From owner-chemistry@ccl.net Wed Mar 21 01:19:01 2012 From: "partha kundu partha1kundu-$-gmail.com" To: CCL Subject: CCL: TDDFT calculation Message-Id: <-46535-120321011603-25810-uohzEWuFj72l/wF/S18Cjw^^server.ccl.net> X-Original-From: partha kundu Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 21 Mar 2012 10:45:16 +0530 MIME-Version: 1.0 Sent to CCL by: partha kundu [partha1kundu=-=gmail.com] Dear All, I am interested in doing exited state calculation for my molecule using TDDFT method. I have some questions regarding this. In ground state calculation, we optimize a structure using lower basis set and use it as a intial structure for the next level.Is it also possible to do for exited state? Is there any other concern in optimizing the higher excited state? I know that at higher excited state since the energy levels are closer, a wrong optimization may lead to different exited state. How to check it and solve?Any other advice is greatly appreciated. Thanks. Partha From owner-chemistry@ccl.net Wed Mar 21 01:54:00 2012 From: "Prof. Curt Breneman brenec(-)rpi.edu" To: CCL Subject: CCL: Emerging Technologies in Computational Chemistry - Competition Award Symposium at Philadelophia ACS Meeting Message-Id: <-46536-120320233815-12056-bqy2sFboJ+w4Fl7bN8aj1Q~~server.ccl.net> X-Original-From: "Prof. Curt Breneman" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 20 Mar 2012 23:38:16 -0400 MIME-Version: 1.0 Sent to CCL by: "Prof. Curt Breneman" [brenec|a|rpi.edu] Call for Papers: 2012 Symposium on Emerging Technologies in Computational Chemistry ("Emerging Technology") at the American Chemical Society National Meeting, Philadelphia, PA Aug. 19-23 2012 >>>> Note: The Deadline for COMP Abstracts for the Philadelphia meeting is April 3th, 2012 <<<< $1,000 prize to be awarded at the end of the symposium! In cooperation with Schrodinger, Inc, the Computers in Chemistry Division (COMP) of the ACS will hold the annual Symposium on Emerging Technologies in Computational Chemistry at the American Chemical Society National Meeting, Philadelphia, PA, Aug. 19-23 2012. The objective of the symposium is to stimulate, reward, and publicize methodological advances in computational chemistry. The talks will be evaluated at the meeting by a panel of experts on the quality of the presentation, and the impact that the research will have on the future of computational chemistry and allied sciences. The symposium is ideal for presenting your latest and best research on new techniques, applications and software development. Schrodinger, Inc., sponsors the $1,000 prize for the best talk at the symposium. All are invited to participate. To take part, it is necessary to submit a regular short ACS abstract the PACS system. It is also necessary to also email a longer (~1000-word) abstract to the organizer. The talks must be original and not be repeats of talks at other ACS symposia. The long abstracts will be evaluated, and those individuals selected for an oral presentation at the symposium will be notified. Applications for the Emerging Technologies Symposium that cannot be accepted will be rescheduled in one of the other COMP sessions at the meeting. Long abstracts must be sent by e-mail to: Prof. Curt M. Breneman ACS Division of Computers in Chemistry Acting Head, RPI Department of Chemistry and Chemical Biology Brenec_at_rpi_dot_edu From owner-chemistry@ccl.net Wed Mar 21 11:08:00 2012 From: "Pierre Archirel pierre.archirel|u-psud.fr" To: CCL Subject: CCL: gas phase entropy Message-Id: <-46537-120321110206-12180-GgaEPfyUgd//l1aefFUTag],[server.ccl.net> X-Original-From: "Pierre Archirel" Date: Wed, 21 Mar 2012 11:02:03 -0400 Sent to CCL by: "Pierre Archirel" [pierre.archirel^u-psud.fr] Dear colleagues, I wish informations on the calculation of gas phase entropies, namely: 1- are the tabulated measured values accurate? In one case (acetonitrile) they are obtained from the addition of condensed phase entropies and vaporisation entropy... Is this general? Is the direct measurement impossible? 2- what is the accuracy of the usual calculations, i.e. Sackur-Tetrode, rigid rotor and harmonic analysis? Is there some work comparing methods, bases, anharmonicities, etc? Thanks in advance, Pierre Archirel LCP, Universite Paris-Sud, Orsay From owner-chemistry@ccl.net Wed Mar 21 14:06:00 2012 From: "Prija Ponnan prija.ponnan:-:gmail.com" To: CCL Subject: CCL: Docking studies with multiple crystal structures of a protein Message-Id: <-46538-120321122156-5654-j4/kCW3ZZPy7I9aAJqu87w%a%server.ccl.net> X-Original-From: Prija Ponnan Content-Type: multipart/alternative; boundary=f46d0444047a102ce004bbc33096 Date: Wed, 21 Mar 2012 21:51:05 +0530 MIME-Version: 1.0 Sent to CCL by: Prija Ponnan [prija.ponnan,+,gmail.com] --f46d0444047a102ce004bbc33096 Content-Type: text/plain; charset=ISO-8859-1 Hello all Its a general query not directly related to Autodock usage.I want to study interaction of certain coumarin molecules with INHA (Enoyl-[acyl-carrier-protein] reductase [NADH]) of *Mycobacterium tuberculosis* In PDB database 36 crystal structure entries of this protein is available.Can anyone please suggest as how should I choose any one/few crystal structure among them or am I supposed to dock my compounds with all the available 36 crystal structures of this protein. Thank you Prija Ponnan PhD Chemistry University of Delhi Delhi-110007,India --f46d0444047a102ce004bbc33096 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Hello all

Its a general query not directly related to Autodock usa= ge.I want to study interaction of certain coumarin molecules with INHA

=

(Enoyl-[acyl-carrier-protein]= reductase [NADH]) of Mycobacterium tuberculosis

I= n PDB database 36 crystal=20 structure entries of this protein is available.Can anyone please suggest as how should I choose any one/few crystal structure among them or am I supposed to dock my compounds with all the available 36 crystal=20 structures of this protein.


Thank you


Prija Pon= nan
PhD Chemistry
University of Delhi
Delhi-110007,India

=A0
--f46d0444047a102ce004bbc33096-- From owner-chemistry@ccl.net Wed Mar 21 14:41:00 2012 From: "James Gary Prudhomme jprudhomme!^!healthtech.com" To: CCL Subject: CCL: First Principles in Binding Kinetics Message-Id: <-46539-120321122600-1723-/kftxhU/CjB0ACoR5KYaOQ]*[server.ccl.net> X-Original-From: "James Gary Prudhomme" Date: Wed, 21 Mar 2012 12:25:58 -0400 Sent to CCL by: "James Gary Prudhomme" [jprudhomme . healthtech.com] ***Please distribute this message to your colleagues. Thank you.*** Dinner Short Course Announcement: First Principles in Binding Kinetics:Towards Predicting Structure-Kinetics Relationships* June 6, 2012 - 6:00-8:00 pm Royal Sonesta Hotel Boston, Cambridge, Massachusetts Instructors: David Swinney, Ph.D., CEO, Institute for Rare and Neglected Diseases Drug Discovery (iRND3) Xavier Barril, Ph.D., ICREA Research Professor, Physical Chemistry Department, University of Barcelona This course will address the questions on why should I care about kinetics and how can I understand and predict Structure-Kinetics relationships? We will first review the role of binding kinetics in drug action and then focus on the particular case of protein-ligand non-covalent complexes, reviewing what is known so far about the structural determinants of binding kinetics. This course will help you with a better understanding and increased awareness of current state of the chemistry and pharmacology of binding kinetics. This course is scheduled at the conclusion of Day One of CHI's co- located "Structure-Based Drug Design" conference. More details and to register: http://www.healthtech.com/sbd For questions or to register for this course and/or conference via telephone, call 781-972-5400. From owner-chemistry@ccl.net Wed Mar 21 15:17:00 2012 From: "gerard boureau gerard.boureau\a/upmc.fr" To: CCL Subject: CCL: entropy Message-Id: <-46540-120321133109-32679-fXYuSZ6ch5Pvi2/jD54yDQ===server.ccl.net> X-Original-From: gerard boureau Content-Type: multipart/mixed; boundary="------------080607090702010106080805" Date: Wed, 21 Mar 2012 18:59:31 +0100 MIME-Version: 1.0 Sent to CCL by: gerard boureau [gerard.boureau]|[upmc.fr] This is a multi-part message in MIME format. --------------080607090702010106080805 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit > From my own recent experience, tabulated values are highly unreliable. I explain my problem in my last paper R.Coustel et al. J. Chem. Phys. 134, 234708 (2011) I was vey happy to find the book of P. Vogel chimie organique:methodes et modeles De Boek universite Paris 1998 P. Vogel details nicely the connections between thermodynamics and organic chemistry. good luck gérard boureau -- gerard boureau Laboratoire de chimie physique (UPMC-Paris 6) 11, rue Pierre et Marie Curie 75231 Paris cedex 5 e-mail gerard.boureau(-)upmc.fr http://www.ccr.jussieu.fr/lcpmr/simulation.html tel 01 44 27 66 26 fax 01 44 27 62 26 --------------080607090702010106080805 Content-Type: text/x-vcard; charset=utf-8; name="gerard_boureau.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="gerard_boureau.vcf" begin:vcard fn;quoted-printable:g=C3=A9rard boureau n;quoted-printable:boureau;g=C3=A9rard email;internet:gerard.boureau(-)upmc.fr tel;work:33 1 44 27 66 26 tel;fax:33 1 44 27 62 26 x-mozilla-html:TRUE version:2.1 end:vcard --------------080607090702010106080805-- From owner-chemistry@ccl.net Wed Mar 21 20:28:00 2012 From: "Vladimir Chupakhin chupvl,gmail.com" To: CCL Subject: CCL: Docking studies with multiple crystal structures of a protein Message-Id: <-46541-120321153006-24577-idjr5HF6EhHiYKDiQm8/BQ!^!server.ccl.net> X-Original-From: Vladimir Chupakhin Content-Type: multipart/alternative; boundary=000e0cdfc78600091d04bbc5d1fa Date: Wed, 21 Mar 2012 15:29:15 -0400 MIME-Version: 1.0 Sent to CCL by: Vladimir Chupakhin [chupvl ~ gmail.com] --000e0cdfc78600091d04bbc5d1fa Content-Type: text/plain; charset=UTF-8 Hello, in my opinion there is no way to choose the "perfect" protein conformation for ligand-receptor interactoin studies. Choose the protein with the best quality (<2.5A), and it will be better to dock to every protein and compare the results. The last one will be the more honest way. If you have some quntitative data - activity for example, try to find correlation between activity and scoring function, the one with the best correlation is "more" correct protein conformation. Best regards, -- *Vladimir Chupakhin*, Independent researcher in chemoinformatics and structural bioinformatics. Mobile: +1-617-943-9710 skype: chupvl ==-0-0-== *Currently looking for job in San Diego area.* On Wed, Mar 21, 2012 at 12:21, Prija Ponnan prija.ponnan:-:gmail.com < owner-chemistry(-)ccl.net> wrote: > Hello all > > Its a general query not directly related to Autodock usage.I want to study > interaction of certain coumarin molecules with INHA > (Enoyl-[acyl-carrier-protein] reductase [NADH]) of *Mycobacterium > tuberculosis* > > In PDB database 36 crystal structure entries of this protein is > available.Can anyone please suggest as how should I choose any one/few > crystal structure among them or am I supposed to dock my compounds with all > the available 36 crystal structures of this protein. > > > Thank you > > Prija Ponnan > PhD Chemistry > University of Delhi > Delhi-110007,India > > > > * * --000e0cdfc78600091d04bbc5d1fa Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hello,

in my opinion there is no way to choose the "perfect&quo= t; protein conformation for ligand-receptor interactoin studies. Choose the= protein with the best quality (<2.5A), and it will be better to dock to= every protein and compare the results. The last one will be the more hones= t way.

If you have some quntitative data - activity for example, try to find c= orrelation between activity and scoring function, the one with the best cor= relation is "more" correct protein conformation.

Best rega= rds,
--
Vladimir Chupakhin,
Independent researcher
in chemoi= nformatics and structural bioinformatics.
Mobile: +1-617-943-9710
sky= pe: chupvl
=3D=3D-0-0-=3D=3D
Currently looking for job in San D= iego area.

On Wed, Mar 21, 2012 at 12:21, Prija Ponnan = prija.ponnan:-:gmail.com <owner-chemistry(-)ccl.net= > wrote:

Hello all

Its a general query not d= irectly related to Autodock usage.I want to study interaction of certain co= umarin molecules with INHA

(Enoyl-[acyl-carrier-protein]= reductase [NADH]) of Mycobacterium tuberculosis

I= n PDB database 36 crystal=20 structure entries of this protein is available.Can anyone please suggest as how should I choose any one/few crystal structure among them or am I supposed to dock my compounds with all the available 36 crystal=20 structures of this protein.


Thank you


Prija Ponnan
PhD Chemis= try
University of Delhi
Delhi-110007,India

=C2=A0







--000e0cdfc78600091d04bbc5d1fa--