From owner-chemistry@ccl.net Thu Dec 6 03:06:00 2007 From: "Alex Wang yawang[a]chem.ubc.ca" To: CCL Subject: CCL: ISTCP-VI, 19-24 July 2008 at UBC, Vancouver, Canada Message-Id: <-35774-071206030357-16093-eUiEw27aDNyOdj4fEPZBhw(a)server.ccl.net> X-Original-From: "Alex Wang" Date: Thu, 6 Dec 2007 03:03:53 -0500 Sent to CCL by: "Alex Wang" [yawang]^[chem.ubc.ca] --------------------------------------------------------------------- PLEASE ACCEPT OUR APOLOGIES IF YOU RECEIVE THIS E-MAIL MORE THAN ONCE --------------------------------------------------------------------- ****************** FIRST ANNOUNCEMENT ****************** Sixth International Congress of the INTERNATIONAL SOCIETY FOR THEORETICAL CHEMICAL PHYSICS July 19-24, 2008 Vancouver, BC, Canada Very soon, the ISTCP-VI website (http://www.chem.ubc.ca/istcp6) will be open for abstract submission. In the coming weeks, please visit the conference website for updated information and details. ------------ Dear Colleague, The Sixth Congress of the International Society for Theoretical Chemical Physics (ISTCP-VI) (http://www.chem.ubc.ca/istcp6) will be held on July 19-24, 2008 in the beautiful campus of the University of British Columbia (UBC) at Vancouver, BC, Canada. The history of ISTCP and its Congresses is available at the following link: http://www.chem.ubc.ca/istcp6/ISTCPstory.htm. Held every three years, ISTCP Congresses continue the tradition of showcasing the achievements and advances in all areas of theoretical chemical physics, with special emphasis on the interaction between experimental and theoretical physical chemistry, chemical physics, and materials and life sciences. The scope of ISTCP-VI will cover a broad range of topics that include Biophysical/Medical Simulations, Statistical Mechanics, Quantum Chemistry, Density-Functional Theory, Coupled Clusters, Quantum Monte Carlo, Quantum/Classical Dynamics, Nanosystems, Coherent Control, Ultra-cold Chemistry, AttoScience, and Novel Materials. As usual, the proceedings of the Congress will be published in the International Journal of Quantum Chemistry (IJQC) and Progress in Theoretical Chemistry and Physics (PTCP). Research papers will appear in IJQC (Wiley) while review papers will appear in PTCP (a book series published by Springer). With extensive advertising all over the world, we anticipate the total number of participants to ISTCP-VI to reach 250. This will definitely be a wonderful opportunity to know the latest cutting- edge advances in theoretical chemical physics and to network with your colleagues worldwide. It is our great pleasure to invite you to join us for a five-day scientific fest at UBC during ISTCP-VI. Several members of the Honorary Board of Directors of ISTCP (which includes 4 Nobel Laureates and 4 Wolf Prize Awardees) have expressed their intention to attend the Congress. With best wishes, The ISTCP-VI Executive Committee Alex Wang (Chair, UBC, Canada) Erkki J. Brandas (Co-chair, President of ISTCP, Sweden) Jean Maruani (Co-chair, France) ------------ About Vancouver Vancouver is the largest city in Western Canada, located at the south- western corner of the province of British Columbia. Situated between the north-shore and coastal mountains and the edge of the Pacific ocean, Vancouver is one of the most beautiful cities in North America, and was recently ranked as "the world's most desirable place to live" in a survey of 127 cities performed by the Intelligence Unit of the magazine The Economist. It is also the hosting city of the 2010 Olympic Winter Games. The vibrant downtown core offers all the amenities of an international destination - from hundreds of restaurants and clubs through countless parks and recreation facilities to world-class sporting and entertainment events (including the Vancouver Symphony Orchestra and the Canucks - the city's major league hockey team). Vancouver's natural surroundings offer limitless opportunities for outdoor pursuits, such as hiking and mountain biking in the Spring and Summer, and skiing at nearby Whistler-Blackcomb resort in Winter. We invite you to explore Vancouver and Beautiful British Columbia at the following web sites: - Tourism Vancouver (http://www.tourismvancouver.com) - Tourism BC (http://www.hellobc.com) ------------ About UBC Highly ranked among the world's best universities, the University of British Columbia holds an international reputation for excellence in advanced research and learning (http://www.ubc.ca/global/index.html). Only 30 minutes from the vibrant heart of downtown Vancouver, the spectacular UBC campus is a 'must-see' for any visitor of the world: snow-capped mountains can be seen meeting the ocean, and breathtaking vistas greet you around every corner. The UBC campus also boasts some of the city's best attractions and recreation facilities, including the Chan Centre for the Performing Arts (mainly music), the Museum of Anthropology, the UBC Botanical Garden, and endless opportunities to explore forested trails in the adjoining 763-hectare Pacific Spirit Regional Park. More attractions of UBC are available at http://www.attractions.ubc.ca. ------------ From owner-chemistry@ccl.net Thu Dec 6 09:56:00 2007 From: "Rob Paton rsp25 .. cam.ac.uk" To: CCL Subject: CCL: Calculating second derivatives in PCM using Jaguar 6.5 Message-Id: <-35775-071206095424-9129-MI9vGdXs0w8o4d06iKnMdA%server.ccl.net> X-Original-From: "Rob Paton" Date: Thu, 6 Dec 2007 09:54:20 -0500 Sent to CCL by: "Rob Paton" [rsp25---cam.ac.uk] Hi all, I'm trying to calculate the frequencies of a species using the PCM model in Jaguar 6.5. i.e. numerically evaluating second derivatives. The job fails (after a while!) with the following message: Mesh_step: Cavity error formation - mesh construction failed for V=6363, nfacelist=0 is less than 4; cvn=5. Vtess_pol: 'mesh_step' failed on 6714th point (gd=6363) with mstat=-1. Hence, something is wrong with the tesserae generation. Has anyone encountered this problem before, and more importantly, is there a quick fix? Many thanks in advance, Rob Paton From owner-chemistry@ccl.net Thu Dec 6 10:30:00 2007 From: "Maxim Kholin maxim.kholin*|*q-pharm.com" To: CCL Subject: CCL: Quantum Docking: New Year Offer Message-Id: <-35776-071206101252-28537-8/uBRLEnlTCrS7r2KxhNfA..server.ccl.net> X-Original-From: "Maxim Kholin" Date: Thu, 6 Dec 2007 10:12:49 -0500 Sent to CCL by: "Maxim Kholin" [maxim.kholin[*]q-pharm.com] Dear Colleagues, Let us invite researchers who have not yet tried Quantum docking module explore it and enjoy a special New Year offerings. As many of you know, Quantum is an industrial docking tool with first principles based free energy calculations, already adopted by many researchers, including those of Top World Pharma. Quantum was created in response of the widely known critical limitations of scoring functions and QSAR based tools, such as False Positives, Low Hit Rate and others. Please download free trial right now from www.q-pharm.com , discover more new inhibitors of novel classes and work with flexible proteins. Special New Year Offers are also there. We wish you New Achievements with New Technology in the New Year. Best regards Quantum Pharmaceuticals Team From owner-chemistry@ccl.net Thu Dec 6 11:09:00 2007 From: "Matthew Cooper mdcooper^^uvic.ca" To: CCL Subject: CCL: General semiempirical method Message-Id: <-35777-071206102656-4236-RSfF1FVInX/bKweCTc2DOA+*+server.ccl.net> X-Original-From: "Matthew Cooper" Date: Thu, 6 Dec 2007 10:26:52 -0500 Sent to CCL by: "Matthew Cooper" [mdcooper~~uvic.ca] Hello all, I am in the process of choosing a semiempirical method to use solely for the generation of point charges on a wide variety of small molecules. My goal is to use the most general and widely available semiempirical method and so would like to choose between AM1, PM3, MNDO or SAM1. I have done a relatively extensive literature survey on where each of these methods are strong and weak but I was hoping to get further evidence (it can be anecdotal if the information has not been published!) on where any of these methods fail to match experimental results especially badly, especially if the failure results in random rather than systematic errors. I am looking not for just large errors, but exceptionally large and unexpected errors. I know about the problems that PM3 has with delocalised nitrogens and the fact that MNDO is very bad at hydrogen bonding. I am really looking for unique and unusual failures that may make me question the use of any single method as a general charge generator. Thanks, Matthew From owner-chemistry@ccl.net Thu Dec 6 11:59:01 2007 From: "Tom de Greef t.f.a.d.greef+/-tue.nl" To: CCL Subject: CCL:G: PCM and dipole Message-Id: <-35778-071206094731-8436-7eLbUZAueechymmo1cTGpA]=[server.ccl.net> X-Original-From: "Tom de Greef" Date: Thu, 6 Dec 2007 09:47:27 -0500 Sent to CCL by: "Tom de Greef" [t.f.a.d.greef(-)tue.nl] Dear all, I have yet another question about the PCM model. I have computed the dipole moments of several tautomers in the gas-phase as well as in CHCl3 using all the standard settings in Gaussian (alfa = 1.21, epsilon = 4.9, use of UA0 to define cavity). In all cases, the tautomers have a high dipole moment in the gas phase (around 5) and this dipole moment ALWAYS (i have examined 5 structures) is higher in CHCl3 (around 6-7). I am aware that the PCM models explicity takes multipole moments into account. However, I cannot reason why the dipole moments of my solute increase when using PCM.Any help (or reference) would be greatly appreciated. thnax! Tom From owner-chemistry@ccl.net Thu Dec 6 12:33:01 2007 From: "miguel escobedo kmiguelescobedo##yahoo.com" To: CCL Subject: CCL: Fractional coordinates Message-Id: <-35779-071206085308-2263-luM187MdJinC4imBWAUZWA|*|server.ccl.net> X-Original-From: miguel escobedo Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1139875523-1196945833=:41297" Date: Thu, 6 Dec 2007 04:57:13 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: miguel escobedo [kmiguelescobedo=-=yahoo.com] --0-1139875523-1196945833=:41297 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit My name is Miguel escobedo. I'm novice in this field and I am trying to convert some fractional coordenates ( x ray coordinates) to cartesian.coordinates . I want a free programan which could do it . Thanks in advance. Regards, Miguel --------------------------------- Never miss a thing. Make Yahoo your homepage. --0-1139875523-1196945833=:41297 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
My name is Miguel escobedo. I'm novice in this field and I am trying to convert some fractional coordenates ( x ray coordinates) to cartesian.coordinates . I want a free programan  which could do it .
 
 Thanks in advance.
 
 
Regards,
Miguel
 

Never miss a thing. Make Yahoo your homepage. --0-1139875523-1196945833=:41297-- From owner-chemistry@ccl.net Thu Dec 6 13:15:01 2007 From: "Jamie Platts platts#cf.ac.uk" To: CCL Subject: CCL: MGMS Spring meeting: 31st March - 2nd April 2008 Message-Id: <-35780-071206115614-1905-Dz/DSR6zbs1p1wuH+j+Abw+*+server.ccl.net> X-Original-From: "Jamie Platts" Date: Thu, 6 Dec 2007 11:56:10 -0500 Sent to CCL by: "Jamie Platts" [platts a cf.ac.uk] Dear Colleague, We are pleased to announce that registration is now open for the MGMS Spring conference on Computational Bio-inorganic Chemistry, which will take place in Cardiff University between 31st March and 2nd April 2008. Registration costs are 70 (50 for students) for MGMS members, and 90 (70) for non-members, before the "early bird" deadline of 31st January 2008, after which a late registration charge of 40 will be added. Student attendees may be eligible for travel bursaries, kindly provided by Chemical Computing Group. If you would like to present your work, the deadline for abstract submission is 22nd February 2008. Further details of registration, the conference location, and accomodation in the area, can be found at the conference website http://theory.chem.cf.ac.uk/~grant/conf/index.html . Best regards, Jamie Platts & Adrian Mulholland From owner-chemistry@ccl.net Thu Dec 6 13:49:01 2007 From: "Close, David M. CLOSED[-]mail.etsu.edu" To: CCL Subject: CCL: Fractional coordinates Message-Id: <-35781-071206132007-4074-Bkz16V4fG3vDqlAr2M2ExQ(-)server.ccl.net> X-Original-From: "Close, David M." Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C83834.9AA11538" Date: Thu, 6 Dec 2007 13:19:55 -0500 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED-*-mail.etsu.edu] This is a multi-part message in MIME format. ------_=_NextPart_001_01C83834.9AA11538 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable The best free program is BABEL. If you just have one set of data, I'll do it for you. If you want to do this routinely, just Google BABEL. =20 ________________________________ > From: owner-chemistry.:.ccl.net [mailto:owner-chemistry.:.ccl.net]=20 Sent: Thursday, December 06, 2007 7:57 AM To: Close, David M. Subject: CCL: Fractional coordinates =20 My name is Miguel escobedo. I'm novice in this field and I am trying to convert some fractional coordenates ( x ray coordinates) to cartesian.coordinates . I want a free programan which could do it . =20 Thanks in advance. =20 =20 Regards, Miguel =20 =20 ________________________________ Never miss a thing. Make Yahoo your homepage. =20 ------_=_NextPart_001_01C83834.9AA11538 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

The best free program is BABEL.  If you just have one = set of data, I’ll do it for you.  If you want to do this routinely, just Google = BABEL.

 

From: owner-chemistry.:.ccl.net [mailto:owner-chemistry.:.ccl.net]
Sent: Thursday, December = 06, 2007 7:57 AM
To: Close, David M.
Subject: CCL: Fractional coordinates

 

My name is Miguel escobedo. I'm novice in this field and = ;I am trying to convert some fractional coordenates ( x ray coordinates) to cartesian.coordinates . I want a free = programan  which could do it .

 

 Thanks in advance.

 

 

Regards,

Miguel

 

 

Never miss a thing. Mak= e Yahoo your homepage.

------_=_NextPart_001_01C83834.9AA11538-- From owner-chemistry@ccl.net Thu Dec 6 14:32:01 2007 From: "Andreas Klamt klamt-.-cosmologic.de" To: CCL Subject: CCL:G: PCM and dipole Message-Id: <-35782-071206142401-30016-kG5VhhWi3X2YezC8xLlChw(~)server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Thu, 06 Dec 2007 20:23:46 +0100 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt::cosmologic.de] Hi Tom, all self consistent solvation models increase the dipole moment because the solvent polarization interacts with the solute density and thus increases the polarity of the solute. A typical value for dipole moments is 30 % increase by this backpolarization in water. Obviously, at eps=4.9 it will be much less, ~15% or so. Regards Andreas Tom de Greef t.f.a.d.greef+/-tue.nl schrieb: > Sent to CCL by: "Tom de Greef" [t.f.a.d.greef(-)tue.nl] > Dear all, > I have yet another question about the PCM model. I have computed the dipole moments of several tautomers in the gas-phase as well as in CHCl3 using all the standard settings in Gaussian (alfa = 1.21, epsilon = 4.9, use of UA0 to define cavity). In all cases, the tautomers have a high dipole moment in the gas phase (around 5) and this dipole moment ALWAYS (i have examined 5 structures) is higher in CHCl3 (around 6-7). I am aware that the PCM models explicity takes multipole moments into account. > However, I cannot reason why the dipole moments of my solute increase when using PCM.Any help (or reference) would be greatly appreciated. > > thnax! > > Tom> > > > > -- ----------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt]![cosmologic.de web: www.cosmologic.de ----------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics ----------------------------------------------------------------------------- From owner-chemistry@ccl.net Thu Dec 6 15:27:01 2007 From: "Jeff Nauss jnauss*|*accelrys.com" To: CCL Subject: CCL: Accelrys Customer Training for December and January Message-Id: <-35783-071206152519-28560-q+WUQD2h2q2VMdhuJYhQXA]~[server.ccl.net> X-Original-From: Jeff Nauss Content-Type: text/plain; charset="US-ASCII" Date: Thu, 6 Dec 2007 12:21:34 -0800 MIME-Version: 1.0 Sent to CCL by: Jeff Nauss [jnauss**accelrys.com] Accelrys Inc. are holding the following training workshops during December 2007 and January 2008. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. Costs for the on-line presentations are the price is $175 per three hour session for all customers. December 2007 Protein Homology Modeling in Discovery Studio 11 Dec (8am PST) Introduction to Material Studio 11 Dec (4pm GMT) Scripting in Materials Studio 12 Dec (4pm GMT) Simulations in Discovery Studio 12 - 13 Dec (8am PST) Catalyst to Discovery Studio Migration 17 Dec (4pm GMT) January 2008 Solvation Models in CHARMm 9 Jan (8am PST) InsightII to Discovery Studio Migration 10 Jan (8am PST) Catalyst to Discovery Studio Migration 11 Jan (8am PST) Introduction to Material Studio 14 Jan (4pm GMT) Scripting in Materials Studio 15 Jan (4pm GMT) Introduction to Discovery Studio 14 Jan (8am PST) Sequence Analysis for Homology Modeling 15 Jan (8am PST) Protein Homology Modeling in Discovery Studio 16 Jan (8am PST) Simulations in Discovery Studio 17-18 Jan (8am PST) Docking & Scoring in Discovery Studio 21 Jan (8am PST) De Novo Design with Discovery Studio 22 Jan (8am PST) Pharmacophore Modeling in Discovery Studio 23-24 Jan (8am PST) Note that some of these events in December are tentative and may be rescheduled. Please check for the latest updates at http://www.accelrys.com/services/training/general/calendar.html. Further details can be found on our website at http://www.accelrys.com/training/general/calendar.html and http://www.accelrys.com/training/general/calendar_online.html Questions regarding scheduling and content should be directed to workshops]^[accelrys.com -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121-4779 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/services/training/ From owner-chemistry@ccl.net Thu Dec 6 16:02:00 2007 From: "Jerome Kieffer jerome.Kieffer^^terre-adelie.org" To: CCL Subject: CCL: Fractional coordinates Message-Id: <-35784-071206144609-25210-fCiHbvz5e6DiYC1IRTpWYQ .. server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-15 Date: Thu, 6 Dec 2007 20:46:24 +0100 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [jerome.Kieffer=-=terre-adelie.org] On Thu, 6 Dec 2007 04:57:13 -0800 (PST) "miguel escobedo kmiguelescobedo##yahoo.com" wrote: >=20 > My name is Miguel escobedo. I'm novice in this field and I am trying to c= onvert some fractional coordenates ( x ray coordinates) to cartesian.coordi= nates . I want a free programan which could do it . Have a look at Mercury from CCDC or Platon (written by Speck in the NL). The first is free, the second is open-source + academic license. Reards --=20 J=E9r=F4me KIEFFER : http://www.terre-adelie.org =C0 v=E9lo, prendre une rue =E0 contre-sens est moins dangeureux que prendre un boulevard dans le sens l=E9gal. =C0 qui la faute ?