From owner-chemistry@ccl.net Fri Feb 8 08:20:02 2008 From: "=?ISO-8859-1?Q?Nicolas_Ferr=E9?= nicolas.ferre ~~ univ-provence.fr" To: CCL Subject: CCL: Visualizing inertia ellipsoid and principal axes Message-Id: <-36248-080208080815-26846-vE5vVC/jTzyqaj0QwLJVZQ~~server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 08 Feb 2008 13:35:17 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= [nicolas.ferre^univ-provence.fr] Hi, Do you know about any software able to display the molecular center of mass, the inertia ellipsoid and its principal axes, given a set of atomic coordinates ? If it can give also the rotational constants (temperatures), it is even better. If not, I'll calculate them myself ! -- Nicolas Ferre' Laboratoire Chimie Provence Universite' de Provence - France Tel: +33 391282733 From owner-chemistry@ccl.net Fri Feb 8 09:08:00 2008 From: "Van Hoorn, Willem Willem.Van.Hoorn-,-pfizer.com" To: CCL Subject: CCL: Another Pipeline Pilot Question: Loops Message-Id: <-36249-080208090614-19679-ZDRgxfoWN6hCff7mniSEug*o*server.ccl.net> X-Original-From: "Van Hoorn, Willem" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Fri, 8 Feb 2008 13:34:57 -0000 MIME-Version: 1.0 Sent to CCL by: "Van Hoorn, Willem" [Willem.Van.Hoorn[*]pfizer.com] I presume you use the "Learn Good Molecules" component (Bayesian learning)? By default the 'Validate Models' option is turned on. This is a leave-one-out cross-validation, the results of which will be in the help text of the model component (which will be in your LearnedProperties tab if your model building was successful). In general, if you want a loop in Pipeline Pilot you will have to put whatever you want to be inside the loop in a subprotocol for which you have set the RunToCompletion to True. There is a download library on the Scitegic/Accelrys website: http://accelrys.org/pipelinepilot/index.html =20 ________________________________ > From: owner-chemistry{}ccl.net [mailto:owner-chemistry{}ccl.net]=20 Sent: 07 February 2008 03:23 To: Van Hoorn, Willem Subject: CCL: Another Pipeline Pilot Question: Loops Hi all, I was wondering if any one would be able to help me. I can not figure out how to "loop" over a PipeLine pilot protocol that I have written. I would like to run it a number of times and generate some statistics.=20 I have written a protocol to build a model to classify drugs from non-drugs. It takes in actives/inactives and splits them into a training and test set. The model is then build using the training set, and then validated on the test set. I am wondering if there is any way I can loop over this procedure, to turn it into a cross validation procedure? As an aside, does anybody know of a good resource for example PipeLine pilot protocols? This is all rather new to me!=20 Thanks for any help :) Iain From owner-chemistry@ccl.net Fri Feb 8 10:30:00 2008 From: "Richard Compton rcompton~~accelrys.com" To: CCL Subject: CCL: Pipeline Pilot Question Message-Id: <-36250-080208102413-23601-VB1IWMwKp9CaTN+XfQazMg###server.ccl.net> X-Original-From: "Richard Compton" Content-type: multipart/related; Boundary="0__=0FBBF97ADFC3F8008f9e8a93df938690918c0FBBF97ADFC3F800" Date: Fri, 8 Feb 2008 14:41:40 +0000 Sent to CCL by: "Richard Compton" [rcompton-.-accelrys.com] --0__=0FBBF97ADFC3F8008f9e8a93df938690918c0FBBF97ADFC3F800 Content-type: multipart/alternative; Boundary="1__=0FBBF97ADFC3F8008f9e8a93df938690918c0FBBF97ADFC3F800" --1__=0FBBF97ADFC3F8008f9e8a93df938690918c0FBBF97ADFC3F800 Content-Transfer-Encoding: quoted-printable Content-type: text/plain; charset=US-ASCII Hi Jeremy, Just to let you know that PipelinePilot is available to Academics for free. You can find more information on our Academic program at http://www.accelrys.com/products/scitegic/pp-student/ Kind regards, Richard. =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F Mr Richard Compton Senior Director, EMEA Accelrys Ltd. 334 Cambridge Science Park Cambridge CB4 0WN |------------> | From: | |------------> >------------------------------------------------------------------------= --------------------------------------------------------------------------| |"Jeremy Besnard j10b84%%hotmail.com" = | >------------------------------------------------------------------------= --------------------------------------------------------------------------| |------------> | To: | |------------> >------------------------------------------------------------------------= --------------------------------------------------------------------------| |"Compton, Richard " = | >------------------------------------------------------------------------= --------------------------------------------------------------------------| |------------> | Date: | |------------> >------------------------------------------------------------------------= --------------------------------------------------------------------------| |06/02/2008 20:24 = | >------------------------------------------------------------------------= --------------------------------------------------------------------------| |------------> | Subject: | |------------> >------------------------------------------------------------------------= --------------------------------------------------------------------------| |CCL: Pipeline Pilot Question = | >------------------------------------------------------------------------= --------------------------------------------------------------------------| Sent to CCL by: "Jeremy Besnard" [j10b84[]hotmail.com] Hi Richard, I used Pipeline Pilot last year (internship) and I managed to do it. Now that I'm back to school, I don't have access to PP, so Ill try to remind (there could be some errors, and I apologize for it). You can use the group component to group by number (for example 5000). Then you add a counter, with (~)counter. Then you create a subprotocol with inside: -a component to define the name of the file, you can use the (~)counter (~)file:=3D"c:\blabla\file=5F".(~)counter."sdf"; -an ungroup component -a sdf writer, and for the destination: $(file) And for the subprotocol you enable the option : "run to completion" (true) And now you will have a new file for each 5000 molecules. Note: 1. to reduce the size of a file, you can write a gz file, Pipeline does it, for the destination you write c:\blabla\file.sdf.gz, and it works. 2. For the number of molecule to group, you can use a global variable, which you can defined at the beginning. I hope you will understand what I said. Jrmy ---------------------------------------------------------------------------= ----- > Sent to CCL by: "Richard L. Wood" [woodx278:-:umn.edu] > Hi all, > > I've written a protocol in Pipeline Pilot that reads in a database in smiles > format, coonverts it to 3D coordinates, then adds hydrogens and minimizes the > structures. After this, I have it write the structures to an SDF file. > > The problem is that if there are a lot of molecules in the original database, this file will be very large. I've generated one that is 34 GB. I would like to be able to do something with this file, so I was wondering how or what I can do in Pipeline Pilot so that I can write out the molecules into multiple files that have fewer molecules per file? I'd like to be able to create something that I can use over and over, as opposed to just going in and having it write out x output files by having x output statements. I'm thinking that it has to be some kind of For Next loop, but I'm not sure how to write that in Pipeline Pilot. > > TIA, > > Richard > > Richard L. Wood, Ph. D. > University of Minnesota > Dept. of Medicinal Chemistry, > College of Pharmacy > 717 Delaware St. SE > Minneapolis, MN 55414-2959 > woodx278^umn.edu > -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessagehttp://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessagehttp://www.ccl.net/chemistry/sub=5Funsub.shtmlhttp://www.ccl.net/spammers.txt-- Click on the link below to report this email as spam https://www.mailcontrol.com/sr/WYclNU+qQ9Lt5QCI!1Gmgdm+Uz1JRLpdYvXAg9Rx98nu= paJqwRTbOMsMyhpD6JxvVC!azz6vDEYeveIpVJoEnvOafiW1rQq5LzMWG28Kjk4OiT2Tq65939w= mqO0X+10xLxJH5J!G9uFBlyaCoBth6!CWs4v5Dm0I3Eao8o3D4YPnhqxZwpIHTSchrUadyKxUbn= 2Iz848ZVPO++Itrau0QFMe58MXgCyH Accelrys Limited (http://www.accelrys.com)=20 Registered office: 334 Cambridge Science Park, Cambridge, CB4 0WN, UK=20 Registered in England: 2326316 = --1__=0FBBF97ADFC3F8008f9e8a93df938690918c0FBBF97ADFC3F800 Content-Transfer-Encoding: quoted-printable Content-type: text/html; charset=US-ASCII Content-Disposition: inline

Hi Jeremy,
Just to let you know that PipelinePilot is ava= ilable to Academics for free.
You can find more information on our Acade= mic program at http://www.accelrys.com/products/scitegic/pp-student/
Kind re= gards,
Richard.
=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F

Mr Richard Compton
Senior Director, EMEA
Ac= celrys Ltd.
334 Cambridge Science Park
Cambridge
CB4 0WN

<= br>

3D"Inactive&= quot;Jeremy Besnard j10b84%%hotmail.com" ---06/02/2008 20:24:40---Sent= to CCL by: "Jeremy Besnard" [j10b84[]hotmail.com]

<= /tr>
3D""From:
"Jeremy Bes= nard j10b84%%hotmail.com" <owner-chemistry]![ccl.net>
3D"=
To:		= 3D""
"Compton,= Richard " <rcompton]![accelrys.com>
3D"=
Date:		3D""
06/02/2008 2= 0:24
3D"=
Subject:		3D""
CCL: Pipe= line Pilot Question





Sent to= CCL by: "Jeremy  Besnard" [j10b84[]hotmail.com]
Hi Richa= rd,

I used Pipeline Pilot last year (internship) and I managed to d= o it.
Now that I'm back to school, I don't have access to PP, so Ill try= to remind (there could be some errors, and I apologize for it).
You can= use the group component to group by number (for example 5000).
Then you= add a counter, with (~)counter.
Then you create a subprotocol with insi= de:
-a component to define the name of the file, you can use the (~)coun= ter
   (~)file:=3D"c:\blabla\file=5F".(~)counter.&q= uot;sdf";
-an ungroup component
-a sdf writer, and for the desti= nation: $(file)

And for the subprotocol you enable the option : &qu= ot;run to completion" (true)

And now you will have a new file = for each 5000 molecules.

Note: 1. to reduce the size of a file, you = can write a gz file, Pipeline does it, for the destination you write c:\bla= bla\file.sdf.gz, and it works.
2. For the number of molecule to group, y= ou can use a global variable, which you can defined at the beginning.
<= br>I hope you will understand what I said.

Jrmy



----= ---------------------------------------------------------------------------= -

> Sent to CCL by: "Richard L. Wood" [woodx278:-:umn.e= du]
> Hi all,
>
> I've written a protocol in Pipeline Pi= lot that reads in a database in smiles
> format, coonverts it to 3D = coordinates, then adds hydrogens and minimizes the
> structures. Afte= r this, I have it write the structures to an SDF file.
>
> The= problem is that if there are a lot of molecules in the original database, = this file will be very large. I've generated one that is 34 GB. I would lik= e to be able to do something with this file, so I was wondering how or what= I can do in Pipeline Pilot so that I can write out the molecules into mult= iple files that have fewer molecules per file? I'd like to be able to creat= e something that I can use over and over, as opposed to just going in and h= aving it write out x output files by having x output statements. I'm thinki= ng that it has to be some kind of For Next loop, but I'm not sure how to wr= ite that in Pipeline Pilot.
>
> TIA,
>
> Richard=
>
> Richard L. Wood, Ph. D.
> University of Minnesota> Dept. of Medicinal Chemistry,
> College of Pharmacy
> 71= 7 Delaware St. SE
> Minneapolis, MN 55414-2959
> woodx278^umn.e= du
>



-=3D This is automatically added to each message = by the mailing script =3D-
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--
Click on the link below to report this email as s= pam
https://www.mail= control.com/sr/WYclNU+qQ9Lt5QCI!1Gmgdm+Uz1JRLpdYvXAg9Rx98nupaJqwRTbOMsMyhpD= 6JxvVC!azz6vDEYeveIpVJoEnvOafiW1rQq5LzMWG28Kjk4OiT2Tq65939wmqO0X+10xLxJH5J!= G9uFBlyaCoBth6!CWs4v5Dm0I3Eao8o3D4YPnhqxZwpIHTSchrUadyKxUbn2Iz848ZVPO++Itra= u0QFMe58MXgCyH 

Accelrys Limited (http://www.accelrys.com)
Registered office: 334 C= ambridge Science Park, Cambridge, CB4 0WN, UK
Registered in England: 2= 326316 --1__=0FBBF97ADFC3F8008f9e8a93df938690918c0FBBF97ADFC3F800-- --0__=0FBBF97ADFC3F8008f9e8a93df938690918c0FBBF97ADFC3F800 Content-type: image/gif; name="graycol.gif" Content-Disposition: inline; filename="graycol.gif" Content-ID: <1__=0FBBF97ADFC3F8008f9e8a93df9]![accelrys.com> Content-Transfer-Encoding: base64 R0lGODlhEAAQAKECAMzMzAAAAP///wAAACH5BAEAAAIALAAAAAAQABAAAAIXlI+py+0PopwxUbpu ZRfKZ2zgSJbmSRYAIf4fT3B0aW1pemVkIGJ5IFVsZWFkIFNtYXJ0U2F2ZXIhAAA7 --0__=0FBBF97ADFC3F8008f9e8a93df938690918c0FBBF97ADFC3F800 Content-type: image/gif; name="ecblank.gif" Content-Disposition: inline; filename="ecblank.gif" Content-ID: <2__=0FBBF97ADFC3F8008f9e8a93df9]![accelrys.com> Content-Transfer-Encoding: base64 R0lGODlhEAABAIAAAAAAAP///yH5BAEAAAEALAAAAAAQAAEAAAIEjI8ZBQA7 --0__=0FBBF97ADFC3F8008f9e8a93df938690918c0FBBF97ADFC3F800-- From owner-chemistry@ccl.net Fri Feb 8 11:04:01 2008 From: "Karine Costuas kcostuas{}univ-rennes1.fr" To: CCL Subject: CCL: Conference announcement Message-Id: <-36251-080208094817-10702-zfr6i50Ech0EWm5iQn4bbA/a\server.ccl.net> X-Original-From: Karine Costuas Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 8 Feb 2008 15:49:40 +0100 MIME-Version: 1.0 Sent to CCL by: Karine Costuas [kcostuas]~[univ-rennes1.fr] Dear CCL Suscribers, please find bellow the a announcement of a French-speaking meeting on=20 theoretical chemistry. Du 30 juin au 4 juillet 2008 =E0 Dinard (France) XI=E8me Rencontre des chimistes th=E9oriciens francophones organis=E9e par l'=E9quipe de Chimie th=E9orique inorganique des Sciences c= himiques=20 de Rennes=20 Site du congr=E8s :=20 http://scienceschimiques.univ-rennes1.fr/theo/RCTF/indexRCTF.htm ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Karine Costuas, charg=E9e de recherche Chimie th=E9orique inorganique UMR-CNRS 6226, Sciences chimiques de Rennes Universit=E9 de Rennes 1, FRANCE Phone: +33 (0)2 23 23 69 73 =46ax: +33 (0)2 23 23 68 40 http://scienceschimiques.univ-rennes1.fr/theo http://recherche-en-danger.apinc.org/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-chemistry@ccl.net Fri Feb 8 11:39:00 2008 From: "ramachandran chelat rcchelat!=!rediffmail.com" To: CCL Subject: CCL: AIM for non minimum structures Message-Id: <-36252-080208053344-21509-gMbwaR/kkwxAvQSw39PSgw+*+server.ccl.net> X-Original-From: "ramachandran chelat" Content-type: multipart/alternative; boundary="Next_1202463037---0-203.199.83.8-25133" Date: 8 Feb 2008 09:30:37 -0000 MIME-Version: 1.0 Sent to CCL by: "ramachandran chelat" [rcchelat]-[rediffmail.com] This is a multipart mime message --Next_1202463037---0-203.199.83.8-25133 Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear Williams, =0AThanks for pointing out that.=0AI have tried the AIM an= alysis and in many cases of nonminimum structures I failed to get the criti= cal points. The points which I got was unexpectable and had the difficulty = for explaining or comparing the results obtained from some other methods, w= hich seems that your point is valid (atleast in some cases)=0A=0A=0AOn Thu,= 07 Feb 2008 Steve Williams willsd#appstate.edu wrote :=0A>=0A>Sent to CCL = by: Steve Williams [willsd[-]appstate.edu]=0A>Following the recent discussi= on of AIM on CCL, I have a question for the AIM experts out there:=0A>In hi= s book (Atoms in Molecules, and Introduction) Popelier, on pages 60 and 61,= makes the point that AIM analysis of bonding is only valid for energy mini= mum structures, and not for such molecular structures as points on an IRC, = or for transition states. There have however, been some recent publications= (like Salazar et al. J. Phys. Chem. A, 2007, 111, p 7848 and Wagner et al.= Tetrahedron, 2007, 63, p5251) that explicity discuss and attribute meaning= to bond critical points for TS or IRC structures.=0A>What is the current o= pinion (and why is it what it is) on AIM applied to molecules in non energy= minimum geometries?=0A>Thanks,=0A>Steve Williams=0A>=0A>=0A>=0A>-=3D This = is automatically added to each message by the mailing script =3D-=0A>To rec= over the email address of the author of the message, please change=0A>the s= trange characters on the top line to the - - sign. You can also=0A>look up th= e X-Original-From: line in the mail header.=0A>=0A>E-mail to subscribers: C= HEMISTRY- -ccl.net or use:=0A> http://www.ccl.net/cgi-bin/ccl/send_ccl_m= essage=0A>=0A=0A==0A>=0A>Subscribe/Uns= ubscribe:=0A>=0A>Before p= osting, check wait time at: http://www.ccl.net=0A>=0A>Job: http://www.ccl.n= et/jobs Conferences: http://server.ccl.net/chemistry/announcements/conferen= ces/=0A>=0A>Search Messages: http://www.ccl.net/htdig (login: ccl, Passwor= d: search)=0A>=0A=0A==0A>=0A>RTFI: http://www.ccl.net/chem= istry/aboutccl/instructions/=0A>=0A>=0A=0A=0ARamachandran Chelat,=0D=0ADept= . of Chemistry,=0D=0AIIT Kanpur=0D=0AKanpur -208016=0D=0APh: +91-512-259736= 7=0D=0A=0D=0Ahttp://home.iitk.ac.in/~ramcn/ --Next_1202463037---0-203.199.83.8-25133 Content-type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline

=0A  Dear Williams,
=0AThanks for pointing out that.
=0AI ha= ve tried the AIM analysis and in many cases of nonminimum structures I fail= ed to get the critical points. The points which I got was unexpectable and = had the difficulty for explaining or comparing the results obtained from so= me other methods, which seems that your point is valid (atleast in some cas= es)
=0A
=0A
=0AOn Thu, 07 Feb 2008 Steve Williams willsd#appstate.= edu wrote :
=0A>
=0A>Sent to CCL by: Steve Williams [willsd[-]a= ppstate.edu]
=0A>Following the recent discussion of AIM on CCL, I hav= e a question for the AIM experts out there:
=0A>In his book (Atoms in= Molecules, and Introduction) Popelier, on pages 60 and 61, makes the point= that AIM analysis of bonding is only valid for energy minimum structures, = and not for such molecular structures as points on an IRC, or for transitio= n states. There have however, been some recent publications (like Salazar e= t al. J. Phys. Chem. A, 2007, 111, p 7848 and Wagner et al. Tetrahedron, 20= 07, 63, p5251) that explicity discuss and attribute meaning to bond critica= l points for TS or IRC structures.
=0A>What is the current opinion (a= nd why is it what it is) on AIM applied to molecules in non energy minimum = geometries?
=0A>Thanks,
=0A>Steve Williams
=0A>
=0A>= ;
=0A>
=0A>-=3D This is automatically added to each message by = the mailing script =3D-
=0A>To recover the email address of the autho= r of the message, please change
=0A>the strange characters on the top= line to the - - sign. You can also
=0A>look up the X-Original-From: li= ne in the mail header.
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=0A>E-mail to subscribers: CHEMISTR= Y- -ccl.net or use:
=0A>      http://www.ccl.net/cgi-bin= /ccl/send_ccl_message
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=0A&g= t;
=0A=0A

=0A=0A=0ARamachandran Chelat,=0D
=0ADept. of Chemis= try,=0D
=0AIIT Kanpur=0D
=0AKanpur -208016=0D
=0APh: +91-512-25973= 67=0D
=0A=0D
=0Ahttp://home.iitk.ac.in/~ramcn/

=0A
3D'Jeevan
--Next_1202463037---0-203.199.83.8-25133-- From owner-chemistry@ccl.net Fri Feb 8 12:14:00 2008 From: "Peter Burger burger]^[chemie.uni-hamburg.de" To: CCL Subject: CCL: Bader Theory & periodic boundary conditions Message-Id: <-36253-080208103414-26495-7dZvHHEF7hnQDsE0aSK+bA- -server.ccl.net> X-Original-From: Peter Burger Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Fri, 08 Feb 2008 15:53:18 +0100 MIME-Version: 1.0 Sent to CCL by: Peter Burger [burger:_:chemie.uni-hamburg.de] Dear all, I am looking for (AIM) software that allows to do Bader theory in conjunnction with periodic boundary condition calculations. Regards Peter -- Prof. Dr. Peter Burger Institut fuer Anorganische und Angewandte Chemie Universitaet Hamburg Martin-Luther-King-Platz 6 D-20146 Hamburg Tel.:+49 040 42838 3662 FAX 6097 email: burger[-]chemie.uni-hamburg.de http://www.chemie.uni-hamburg.de/ac/AKs/Burger From owner-chemistry@ccl.net Fri Feb 8 12:53:00 2008 From: "Carlos Simmerling carlos.simmerling~!~gmail.com" To: CCL Subject: CCL: $1,150 CCG Excellence Student Travel Awards for Fall ACS Meeting Message-Id: <-36254-080208111309-18788-XoD/hx10ws1Pgm8iiiAYnw..server.ccl.net> X-Original-From: "Carlos Simmerling" Date: Fri, 8 Feb 2008 11:13:06 -0500 Sent to CCL by: "Carlos Simmerling" [carlos.simmerling-.-gmail.com] 5 $1,150 CCG Excellence Student Travel Award Stipends Available for the Fall 2008 Philadelphia ACS National Meeting The CCG Excellence Awards have been created to stimulate graduate student participation in ACS COMP Division activities (symposia and poster sessions) at ACS National Meetings. Those eligible for a CCG Excellence Award are American graduate students in good standing who present work within the COMP program, either in oral or poster format. Winners receive $1,150, as well as a copy of CCG's MOE (Molecular Operating Environment) software with a one-year license. They are also honored during a ceremony at the COMP Division Poster Session. The application consists of an extended abstract (no more than 2 pages) of the poster or presentation along with a letter of support from the research advisor, a two page CV, and a personal statement (no more than 1 page). The awardees are chosen on the basis of the quality and significance of the research to be presented, as well as the strength of the supporting letter and other materials. All graduate students of the Americas are encouraged to submit applications. Awards will be given only to those individuals making presentations, not co-authors. Closing date for entries (including all required supporting info.) is Friday, March 7, 2008 at 5PM Eastern time. Note that the award application deadline is BEFORE the normal deadline for submission of abstracts for the meeting. Applicants will receive email confirmation of receipt of materials. If you do not receive confirmation by March 10, 2008, please contact the organizer immediately by telephone (see below). In addition, you must submit your normal abstract to the " Chemical Computing Group Excellence Award" symposium on the OASYS system (the COMP OASYS deadline is March 17, 2008 for the Philadelphia ACS Meeting) More information on awards offered by the ACS COMP division can be found on the web site at http://membership.acs.org/c/Comp/awards.html Carlos Simmerling Professor, Department of Chemistry Stony Brook University Stony Brook, NY 11794-3400 631-384-9248 carlos.simmerling]^[gmail.com From owner-chemistry@ccl.net Fri Feb 8 13:25:01 2008 From: "Carlos Simmerling carlos.simmerling##gmail.com" To: CCL Subject: CCL: 2008 ACS Symposium on Emerging Technologies in Computational Chemistry Message-Id: <-36255-080208111720-21906-WcTWOk8sIDLxY8+6DbBjXg^^server.ccl.net> X-Original-From: "Carlos Simmerling" Date: Fri, 8 Feb 2008 11:17:17 -0500 Sent to CCL by: "Carlos Simmerling" [carlos.simmerling]=[gmail.com] 2008 Symposium on Emerging Technologies in Computational Chemistry $1,000 prize to be awarded at the ACS national meeting, Philadelphia, PA. 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. 17-21 2008. 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 a $1,000 prize for the best talk at the symposium. All are invited to participate. To participate, it is necessary to submit a regular short ACS abstract via http://oasys.acs.org/ . 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 carlos.simmerling-at-gmail.com Please use a subject of "ACS Emerging Tech Abstract". THE LONG ABSTRACT MUST BE SENT BY 5PM EASTERN TIME ON FRIDAY, MARCH 7, 2008. The short abstract must be submitted to OASYS by the normal deadline of March 17, 2008. You will receive a confirmation of receipt of your application via email. Please contact the organizer immediately if you do not receive confirmation by March 10. More information on awards offered by the ACS COMP division can be found on the web site at http://membership.acs.org/c/Comp/awards.html Carlos Simmerling Professor, Department of Chemistry Stony Brook University Stony Brook, NY 11794-3400 631-632-1336 From owner-chemistry@ccl.net Fri Feb 8 14:06:01 2008 From: "Carlos Simmerling carlos.simmerling.:.gmail.com" To: CCL Subject: CCL: HP Outstanding Junior Faculty Awards in Computational Chemistry Message-Id: <-36256-080208111003-16036-3FGNnPUlwe5pwOlFssdnsQ^server.ccl.net> X-Original-From: "Carlos Simmerling" Date: Fri, 8 Feb 2008 11:09:58 -0500 Sent to CCL by: "Carlos Simmerling" [carlos.simmerling]~[gmail.com] The HP Outstanding Junior Faculty Award program provides $1,000 to each of four outstanding tenure-track junior faculty members to present their work in COMP symposia at ACS National Meetings. The Awards are designed to assist new faculty members in gaining visibility within the COMP community. Award certificates and $1,000 prizes will be presented at the COMP Poster session. While special consideration will be given to Assistant Professors presenting work in the area of algorithm and methods development, applications for HP Outstanding Junior Faculty Awards are invited from all current tenure-track junior faculty who are members of ACS and the ACS Division of Computers in Chemistry. Postdoctoral researchers in transition to faculty appointments may also be considered. Selection criteria will include the novelty and importance of the work to be presented, as well as the level of Departmental support as indicated by a letter of support by the Chair or Chair designee. To apply for an award for the ACS National Meeting In Philadelphia, PA, Aug. 17-21, 2008, an extended abstract of the work (no more than 2 pages) and the letter of departmental support should be sent to carlos.simmerling%x%gmail.com IMPORTANT: EXTENDED ABSTRACT AND SUPPORT LETTER MUST BE RECEIVED BY 5PM EASTERN TIME ON MARCH 7, 2008. Applicants will receive email confirmation of receipt of materials. If you do not receive confirmation by March 10, 2008, please contact the organizer immediately by telephone (see below). In addition, you must submit your normal abstract to the "HP Outstanding Junior Faculty Award" symposium on the OASYS system (the COMP OASYS deadline is March 17, 2008 for the Philadelphia ACS Meeting) More information on awards offered by the ACS COMP division can be found on the web site at http://membership.acs.org/c/Comp/awards.html Carlos Simmerling Professor, Department of Chemistry Stony Brook University Stony Brook, NY 11794-3400 631-384-9248 From owner-chemistry@ccl.net Fri Feb 8 14:34:01 2008 From: "Aron Walsh aronjwalsh[a]gmail.com" To: CCL Subject: CCL:G: Bader Theory & periodic boundary conditions Message-Id: <-36257-080208135321-21855-UfkgLw0gPYi/nBhRb7yUsA-$-server.ccl.net> X-Original-From: "Aron Walsh" Content-Type: multipart/alternative; boundary="----=_Part_30810_29357527.1202493136181" Date: Fri, 8 Feb 2008 10:52:16 -0700 MIME-Version: 1.0 Sent to CCL by: "Aron Walsh" [aronjwalsh..gmail.com] ------=_Part_30810_29357527.1202493136181 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline A group at the university of texas have developed a nice implementation that can read in charge densities generated from VASP and Gaussian. http://theory.cm.utexas.edu/vtsttools/bader/ Whether you believe the Bader numbers for covalent solids is another issue. Best, Aron -- Dr. Aron Walsh Theoretical Materials Science Section National Renewable Energy Laboratory Golden, CO 80401 USA Phone: 303-384-6833; Mailstop: 3203 On Feb 8, 2008 7:53 AM, Peter Burger burger]^[chemie.uni-hamburg.de < owner-chemistry:_:ccl.net> wrote: > > Sent to CCL by: Peter Burger [burger:_:chemie.uni-hamburg.de] > Dear all, > > I am looking for (AIM) software that allows to do Bader theory in > conjunnction > with periodic boundary condition calculations. > > Regards > > Peter > > -- > Prof. Dr. Peter Burger > Institut fuer Anorganische und Angewandte Chemie > Universitaet Hamburg > Martin-Luther-King-Platz 6 > D-20146 Hamburg > Tel.:+49 040 42838 3662 > FAX 6097 > email: burger[A]chemie.uni-hamburg.de > http://www.chemie.uni-hamburg.de/ac/AKs/Burger> > > > ------=_Part_30810_29357527.1202493136181 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
A group at the university of texas have developed a nice implementation that can read in charge densities generated from VASP and Gaussian.

http://theory.cm.utexas.edu/vtsttools/bader/

Whether you believe the Bader numbers for covalent solids is another issue.

Best,
Aron

--
Dr. Aron Walsh
Theoretical Materials Science Section
National Renewable Energy Laboratory
Golden, CO 80401 USA
Phone: 303-384-6833; Mailstop: 3203

On Feb 8, 2008 7:53 AM, Peter Burger burger]^[chemie.uni-hamburg.de <owner-chemistry:_:ccl.net> wrote:

Sent to CCL by: Peter Burger [burger:_:chemie.uni-hamburg.de]
Dear all,

I am looking for (AIM) software that allows to do Bader theory in
conjunnction
with periodic boundary condition calculations.

Regards

Peter

--
Prof. Dr. Peter Burger
Institut fuer Anorganische und Angewandte Chemie
Universitaet Hamburg
Martin-Luther-King-Platz 6
D-20146 Hamburg
Tel.:+49 040 42838 3662
FAX                6097
email: burger[A]chemie.uni-hamburg.de
http://www.chemie.uni-hamburg.de/ac/AKs/Burger



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