From owner-chemistry@ccl.net Mon Oct 27 03:53:00 2008 From: "ewe:_:inbox.ru" To: CCL Subject: CCL: =?koi8-r?Q?Re=3A_CCL=3A_Where_to_find_drug_half_life_prediction_software?= Message-Id: <-37982-081025001709-7193-jHTzCSFHZ8ys4bEkCZBC+g * server.ccl.net> X-Original-From: ewe. * .inbox.ru Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=koi8-r Date: Sat, 25 Oct 2008 07:26:37 +0400 Mime-Version: 1.0 Sent to CCL by: ewe^_^inbox.ru hi i use q-ADME for drug half-life prediction it is downloadable from http://www.q-lead.com/adme_pk From owner-chemistry@ccl.net Mon Oct 27 08:28:01 2008 From: "James Robinson James.Robinson-,-prosonix.co.uk" To: CCL Subject: CCL: FW: dielectric constants Message-Id: <-37983-081027082354-15710-em5pTxP4vAx7vF19ejgd+A{:}server.ccl.net> X-Original-From: "James Robinson" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C93819.1B87E2DF" Date: Mon, 27 Oct 2008 09:48:04 -0000 MIME-Version: 1.0 Sent to CCL by: "James Robinson" [James.Robinson*prosonix.co.uk] This is a multi-part message in MIME format. ------_=_NextPart_001_01C93819.1B87E2DF Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable =20 Hi Dr Borosy, =20 Please consider the context of the molecule, is it in solution or solid = state. It should be possible to calculate the dipole moment. You may = have to use the relationship developed by Debye and extended by = Halverstadt and Kulmer. A good phys chem book should point you in the = right direction.=20 =20 I have also wondered if applying two point charges within a calculation, = in the direction of the permanent dipole can shed any light? =20 =20 Dr James J Robinson Senior Scientist Prosonix Ltd Magdalen Centre Robert Robinson Avenue Oxford Science Park Oxford, Oxon. OX4 4GA, UK. +44(0) 1865 784243 http://www.prosonix.co.uk =20 =20 P Please consider the environment - do you really need to print this = email? =20 =20 ________________________________ > From: owner-chemistry,ccl.net [mailto:owner-chemistry,ccl.net]=20 Sent: 23 October 2008 08:49 To: James Robinson Subject: CCL: dielectric constants =20 -=20 Dear Colleagues,=20 How can dielectric constants of small organic molecules be estimated by = any computational method?=20 Regards,=20 Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf = - Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com ------_=_NextPart_001_01C93819.1B87E2DF Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi Dr = Borosy,

Please consider the context of the molecule, is it in solution or solid state. It should be possible to = calculate the dipole moment. You may have to use the relationship developed by = Debye and extended by Halverstadt and Kulmer. A good phys chem book should point = you in the right direction.

I have also wondered if applying = two point charges within a calculation, in the direction of the permanent dipole = can shed any light?

Dr James J = Robinson

Senior = Scientist

Prosonix = Ltd

Magdalen = Centre

Robert Robinson = Avenue

Oxford Science = Park

Oxford, Oxon.

OX4 4GA, = UK.

+44(0) 1865 = 784243

http://www.prosonix.co.uk

=

P Please consider the environment - = do you really need to print this email?

=

=

From: = owner-chemistry,ccl.net = [mailto:owner-chemistry,ccl.net]
Sent: 23 October 2008 = 08:49
To: James Robinson
Subject: CCL: dielectric = constants

-
Dear Colleagues,

How can dielectric constants of small organic molecules be estimated = by any computational method?

Regards,

Dr. Andr=E1s P=E9ter Borosy
Scientific Modelling Expert
Fragrance Research
Givaudan Schweiz AG - Ueberlandstrasse 138 - = CH-8600 - D=FCbendorf - Switzerland
T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com

------_=_NextPart_001_01C93819.1B87E2DF-- From owner-chemistry@ccl.net Mon Oct 27 12:08:01 2008 From: "Andrew Dalke dalke . dalkescientific.com" To: CCL Subject: CCL: Python training for cheminformatics Message-Id: <-37984-081027114817-1343-Sn+hYpE3sXTOKeEMHncZvg|server.ccl.net> X-Original-From: Andrew Dalke Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Date: Mon, 27 Oct 2008 12:48:02 -0200 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Andrew Dalke [dalke- -dalkescientific.com] I will be teaching several training courses in Python programming, designed for cheminformatics researchers who want to be more effective at the software side of their work. These courses will be in San Francisco in December, in Leipzig in March and in Boston in April. The next course is in San Francisco on December 4-5, 2008 and space is still available. Topics I will cover include: - an overview of the Python language - the IPython interactive shell - plotting with matplotlib - OpenEye's OEChem - parsing CSV, SMILES and SD files with Python and OEChem - substructure matching with SMARTS, using OEChem - calling other programs - working with a SQL database I am planning a course for Leipzig on 2-4 March 2009, although the dates are not yet finalized. This three-day course will cover a few additional topics, like working with Excel, and include more time for hands-on and self-directed work. Please contact me if you are interested and I'll notify you on the details when they are finalized. I have started planning a course for Boston in April, 2009 and am working on finding a location and time. Please contact me if you are interested in this class or have a suggestion for a location. All courses are limited to 8 people. Registration includes all teaching materials, coffee breaks, and lunch. For full details including course topics and prerequisite experience, see http://dalkescientific.com/training/ . Andrew Dalke dalke,dalkescientific.com From owner-chemistry@ccl.net Mon Oct 27 18:53:01 2008 From: "Jacqueline Cawthray jacqueline.cawthray|a|adelaide.edu.au" To: CCL Subject: CCL:G: Atoms in Molecules calculation Message-Id: <-37985-081026043551-25898-OaGWYa/oN2V+ngBrcEu8uA^^^server.ccl.net> X-Original-From: Jacqueline Cawthray Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 26 Oct 2008 18:34:44 +1030 MIME-Version: 1.0 Sent to CCL by: Jacqueline Cawthray [jacqueline.cawthray++adelaide.edu.au] Hi there I've been using Todd Keith's AIMALL which is freely available from his website: http://aim.tkgristmill.com You need to email him for a password before you can download the program. It uses wfn files from Gaussian and is simple to use. Regards JC Quoting "Emilio J Ju rez-P rez ejjuarezperez+*+gmail.com" : > > Sent to CCL by: "Emilio J Ju rez-P rez" [ejjuarezperez++gmail.com] > Hello CCL users, > > This is my first post in the forum. > > > Problem: tipical Atoms in Molecules calculation (bcp,rcp...,e density, > laplacian...) for a molecule in gas phase with less 20 atoms (some from 4th > row period) Full electron optimization accounting for relativistic effect is > needed. > > And I have two main options: > > > a)Gaussian03(mp2?,cc-pVTZ?, AIMPAC (or XAIM, aimall) > > b)ADF2007(ZORA,TZ2P), XAIM (aimall?) > > > First question: What option (or combination) will be good? > (I have not Morphy98 nor AIM2000) > > Second question:How it be correct to do a single point calculation in a > crystal structure to determine the electronic density(the .wfn file)? > > Thank you!> > >