From owner-chemistry@ccl.net Fri Dec 7 00:53:01 2007 From: "info info|seascapelearning.com" To: CCL Subject: CCL: PuneUniversity-OpenEye-Seascape Workshop on Molecular Modeling: Dec 12-16, Pune - India! Message-Id: <-35785-071206181634-8922-jfV6tO3fFToEnzxvQTowRw- -server.ccl.net> X-Original-From: info Content-Type: multipart/alternative; boundary="------------000605080304080801080502" Date: Thu, 06 Dec 2007 14:16:19 -0800 MIME-Version: 1.0 Sent to CCL by: info [info\a/seascapelearning.com] This is a multi-part message in MIME format. --------------000605080304080801080502 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Seascape is pleased to announce a "Knowledge Discovery in Life Sciences: Modeling of Small Molecules to Macromolecules" workshop as detailed below. Key Faculty/Lecturers This 5 day workshop will be led by Prof. Indira Ghosh and supported by Prof. Kolaskar, Prof. Balaji of IIT Bombay, Prof. Devipriya of JNU and Scientists from OpenEye Scientific and Seascape. Workshop Overview > > Understanding and characterisation of the phenomenon of molecular > associations like DNA-Protein, Protein-Carbohydrate and > receptor-ligand complex formation is one of the important steps in any > successful rational drug discovery process. The use of computational > tools and algorithms can facilitate knowledge extraction from the > structural aspects of macromolecules. Alongside the importance of > protein in biological interaction, this workshop will emphasize the > structure of DNA, RNA and Carbohydrate, considering the emerging > importance of glyco-biology, transcription factor and anti-sense RNA. > This can help in understanding of the critical conformational changes > that affect the biological functioning on macroscale. > > The importance of shape and electrostatics as primary variables for > describing the chemistry of molecular interactions will be emphasized > by OpenEye Scientific Software. > > The topics covered would include (but are not limited to): > > * Understanding Protein, DNA, RNA and Carbohydrate structure > * Description of the potential energy of a system of particles- > Basics of Force fields > * Principles and basic techniques in Molecular Dynamics simulation > of biomolecules > * Small molecules as drug and their physico-chemical properties > * Docking, lead identification and lead optimization > > Registration/Information > > http://bioinfo.ernet.in/workshopdec07/ > http://www.seascapelearning.com --------------000605080304080801080502 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Seascape is pleased to announce a "Knowledge Discovery in Life Sciences: Modeling of Small Molecules to Macromolecules" workshop as detailed below.

Key Faculty/Lecturers

This 5 day workshop will be led by Prof. Indira Ghosh and supported by Prof. Kolaskar, Prof. Balaji of IIT Bombay, Prof. Devipriya of JNU and Scientists from OpenEye Scientific and Seascape.

Workshop Overview

Understanding and characterisation of the phenomenon of  molecular associations like DNA-Protein, Protein-Carbohydrate and receptor-ligand complex formation is one of the important steps in any successful rational drug discovery process. The use of computational tools and algorithms can facilitate knowledge extraction from the structural aspects of macromolecules. Alongside the importance of protein in biological interaction, this workshop will  emphasize the structure of DNA, RNA and Carbohydrate, considering the emerging importance of glyco-biology, transcription factor and anti-sense RNA. This can help in understanding of the critical conformational changes that affect the biological functioning on macroscale.

The importance of shape and electrostatics as primary variables for describing the chemistry of molecular interactions will be emphasized by OpenEye Scientific Software.

The topics covered would include (but are not limited to):
  • Understanding Protein, DNA, RNA and Carbohydrate structure
  • Description of the potential energy of a system of particles- Basics of Force fields
  • Principles and basic techniques in Molecular Dynamics simulation of biomolecules
  • Small molecules as drug and their physico-chemical properties
  • Docking, lead identification and lead optimization
Registration/Information

http://bioinfo.ernet.in/workshopdec07/  
http://www.seascapelearning.com
--------------000605080304080801080502-- From owner-chemistry@ccl.net Fri Dec 7 08:35:01 2007 From: "David Cornil cornildavid . yahoo.fr" To: CCL Subject: CCL: poisson_equation Message-Id: <-35786-071207080155-23435-IdwwST7Z5mJR9wy+WDCrRQ**server.ccl.net> X-Original-From: "David Cornil" Date: Fri, 7 Dec 2007 08:01:51 -0500 Sent to CCL by: "David Cornil" [cornildavid__yahoo.fr] Dear CCL's users, I have calculated the plane-integrated charge density for a molecule adsorbed on a metal surface i.e. the density for a series of points along z axis perpendicular to the surface. Now I want to estimate the potential variation induced by this density distribution. The solution is to integrating numerically the one-dimensional Poisson equation (d^2V/dx2 = - rho/e0) but how can I easily do that? As somebody know a way to resolve this problem ? Thanks in advance David Cornil Ph Student University of Mons-Hainaut Belgium From owner-chemistry@ccl.net Fri Dec 7 09:09:00 2007 From: "Matthieu Montes matthieu.montes+*+cnam.fr" To: CCL Subject: CCL: flexibility of a macrocyclic system Message-Id: <-35787-071207061959-14430-Tixf4Kam84fPqpXBXzr6kg ~~ server.ccl.net> X-Original-From: Matthieu Montes Content-Type: multipart/alternative; boundary=Apple-Mail-1--327535331 Date: Fri, 7 Dec 2007 11:23:16 +0100 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Matthieu Montes [matthieu.montes~~cnam.fr] --Apple-Mail-1--327535331 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Hi all, I am looking for a free software to evaluate the flexibility of =20 macrocyclic systems. Do you know free softwares that can do such a =20 thing ? Thanks regards, Matthieu -- Matthieu Montes, PhD Teaching and Research Associate Chair of Bioinformatics Conservatoire National des Arts et M=E9tiers 292 Rue saint Martin 75003 Paris, France mailto:matthieu.montes],[cnam.fr --Apple-Mail-1--327535331 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Hi all,

I am = looking for a free software to evaluate the flexibility of macrocyclic = systems. Do you know free softwares that can do such a thing = ?

Thanks

regards,

Matthieu

=
Matthieu Montes, = PhD
Teaching and Research Associate
Chair of = Bioinformatics
Conservatoire National des Arts et = M=E9tiers
292 Rue saint Martin
75003 Paris, = France


=

= --Apple-Mail-1--327535331-- From owner-chemistry@ccl.net Fri Dec 7 10:01:01 2007 From: "Rob Paton rsp25++cam.ac.uk" To: CCL Subject: CCL: PCM and dipole Message-Id: <-35788-071207094138-2539-n00+Rkv0puiljsa5u3KXIw||server.ccl.net> X-Original-From: "Rob Paton" Date: Fri, 7 Dec 2007 09:41:35 -0500 Sent to CCL by: "Rob Paton" [rsp25[A]cam.ac.uk] Solvation stabilises the polarization of a solute molecule relative to the gas phase. There is a discussion of the increase in dipole moment of nucleic acid bases on P349-350 in Cramer's Essentials of Comp. Chem book. Rob From owner-chemistry@ccl.net Fri Dec 7 13:36:00 2007 From: "Aleksandra N Rudnitskaya aleksandra.rudnit001|-|umb.edu" To: CCL Subject: CCL:G: pqs 3.3 and PQSMol 1.2 Message-Id: <-35789-071207131304-21531-lmrbvm0SFhg9rl5JRrhccQ/./server.ccl.net> X-Original-From: "Aleksandra N Rudnitskaya" Date: Fri, 7 Dec 2007 13:13:01 -0500 Sent to CCL by: "Aleksandra N Rudnitskaya" [aleksandra.rudnit001(_)umb.edu] Hi, All What do you think about sofware PQS 3.3 and PQSMol 1.2? Is it appropriate for academic calculation? I mean is it a good idea to switch from Gaussian03 to PQS software? I work with G03 on my laptop and we want to start our unix machine but its expansive for department because we have to buy a license for the whole departmentso, can you make any recommendations. If this particular software is not good enough you wouldnt switch to it what is a good cheap alternative? Thank you very much Aleksandra From owner-chemistry@ccl.net Fri Dec 7 17:45:00 2007 From: "Jozsef Csontos jozsefcsontos(0)creighton.edu" To: CCL Subject: CCL:G: pqs 3.3 and PQSMol 1.2 Message-Id: <-35790-071207170043-1233-4lyz0IBpZeA9BL59XgYnyQ|a|server.ccl.net> X-Original-From: Jozsef Csontos Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Fri, 07 Dec 2007 15:24:49 -0600 Mime-Version: 1.0 Sent to CCL by: Jozsef Csontos [jozsefcsontos+/-creighton.edu] Hi, it depends on what you want to calculate. I'm sure that you are gonna get meaningful suggestions if you give us a little bit more details. Every package has its benefits and shortcomings. General suggestions, which are free of charge and can cover large part of the possibilities available in Gaussian, are: NWChem, Orca, Gamess-US. They also have extra capabilities, which are not implemented in Gaussian. There are several other possibilities including free (MPQC, Dalton, Abinit, CPMD, deMon, etc) and commercial competitors as well. All the best, Jozsef On Fri, 2007-12-07 at 13:13 -0500, Aleksandra N Rudnitskaya aleksandra.rudnit001|-|umb.edu wrote: > Sent to CCL by: "Aleksandra N Rudnitskaya" [aleksandra.rudnit001(_)umb.edu] > Hi, All > > What do you think about sofware PQS 3.3 and PQSMol 1.2? > Is it appropriate for academic calculation? I mean is it a good idea to switch from Gaussian03 to PQS software? I work with G03 on my laptop and we want to start our unix machine but its expansive for department because we have to buy a license for the whole departmentso, can you make any recommendations. If this particular software is not good enough you wouldnt switch to it what is a good cheap alternative? > > Thank you very much > > Aleksandra> > -- Jozsef Csontos, Ph.D. (jozsefcsontos_at_creighton.edu) Department of Biomedical Sciences Creighton University, Omaha, NE From owner-chemistry@ccl.net Fri Dec 7 18:24:01 2007 From: "=?ISO-8859-1?Q?=D6d=F6n?= Farkas farkas * chem.elte.hu" To: CCL Subject: CCL: flexibility of a macrocyclic system Message-Id: <-35791-071207171302-2140-52gVL7VscTzArpZ7vH4KCw{:}server.ccl.net> X-Original-From: =?ISO-8859-1?Q?=D6d=F6n?= Farkas Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Fri, 07 Dec 2007 23:12:28 +0100 Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas*|*chem.elte.hu] Hi Matthieu, ChemAxon's Marvin (http://www.chemaxon.com/marvin) has a conformer plugin which is capable of generating multiple conformers for macrocyclic systems. It can be downloaded and tried through the GUI, and the license for permanent use is free for academic users. It also comes with command line tools and Java API. I hope it will fit your needs. Best wishes, Ödön -- Ödön Farkas Associate professor Deparment of Organic Chemistry and Laboratory of Chemical Informatics, Institute of Chemistry, Eötvös Loránd University, Budapest Address: 1/A Pázmány Péter sétány, H-1117 Budapest, Hungary Phone: +36-1-372-2570 Cell phone: +36-30-255-3111 Fax: +36-1-372-2620 URL: http://organ.elte.hu/farkas