkanmi Lukman Olawale walecomuk : yahoo.co.uk a écrit : > Does presence of a horizontal plane of symmetry in a molecule suggests > that it is PLANAR: e.g. Cnh and Dnh molecules? I had a molecule in which > some atoms are not in the same plane and yet it has a C2h point group. > Should I say it is a planar molecule even though some atoms are not in > the same plane? > Thank you in anticipation of your contributions. > Olasunkanmi Lukman Olawale > ------------------------------------------------------------------------ > Current Address: > Department of Chemistry, > Obafemi Awolowo University, > Ile-Ife, Osun State. > Nigeria. > +234-0-80-52401564 Or +234-0-80-67161091 > ------------------------------------------------------------------------ -- From owner-chemistry@ccl.net Thu Jun 7 07:34:00 2012 From: "Alexander Genaev genaev.,.gmail.com" To: CCL Subject: CCL: Initrot Problem in Tinker Message-Id: <-47056-120607062024-19704-T5phcj/A6T2YPawOok8Fsw,server.ccl.net> X-Original-From: "Alexander Genaev" Date: Thu, 7 Jun 2012 06:20:15 -0400 Sent to CCL by: "Alexander Genaev" [genaev:-:gmail.com] Hi, Max You may renumerate atoms in the molecule to fix this problem 41 indomethacin 1 C 1.584800 1.687700 1.180400 133 2 6 38 2 C 0.899400 1.618000 -0.039400 133 1 3 7 3 C 0.861800 2.731200 -0.888400 133 2 4 35 4 C 1.544200 3.898400 -0.537200 133 3 5 36 5 C 2.246600 3.954700 0.666700 133 4 6 9 6 C 2.266800 2.857000 1.527500 133 1 5 37 7 C 0.142400 0.399100 -0.413600 8 2 8 10 8 O -0.963700 0.562100 -0.926600 43 7 9 Cl 3.086700 5.392300 1.098300 57 5 10 N 0.588200 -0.929900 -0.189600 135 7 11 14 11 C -0.248600 -2.021300 0.069700 170 10 12 15 12 C 0.558600 -3.103500 0.429600 171 11 13 18 13 C 1.917500 -2.695300 0.294000 171 12 14 21 14 C 1.909300 -1.388100 -0.174700 170 10 13 24 15 C -1.655700 -2.125600 0.079600 133 11 16 26 16 C -2.239800 -3.337300 0.455700 133 15 17 27 17 C -1.445100 -4.406600 0.838200 133 16 18 19 18 C -0.052600 -4.317000 0.814500 133 12 17 28 19 O -2.038400 -5.593100 1.178100 27 17 20 20 C -2.213700 -5.660000 2.593500 1 19 39 40 41 21 C 3.119900 -3.553200 0.563100 1 13 22 29 30 22 C 3.655400 -3.366600 1.964000 11 21 23 25 23 O 3.449400 -2.443900 2.735600 45 22 24 C 3.077100 -0.579200 -0.637600 1 14 32 33 34 25 O 4.492500 -4.366100 2.320600 26 22 31 26 H -2.289500 -1.288200 -0.200200 23 15 27 H -3.321600 -3.437500 0.451800 23 16 28 H 0.545700 -5.182100 1.082500 23 18 29 H 2.856500 -4.608400 0.429400 23 21 30 H 3.925500 -3.322400 -0.141200 23 21 31 H 4.774800 -4.124600 3.228100 83 25 32 H 3.559300 -0.075100 0.204300 23 24 33 H 2.793500 0.158300 -1.393400 23 24 34 H 3.827000 -1.223500 -1.108400 23 24 35 H 0.299800 2.692500 -1.819900 23 3 36 H 1.517200 4.759400 -1.200300 23 4 37 H 2.804000 2.907700 2.471700 23 6 38 H 1.591600 0.845300 1.869900 23 1 39 H -2.712200 -6.606300 2.824700 23 20 40 H -1.249000 -5.649700 3.112800 23 20 41 H -2.851000 -4.844500 2.953100 23 20 At first I draw indomethacin in MarvinSketch, but this molecule was bad for INITROT. Then I open it in molden and click Z-mat Editor button. Automatically renumerated molecule is OK. In some other cases molden helped too. Concerning ANALYZE, it program does not use INITROT routine. Good luck, Alexander > "Max j J Prendergast eneas{}usal.es" wrote: > > Sent to CCL by: "Max j J Prendergast" [eneas++usal.es] > > Hi everyone, > > im trying to perform a conformational search of indomethacin using the SCAN application of Tinker. Ive draw it with Chem3D and later transform the sdf file to xyz with MMFF atom types using sdf2tinkerxyz. > > The ANALYZE program runs without problems, but when ive started the SCAN routine, a message appeared: > > INITROT: rotation in atoms 10 and 11 occurs more than once in Z-matrix > > Tinker is unable to continue. > > Ive checked the atom types again and again, but its ok. > > Any idea of how to fix it? > > Thanks a lot. > > From owner-chemistry@ccl.net Thu Jun 7 09:22:00 2012 From: "Vera Cathrine vera.cathrine : yahoo.com" To: CCL Subject: CCL:G: G09 ONIOM: MM missing parameters Message-Id: <-47057-120607092036-9037-EKAO+3Nd3yugQbCOoFA3uw_+_server.ccl.net> X-Original-From: "Vera Cathrine" Date: Thu, 7 Jun 2012 09:20:16 -0400 Sent to CCL by: "Vera Cathrine" [vera.cathrine**yahoo.com] Dear All, I wold like to carry out a geometry optimization of a protein using ONIOM method in Gaussian 09. I have portioned my system into two layers. First, after running the job, the Gaussian gives some warnings about some missing amber MM parameters for the QM region of my system. I am wondered to ask are this MM parameters are important to be included? the parameters composed of some bond stretching, bending and van der waals parameters. The fact is that the job is not failed. Second, I faced with this warning inmy job without crashing the job. Is this warning serious? WARNING -- The following centers have non-zero partial charges, but zero Vanderwaals parameters. These centers can collapse onto other centers with non-zero charge Any comments is greatly appreciated. Best wishes, Vera From owner-chemistry@ccl.net Thu Jun 7 10:21:00 2012 From: "Dan Maftei dan.maftei|*|uaic.ro" To: CCL Subject: CCL: G09, TD, Homo-1->excited state Message-Id: <-47058-120607101943-9756-Z++kACqIuFv0PqdvZsMcig=server.ccl.net> X-Original-From: Dan Maftei Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 07 Jun 2012 17:19:31 +0300 MIME-Version: 1.0 Sent to CCL by: Dan Maftei [dan.maftei#uaic.ro] On 06/06/2012 09:30 PM, Ronald Bakus rbakus_._chem.ucsb.edu wrote: Dear Ronald, If you are using CIS or TD-DFT, you may request additional excitations (nstate=number) to be computed. Then inspect the contribution to each excitation, in terms of occupied->virtual molecular orbital pairs. Excepting the first excited state (which arise in many simple cases from almost pure HOMO->LUMO excitation), excitations to higher states involve multiple MO pairs. A listing of all significant pairs involved in each excitation requested (see nstate above) together with the contribution from each pair is printed after the "Excited State ..." line in the log file (to actually estimate the contribution of a specific pair simply square the coefficient and multiply by a factor of 2). So the short answer is to request additional states in the computation and look for an excited state with contribution from a HOMO-x -> virtual pair. For instance, in the following example the HOMO-1 (MO no. 79 which is actually a lone pair) is involved in the third electronic transition: Excited State 1: Singlet-A 2.7758 eV 446.67 nm f=0.0176 =0.000 81 -> 82 0.55299 <-- HOMO -> LUMO 81 -> 83 0.40309 <-- HOMO -> LUMO+1 This state for optimization and/or second-order correction. Total Energy, E(TD-HF/TD-KS) = -1410.34699336 Copying the excited state density for this state as the 1-particle RhoCI density. Excited State 2: Singlet-A 2.9282 eV 423.41 nm f=0.0408 =0.000 81 -> 82 -0.41695 81 -> 83 0.55186 Excited State 3: Singlet-A 3.6912 eV 335.89 nm f=0.0014 =0.000 76 -> 82 -0.23728 76 -> 83 -0.27683 79 -> 82 -0.32813 <--- here as HOMO-1 -> LUMO 79 -> 83 -0.36153 <--- and here HOMO-1 -> LUMO+1 80 -> 82 -0.17789 80 -> 83 -0.19123 81 -> 83 0.13833 ..................... Best regards, Dan. > Sent to CCL by: "Ronald Bakus" [rbakus#,#chem.ucsb.edu] > I'm trying to look at excitations from states other than the HOMO in G09. Is there an option to get G09 to look at HOMO-1 etc states? Ive tried using 'root=n' but that didn't seem to work.> > From owner-chemistry@ccl.net Thu Jun 7 11:38:01 2012 From: "Wilson Rodriguez wilson.rodriguez[*]uam.es" To: CCL Subject: CCL: Surface Dynamics: Beyond the Born-Oppenheimer Static Surface Approxima Message-Id: <-47059-120607082006-11404-CJsGUgVCvL4fiuFFg+7lIg(!)server.ccl.net> X-Original-From: "Wilson Rodriguez" Date: Thu, 7 Jun 2012 08:20:03 -0400 Sent to CCL by: "Wilson Rodriguez" [wilson.rodriguez[-]uam.es] CECAM Workshop "Surface Dynamics: Beyond the Born-Oppenheimer Static Surface Approximation". We are pleased to inform you that it is open the registration to attend at the : CECAM Workshop "Surface Dynamics: Beyond the Born-Oppenheimer Static Surface Approximation" It will be held from 24st October to 26th October 2012, in Zaragoza Spain and the organizers are: Cristina Daz (Autonomous University of Madrid, Spain) Manuel Alcam (Autonomous University of Madrid, Spain) Sergio Daz-Tendero (Autonomous University of Madrid, Spain) Maite Alducin (CSIC-UPV Center of Materials Physics and DIPC, San Sebastin, Spain) Roar A. Olsen (SINTEF Materials and Chemistry, Oslo, Norway) To register please go to the following link: http://www.cecam.org/workshop-0-754.html The abstract submission deadline for contributions to be considered as a hot topic presentation is July 1st, 2012. The applying authors will be notified about the final selection shortly after this deadline. The workshop sponsors will cover the accommodations expenses of the selected 'hot topic' presenters at the hotel arranged by the organizers. From owner-chemistry@ccl.net Thu Jun 7 12:13:01 2012 From: "Jaime Martell jaime_martell[*]cbu.ca" To: CCL Subject: CCL: Cnh & Dnh molecules: planar or non-planar Message-Id: <-47060-120607104707-22442-PfkhTbAtwIz5NqbE9j6DVw===server.ccl.net> X-Original-From: "Jaime Martell" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01CD44BC.6459A6CD" Date: Thu, 7 Jun 2012 11:46:58 -0300 MIME-Version: 1.0 Sent to CCL by: "Jaime Martell" [jaime_martell!=!cbu.ca] This is a multi-part message in MIME format. ------_=_NextPart_001_01CD44BC.6459A6CD Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 IA0KDQpZb3UgbmVlZCB0byBsZWFybiB0aGUgc3ltbWV0cnkgZWxlbWVudHMgb2YgcG9pbnQgZ3Jv dXBzLCB3aGljaCBjYW4gYmUgZ2xlYW5lZCBieSBsb29raW5nIGF0IHBvaW50IGdyb3VwIHRhYmxl cy4gIFlvdSBjYW4gaGF2ZSBhIGhvcml6b250YWwgcGxhbmUgb2Ygc3ltbWV0cnkgd2l0aG91dCBo YXZpbmcgYWxsIGF0b21zIGluIHRoYXQgcGxhbmUuICBUaGUgcmVtYWluaW5nIGF0b21zIGFyZSBh 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+0200 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?Q?Adri=C3=A0_Cereto_Massagu=C3=A9?= [adrian.cereto]=[gmail.com] --14dae9340ec974ad4604c1e3031d Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear CCL subscribers, the Nutrigenomics research group at the Rovira i Virgili Universityand the Technological Center for Nutrition & Health are proud to announce the release of DecoyFinder, a graphical tool which helps finding sets of decoy molecules for a given group of active ligands. *DESCRIPTION:* Decoys are molecules that are presumed to be inactive against a target (*i.e.*, will not likely bind to the target) and are used to validate the performance of molecular docking or a virtual screening workflow. The DUD database provides a free directory of decoys for use in virtual screening, though it only contains a limited set of decoys for 40 targets. To overcome this limitation, we have developed an application called DecoyFinderthat selects, for a given collection of active ligands of a target, a set of decoys from a database of compounds. Decoys are selected if they are similar to active ligands according to five physical descriptors (molecular weight, number of rotational bonds, total hydrogen bond donors, total hydrogen bond acceptors and the octanol-water partition coefficient) without being chemically similar to any of the active ligands used as an input (according to the Tanimoto coefficient between MACCS fingerprints). To the best of our knowledge, DecoyFinderis the first application designed to build target-specific decoy sets and a complete description of the software is included on the application home page . *AVAILABILITY:* DecoyFinderis freely available at http://URVnutrigenomica-CTNS.github.com/DecoyFinder *MORE INFORMATION:* - Cereto-Massague, A., Guasch, L., Valls, C., Mulero, M., Pujadas, G., & Garcia-Vallve, S. (2012). DecoyFinder: an easy-to-use python GUI application for building target-specific decoy sets. Bioinformatics, 2-3= . doi:10.1093/bioinformatics/bts249 - Video introducing DecoyFinder - DecoyFinder wiki If you would like to suggest new features for future releases of the program, please contact us at adrian.cereto[at]urv.cat The DecoyFinder team. --=20 *Adri=C3=A0 Cereto Massagu=C3=A9* Ph.D Student Nutrigenomics Research Group Biochemistry and Biotechnology Department Building N4, Campus Sescelades Universitat Rovira i Virgili Tarragona, Catalonia Languages: Catal=C3=A0, Espa=C3=B1ol, English, Fran=C3=A7ais, Deutsch, Port= ugu=C3=AAs Nota importante | Important Notice --14dae9340ec974ad4604c1e3031d Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear CCL subscribers,

the Nutrigenomics research group at the Rovira i Virgili University a= nd the Technological Cent= er for Nutrition & Health are proud to announce the release of DecoyFinder, a graphical tool which helps finding sets of decoy mol= ecules for a given group of active ligands.

DESCRIPTION: Decoys are molecules that are presumed to be= inactive against a target (i.e., will not likely bind to the target= ) and are used to validate the performance of molecular docking or a virtua= l screening workflow. The DUD database provides a free directory of decoys for use in virtua= l screening, though it only contains a limited set of decoys for 40 targets= . To overcome this limitation, we have developed an application called DecoyFinder that selects, for a given collection of active ligands = of a target, a set of decoys from a database of compounds. Decoys are selec= ted if they are similar to active ligands according to five physical descri= ptors (molecular weight, number of rotational bonds, total hydrogen bond do= nors, total hydrogen bond acceptors and the octanol-water partition coeffic= ient) without being chemically similar to any of the active ligands used as= an input (according to the Tanimoto coefficient between MACCS fingerprints= ). To the best of our knowledge, DecoyFinder is the first appli= cation designed to build target-specific decoy sets and a complete description of the software is included on the application=20 home page.

AVAILABILITY:=C2=A0 DecoyFinder is freely available at http://URVnutrigenomica-C= TNS.github.com/DecoyFinder

MORE INFORMATION:

If you would like to suggest new features for future releases= of the program, please contact us at adrian.cereto[at]urv.cat


The Dec= oyFinder team.


--
Adri=C3=A0 Cereto Massagu=C3=A9
Ph.D Student
Nutrigenomics Research Group<= br style=3D"color:rgb(102,102,102)">= Biochemistry and Biotechnology Department
Building N4,= Campus Sescelades
Universitat Rovira i Virgili
Tarragona, Catalonia

Languages: Catal=C3= =A0, Espa=C3=B1ol, English, Fran=C3=A7ais, Deutsch, Portugu=C3=AAs

Nota importante | Important Notice<= /a>


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