From owner-chemistry@ccl.net Thu Jun 16 07:57:00 2011 From: "Tobias Kraemer tobias.kraemer(0)chem.ox.ac.uk" To: CCL Subject: CCL: ASyTop Error in Gaussian09 Message-Id: <-44907-110616050159-32690-KIOz1CjwtzHKBtg7Z07rEw]~[server.ccl.net> X-Original-From: Tobias Kraemer Content-Type: multipart/alternative; boundary="------------000402060709020308010403" Date: Thu, 16 Jun 2011 10:01:41 +0100 MIME-Version: 1.0 Sent to CCL by: Tobias Kraemer [tobias.kraemer(0)chem.ox.ac.uk] This is a multi-part message in MIME format. --------------000402060709020308010403 Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 8bit Dear Ol Ga... * Thanks for the suggestion but this does unfortunately not solv the problem. Interestingly, I did manage to optimise the structure of this 4,4'-bipyridine before, and it worked. What I was actually trying to do was to calculate a single point energy on the planar structure (in the optimised structure the dihedral angle between the two pyridyl rings is 38 degrees). In the single point calc the error occured for the first time, and I started playing around with different dihedral angles, and also tried reoptimise the structure, but all with the same result. Tobi * _______________________________________ dipl.-chem. tobias krämer department of chemistry inorganic chemistry laboratory university of oxford south parks road oxford OX1 3QR united kingdom |phone| +44 (0)1865 272 135 |email| tobias.kraemer.:.chem.ox.ac.uk |email| tobias.kraemer.:.linacre.ox.ac.uk _________________________________________ --------------000402060709020308010403 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 8bit Dear Ol Ga...


Thanks for the suggestion but this does unfortunately not solv the problem.

Interestingly, I did manage to optimise the structure of this 4,4'-bipyridine before, and it worked.

What  I was actually trying to do was to calculate a single point energy on the planar structure

(in the optimised structure the dihedral angle between the two pyridyl rings is 38 degrees).

In the single point calc the error occured for the first time, and I started playing around with different dihedral angles,

and also tried reoptimise the structure, but all with the same result.


Tobi

 


_______________________________________

  dipl.-chem. tobias krämer
  department of chemistry
  inorganic chemistry laboratory 
  university of oxford
  south parks road
  oxford OX1 3QR
  united kingdom
   	
  |phone| +44 (0)1865 272 135
  |email| tobias.kraemer.:.chem.ox.ac.uk
  |email| tobias.kraemer.:.linacre.ox.ac.uk
_________________________________________
--------------000402060709020308010403-- From owner-chemistry@ccl.net Thu Jun 16 08:32:00 2011 From: "Will Pitt wrp24 : cam.ac.uk" To: CCL Subject: CCL: PDB Survey Message-Id: <-44908-110616041308-20092-tMecKnlm0BeiKN+6dG/9qA!=!server.ccl.net> X-Original-From: Will Pitt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 16 Jun 2011 09:13:09 +0100 MIME-Version: 1.0 Sent to CCL by: Will Pitt [wrp24===cam.ac.uk] You could try Credo. It's a mysql database of protein-ligand interactions in the pdb. There is also a python and pymol API's. No web access as yet I'm afraid. See : http://www-cryst.bioc.cam.ac.uk/databases/credo for more details. -Will On 14/06/11 15:09, Eliac Brown Eliacbrown _ yahoo.com wrote: > 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> > -- Dr Will Pitt Visiting Research Associate Cambridge University Department of Biochemistry 80 Tennis Court Road Cambridge CB2 1GA UK 44(0)1223 766028 From owner-chemistry@ccl.net Thu Jun 16 09:07:01 2011 From: "Rakesh Kumar rakesh.kumar\a/execs.com" To: CCL Subject: CCL: ONTOMINE for virtual screening of bioactivity, drug targets, toxicity Message-Id: <-44909-110616022143-8859-6iwh+f173ZkDPSgDAFHvvQ__server.ccl.net> X-Original-From: "Rakesh Kumar" Date: Thu, 16 Jun 2011 02:21:41 -0400 Sent to CCL by: "Rakesh Kumar" [rakesh.kumar]^[execs.com] Dear CCLers I would like to announce the release of our Chemoinformatics software ONTOMINE for Virtual screening. Ontomine is early stage drug discovery software used for automated Molecular Mining for BioActivity, Drug targets, Toxicity, Side effects, scaffold hopping and ADME prediction. The dataset in Ontomine is formulated into hierarchical trees composed of several thousands of classes of bioactivities, drug targets, therapeutics areas, adverse effects and toxicities. Each class is represented by a fingerprint for the related molecules for their molecular properties, like presence/absence/counts of side-chains/chemical activities, ring structures etc. The fingerprints of molecules in these endpoints allows fast prediction for toxicities, adverse effects, biological activities etc., for flagging toxic effects, HTS library selection, identification of promiscuous hits, scaffold hopping. Ontomine features: Biological Activity Spectrum prediction for small molecules using Ontomine includes :- 1. Drug targets ( Enzyme, receptors, ion channel, growth factor etc. ) 2. Biological processes ( e.g. adjuvant, alkaloid, anti-spasmodic, reducing agents etc.) 3. Therapeutic areas ( Anti Allergic, Anti cancer, Anti infective, Anti- Inflammatory etc.) 4. Toxicity (systemic, organ specific and genetic) and side effect prediction using Ontomine Tox module. Example include hepatotoxicity, mutagenecity, and QT elongation. 5. ADME and physicochemical property prediction (including Solubility, logP, logD, pKa) using Ontomine ADME module. 6. Scaffold hopping for finding new isofunctional, chemotypes. Please contact me for more information and web demo. Rakesh Kumar Manager (Business Development & Corporate Relations) SBW Ltd. Ph:- +91-9810448375 Email: - rakesh.kumar!=!sbw.fi Web: - www.sbw.fi From owner-chemistry@ccl.net Thu Jun 16 09:41:00 2011 From: "Eliac Brown Eliacbrown-x-yahoo.com" To: CCL Subject: CCL: Non-covalent vs Covalent bond Message-Id: <-44910-110616092755-22361-sX6VHTxy7t0ZLLIfO2qvyg ~ server.ccl.net> X-Original-From: "Eliac Brown" Date: Thu, 16 Jun 2011 09:27:54 -0400 Sent to CCL by: "Eliac Brown" [Eliacbrown-,-yahoo.com] Dear All First of all, thanks for your help over my last post (especial thanks to Nicho Demus and Serghei Glinca) I have a fundamental question here, I have searched for its answer but couldn't find one. * Is there a relation/equation can be used to distinguish a bond as a non- covalent bond or Covalent bond? the problem is that I used a software to get contact between two atoms in crystal structures (inter-molecular contact), but I found some of the results have distance very short compared to the vdw radii. I think it is a technical error, so I need to clean the data. what can I do? In addition, what is the scientific difference between Contact, bond, and interaction? A lot of papers using contact in the position of bond, is that right scientifically? Thanks in advance and forgive me if my questions were not at the same level of the mailing list. Eliac From owner-chemistry@ccl.net Thu Jun 16 11:44:01 2011 From: "Srikanth Patala srikanth.patala ~~ gmail.com" To: CCL Subject: CCL: Algorithm for the point group determination of arbitrary molecules Message-Id: <-44911-110616083545-29282-lFz5rIvY5Yc2UhtpVY6OjQ^server.ccl.net> X-Original-From: "Srikanth Patala" Date: Thu, 16 Jun 2011 08:35:43 -0400 Sent to CCL by: "Srikanth Patala" [srikanth.patala-*-gmail.com] Hello all, I am trying to write a code to determine the point group of arbitrary shapes (clusters of atoms). I am very well aware of all the point symmetries and I did find some suggestions online (flowcharts) for developing such a code. The main problem now is that I have temperature in my system and hence the shape of the clusters fluctuates. I am not sure how to have a code while allowing for deviation from symmetric structure. There is an applet online that allows for this deviation: http://www.colby.edu/chemistry/PChem/scripts/ABC.html I would like to perform the exact same calculations using a code. Any suggestions?? Thanks in advance for your time. Thanks, Srikanth From owner-chemistry@ccl.net Thu Jun 16 12:18:01 2011 From: "Ron Cook cookrl:tda.com" To: CCL Subject: CCL: Non-covalent vs Covalent bond Message-Id: <-44912-110616115425-13776-+vylA6+JLTkZrey/vSKEhg]_[server.ccl.net> X-Original-From: "Ron Cook" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 16 Jun 2011 09:54:15 -0600 MIME-Version: 1.0 Sent to CCL by: "Ron Cook" [cookrl^^^tda.com] Hi Using the information provided by Atoms in Molecules software (e.g. AIMALL or AIMPAC) specifically information provided on the bond critical points will answer your questions Ronald Cook Principal Scientist TDA Research, Inc. -----Original Message----- > From: owner-chemistry+cookrl==tda.com * ccl.net [mailto:owner-chemistry+cookrl==tda.com * ccl.net] On Behalf Of Eliac Brown Eliacbrown-x-yahoo.com Sent: Thursday, June 16, 2011 7:28 AM To: Cook, Ronald L Subject: CCL: Non-covalent vs Covalent bond Sent to CCL by: "Eliac Brown" [Eliacbrown-,-yahoo.com] Dear All First of all, thanks for your help over my last post (especial thanks to Nicho Demus and Serghei Glinca) I have a fundamental question here, I have searched for its answer but couldn't find one. * Is there a relation/equation can be used to distinguish a bond as a non- covalent bond or Covalent bond? the problem is that I used a software to get contact between two atoms in crystal structures (inter-molecular contact), but I found some of the results have distance very short compared to the vdw radii. I think it is a technical error, so I need to clean the data. what can I do? In addition, what is the scientific difference between Contact, bond, and interaction? A lot of papers using contact in the position of bond, is that right scientifically? Thanks in advance and forgive me if my questions were not at the same level of the mailing list. Eliachttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Jun 16 13:32:00 2011 From: "Gustavo L.C. Moura gustavo.moura^ufpe.br" To: CCL Subject: CCL: Weaknesses of the INDO/S method Message-Id: <-44913-110616133031-26753-oB4mxsLHohZUVKDDCjYRGw.:.server.ccl.net> X-Original-From: "Gustavo L.C. Moura" Date: Thu, 16 Jun 2011 13:30:30 -0400 Sent to CCL by: "Gustavo L.C. Moura" [gustavo.moura,,ufpe.br] Dear CCL Readers, I am looking for a reference that discusses the strong points and the weaknesses of the semiempirical INDO/S method for calculating electronic spectra. Where does the method work really well? Where does the method perform poorly? I need such reference to add to a manuscript I am writing right now. Any pointers are welcome. Thank you very much in advance. Sincerely yours, Gustavo L.C. Moura From owner-chemistry@ccl.net Thu Jun 16 14:06:00 2011 From: "Michel Petitjean petitjean.chiral]~[gmail.com" To: CCL Subject: CCL: Algorithm for the point group determination of arbitrary molecules Message-Id: <-44914-110616131334-11607-cy9PbAnPL6H0G4Vcf8VcmA : server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 16 Jun 2011 19:13:24 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral!=!gmail.com] Dear Srikanth, Such a code would work under the assumption that the symmetry is not too much distorted. You may check the deviation from direct symmetry with the direct symmetry index (DSI) and the deviation from achirality with the chiral index (CHI), both computable with the QCM freeware: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html 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[A]gmail.com (preferred), michel.petitjean[A]univ-paris-diderot.fr http://petitjeanmichel.free.fr/itoweb.petitjean.html 2011/6/16 Srikanth Patala srikanth.patala ~~ gmail.com : > > Sent to CCL by: "Srikanth  Patala" [srikanth.patala-*-gmail.com] > Hello all, > > I am trying to write a code to determine the point group of arbitrary shapes (clusters of atoms). I am very well aware of all the point symmetries and I did find some suggestions online (flowcharts) for developing such a code. The main problem now is that I have temperature in my system and hence the shape of the clusters fluctuates. I am not sure how to have a code while allowing for deviation from symmetric structure. There is an applet online that allows for this deviation: http://www.colby.edu/chemistry/PChem/scripts/ABC.html > > I would like to perform the exact same calculations using a code. Any suggestions?? Thanks in advance for your time. > > Thanks, > Srikanth > From owner-chemistry@ccl.net Thu Jun 16 14:42:00 2011 From: "Aniko Simon aniko . simbiosys.ca" To: CCL Subject: CCL: PDB Survey Message-Id: <-44915-110616135811-19707-fP2ARbDalyuVwuscDc1M5Q{=}server.ccl.net> X-Original-From: "Aniko Simon" Date: Thu, 16 Jun 2011 13:58:09 -0400 Sent to CCL by: "Aniko Simon" [aniko###simbiosys.ca] Dear Eliac, Worth checking out eHiTS, it's a flexible docking program: http://www.simbiosys.com/ehits/index.html and eHiTS Score a separate tool for protein-ligand interaction scoring only (i.e. without redocking) using the same eHiTS principles: http://www.simbiosys.com/ehits/ehits_score.html Best wishes, Aniko On June 14, 2011 10:09:52 am Eliac Brown Eliacbrown _ yahoo.com wrote: > 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> -- Aniko Simon, Ph.D. | SimBioSys Inc. | Tel: 1-416-741-4263 | http://www.simbiosys.com/ Check out the most recent customer quotes about SimBioSys: http://www.simbiosys.com/support/index.html#quotes From owner-chemistry@ccl.net Thu Jun 16 16:12:00 2011 From: "Srikanth Patala srikanth.patala ~~ gmail.com" To: CCL Subject: CCL: Algorithm for the point group determination of arbitrary molecules Message-Id: <-44916-110616160120-29352-u9tGJiZjnb+6cnPNmzyCHA^_^server.ccl.net> X-Original-From: Srikanth Patala Content-Type: multipart/alternative; boundary=20cf3071c6eee8eba204a5d9bade Date: Thu, 16 Jun 2011 15:00:49 -0500 MIME-Version: 1.0 Sent to CCL by: Srikanth Patala [srikanth.patala|*|gmail.com] --20cf3071c6eee8eba204a5d9bade Content-Type: text/plain; charset=ISO-8859-1 Dear Michel, Thank you very much for your response and the link to the freeware. I also realized that my question is slightly misleading. I do not yet have a working code for determination of point group symmetries of arbitrary molecules (symmetric without deviations). I am still working on it and I jumped a couple of steps ahead and posted a question about deviation from symmetries (which is also something that I absolutely require). I am basically trying to calculate the moment of inertia tensor to determine the point groups but I am not aware of a good (efficient) algorithm to determine point symmetries for static, symmetric molecules. Any help with this first step is also greatly appreciated. Thanks, Srikanth On Thu, Jun 16, 2011 at 12:13 PM, Michel Petitjean petitjean.chiral]~[ gmail.com wrote: > > Sent to CCL by: Michel Petitjean [petitjean.chiral!=!gmail.com] > Dear Srikanth, > Such a code would work under the assumption that the symmetry is not > too much distorted. > You may check the deviation from direct symmetry with the direct > symmetry index (DSI) and the deviation from achirality with the chiral > index (CHI), both computable with the QCM freeware: > http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html > 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 > > > 2011/6/16 Srikanth Patala srikanth.patala ~~ gmail.com > : > > > > Sent to CCL by: "Srikanth Patala" [srikanth.patala-*-gmail.com] > > Hello all, > > > > I am trying to write a code to determine the point group of arbitrary > shapes (clusters of atoms). I am very well aware of all the point symmetries > and I did find some suggestions online (flowcharts) for developing such a > code. The main problem now is that I have temperature in my system and hence > the shape of the clusters fluctuates. I am not sure how to have a code while > allowing for deviation from symmetric structure. There is an applet online > that allows for this deviation: > http://www.colby.edu/chemistry/PChem/scripts/ABC.html > > > > I would like to perform the exact same calculations using a code. Any > suggestions?? Thanks in advance for your time. > > > > Thanks, > > Srikanth> > > -- Srikanth --20cf3071c6eee8eba204a5d9bade Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Michel,

Thank you very much for your response and the link to t= he freeware. I also realized that my question is slightly misleading. I do = not yet have a working code for determination of point group symmetries of = arbitrary molecules (symmetric without deviations). I am still working on i= t and I jumped a couple of steps ahead and posted a question about deviatio= n from symmetries (which is also something that I absolutely require). I am= basically trying to calculate the moment of inertia tensor to determine th= e point groups but I am not aware of a good (efficient) algorithm to determ= ine point symmetries for static, symmetric molecules. Any help with this fi= rst step is also greatly appreciated.

Thanks,
Srikanth

On Thu, Jun 16, 2= 011 at 12:13 PM, Michel Petitjean petitjean.chiral]~[gmail.com <owner-chemistry[A]ccl.net> wrote:

Sent to CCL by: Michel Petitjean [petitjean.chiral!=3D!gmail.com]
Dear Srikanth,
Such a code would work under the assumption that the symmetry is not
too much distorted.
You may check the deviation from direct symmetry with the direct
symmetry index (DSI) and the deviation from achirality with the chiral
index (CHI), both computable with the QCM freeware:
http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.h= tml
Best regards,
Michel.

Michel Petitjean
MTi, INSERM UMR-S 973, University Paris 7
35 rue Helene Brion, 75205 Paris Cedex 13, France.
Phone: +331 572= 7 8434; Fax: +331 5727 8372
E-mail: petitjean.chiral=3D-=3Dgmail.com (preferred),
michel.petitjean=3D-=3Duniv-paris-diderot.fr
http://petitjeanmichel.free.fr/itoweb.petitjean.html


2011/6/16 Srikanth Patala srikanth.patala ~~ gmail.com
<owner-chemistry=3D-=3Dccl.= net>:
>
> Sent to CCL by: "Srikanth =A0Patala" [srikanth.patala-*-gmail.com]
> Hello all,
>
> I am trying to write a code to determine the point group of arbitrary = shapes (clusters of atoms). I am very well aware of all the point symmetrie= s and I did find some suggestions online (flowcharts) for developing such a= code. The main problem now is that I have temperature in my system and hen= ce the shape of the clusters fluctuates. I am not sure how to have a code w= hile allowing for deviation from symmetric structure. There is an applet on= line that allows for this deviation: http://www.colby.edu/chemistr= y/PChem/scripts/ABC.html
>
> I would like to perform the exact same calculations using a code. Any = suggestions?? Thanks in advance for your time.
>
> Thanks,
> Srikanth
>



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--
Srikanth --20cf3071c6eee8eba204a5d9bade-- From owner-chemistry@ccl.net Thu Jun 16 18:27:01 2011 From: "vandestreek-*-avmatsim.de" To: CCL Subject: CCL: Algorithm for the point group determination of arbitrary molecules Message-Id: <-44917-110616181000-32287-Tt7RyEhquIZHex2DXXYSFw_._server.ccl.net> X-Original-From: vandestreek===avmatsim.de Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Fri, 17 Jun 2011 00:09:48 +0200 MIME-Version: 1.0 Sent to CCL by: vandestreek###avmatsim.de Quoting "Srikanth Patala srikanth.patala ~~ gmail.com" : > I am not aware of a good (efficient) algorithm to determine > point symmetries for static, symmetric molecules. Any help with this first > step is also greatly appreciated. http://dx.doi.org/10.1107/S010876810001380X Best wishes, -- Dr Jacco van de Streek Senior Scientist Avant-garde Materials Simulation Freiburg im Breisgau, Germany