From owner-chemistry@ccl.net Tue Sep 22 03:31:01 2009 From: "Michel Petitjean petitjean.chiral##gmail.com" To: CCL Subject: CCL: surface area calculator Message-Id: <-40314-090922032515-31120-2RDTRT2msSiDENvGEGjzDA[a]server.ccl.net> X-Original-From: Michel Petitjean Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 22 Sep 2009 08:55:33 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral(_)gmail.com] Please look at: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ASV (freeware) http://petitjeanmichel.free.fr/itoweb.petitjean.spheres.html (theory) Hope this helps. Michel Petitjean, CEA/DSV/iBiTec-S/SB2SM (CNRS URA 2096), 91191 Gif-sur-Yvette Cedex, France. Phone: +331 6908 4006 / Fax: +331 6908 4007 E-mail: michel.petitjean[*]cea.fr, petitjean.chiral[*]gmail.com (preferred) http://petitjeanmichel.free.fr/itoweb.petitjean.html ---------- Forwarded message ---------- > From: Yun Wang wangyun22{=}yahoo.com Date: 2009/9/21 Subject: CCL: surface area calculator To: "Petitjean, Michel " Dear Madam/Sir, Do you know whether there is a program to calculate the surface area with 3D coordinates? Thank you for your help. Best wishes. Yun ________________________________ Get more done like never before with Yahoo!7 Mail. Learn more. From owner-chemistry@ccl.net Tue Sep 22 04:09:01 2009 From: "Inbal Tuvi-Arad inbaltu%a%openu.ac.il" To: CCL Subject: CCL: Web Tutorials for High and Middle School Students Message-Id: <-40315-090922032622-31231-MymRVMRwFi8gHCaco9PvAQ\a/server.ccl.net> X-Original-From: "Inbal Tuvi-Arad" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Tue, 22 Sep 2009 09:52:40 +0300 MIME-Version: 1.0 Sent to CCL by: "Inbal Tuvi-Arad" [inbaltu+*+openu.ac.il] Hi Anatoli, Here are few links related to atomic structure and more: Physics 2000: http://www.colorado.edu/physics/2000/cover.html Miami museum of science: The Atom Family: http://www.miamisci.org/af/sln/ Chem4kids: http://www.chem4kids.com/ The Particle Adventure: http://particleadventure.org/ A look inside the atom (history of physics from aip.org with original recording of J. J. Thomson): http://www.aip.org/history/electron/jjhome.htm Science is Fun! (Home experiments and much more): http://www.scifun.org/ Molecule of the Month: http://www.chm.bris.ac.uk/motm/motm.htm Webelements (a really good periodic table site): http://www.webelements.com/ Merlot (multimedia educational resources): http://www.merlot.org/merlot/index.htm There are plenty more excellent educational websites. Perhaps you can try searching for a specific scientific topic. You may also want to list other websites that list educational websites. All the best, Inbal -----Original Message----- > From: owner-chemistry+inbaltu=3D=3Dopenu.ac.il+*+ccl.net [mailto:owner-chemistry+inbaltu=3D=3Dopenu.ac.il+*+ccl.net] On Behalf Of Anatoli Korkin a_korkin%x%yahoo.com Sent: Monday, September 21, 2009 7:00 PM To: Inbal Tuvi-Arad Subject: CCL: Web Tutorials for High and Middle School Students Sent to CCL by: Anatoli Korkin [a_korkin]*[yahoo.com] Dear CCLers, I will appreciate if you could point on web based tutorials in atomic scale science (physics, chemistry, biology) and related areas such as nanotechnology, which are made for high and middle school students.=20 I have started to collect some on this web page: http://asdn.net/asdn/links/nanokids.shtml Unfortunately, google search with the relevant key words are dominated by irrelevant web pages promoted with help of "smart algorithms" and "cross farm" links. Thank you for your collaboration, Anatoli Korkin korkin-/at/-nanoandgiga-/dot/-com -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Sep 22 05:34:01 2009 From: "Yun Wang wangyun22]-[yahoo.com" To: CCL Subject: CCL: surface area calculator Message-Id: <-40316-090922053158-27633-3e8g15G3o6S5s7lXwLSf9A+*+server.ccl.net> X-Original-From: Yun Wang Content-Type: multipart/alternative; boundary="0-1390094685-1253611906=:38931" Date: Tue, 22 Sep 2009 02:31:46 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Yun Wang [wangyun22#,#yahoo.com] --0-1390094685-1253611906=:38931 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear Michel,=0A=0A Thank you very much for the helpful information. =0A= =0ABest wishes,=0AYun=0A=0A=0A=0A=0A________________________________=0AFrom= : Michel Petitjean petitjean.chiral##gmail.com =0A= To: "Wang, Yun " =0ASent: Tuesday, 22 Septembe= r, 2009 4:55:33 PM=0ASubject: CCL: surface area calculator=0A=0A=0ASent to = CCL by: Michel Petitjean [petitjean.chiral(_)gmail.com]=0APlease look at:= =0Ahttp://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ASV (freew= are)=0Ahttp://petitjeanmichel.free.fr/itoweb.petitjean.spheres.html (theory= )=0AHope this helps.=0A=0AMichel Petitjean,=0ACEA/DSV/iBiTec-S/SB2SM (CNRS = URA 2096),=0A91191 Gif-sur-Yvette Cedex, France.=0APhone: +331 6908 4006 / = Fax: +331 6908 4007=0AE-mail: michel.petitjean : cea.fr, petitjean.chiral := gmail.com (preferred)=0Ahttp://petitjeanmichel.free.fr/itoweb.petitjean.ht= ml=0A=0A=0A---------- Forwarded message ----------=0A> From: Yun Wang wangy= un22{=3D}yahoo.com =0ADate: 2009/9/21=0ASubject:= CCL: surface area calculator=0ATo: "Petitjean, Michel " =0A=0A=0ADear Madam/Sir,=0A=0A Do you know whether there is a = program to calculate the surface area=0Awith 3D coordinates? Thank you for = your help.=0A=0ABest wishes.=0AYun=0A=0A=0A________________________________= =0AGet more done like never before with Yahoo!7 Mail. Learn more.=0A=0A=0A= =0A-=3D This is automatically added to each message by the mailing script = =3D-=0ATo recover the email address of the author of the message, please ch= ange=0A= =0A=0A=0AE-mail to sub= scribers: CHEMISTRY-.-ccl.net or use:=0A http://www.ccl.net/cgi-bin/ccl/= send_ccl_message=0A=0AE-mail to administrators: CHEMISTRY-REQUEST-.-ccl.net o= r use=0A=0A=0ASubscrib= e/Unsubscribe: =0A=0A=0AB= efore posting, check wait time at: http://www.ccl.net=0A=0AJob: http://www.= ccl.net/jobs =0AConferences: http://server.ccl.net/chemistry/announcements/= conferences/=0A=0ASearch Messages: http://www.ccl.net/chemistry/searchccl/i= ndex.shtml=0A=0A=0A ==0A=0ARTFI: http://www.ccl.net/chemistry= /aboutccl/instructions/=0A=0A=0A _____________________________________= _____________________________________________=0AGet more done like never be= fore with Yahoo!7 Mail.=0ALearn more: http://au.overview.mail.yahoo.com/ --0-1390094685-1253611906=:38931 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Dear Michel,

   Thank you very much for = the helpful information.

Best wishes,
Yun

<= div style=3D"font-family: arial,helvetica,sans-serif; font-size: 13px;">
From: Michel Petitjean petitjean.chiral##gmail.com <o= wner-chemistry-.-ccl.net>
To: "Wang, Yun " <wangyun22-.-yahoo.com>
Sent: Tuesday, 22 September, 2009 4:55:3= 3 PM
Subject: CCL: surf= ace area calculator


Sent to CCL by: Michel Petitjean [petitjean.chiral(_)gmail.com]
Please look at:
= http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ASV (free= ware)
http://petitjeanmichel.free.fr/itoweb.petitjean.sp= heres.html (theory)
Hope this helps.

Michel Petitjean,
CEA= /DSV/iBiTec-S/SB2SM (CNRS URA 2096),
91191 Gif-sur-Yvette Cedex, France.=
Phone: +331 6908 4006 / Fax: +331 6908 4007
E-mail: michel.petitjean= : cea.fr, petitjean.chiral : gmail.com (preferred)
http://petit= jeanmichel.free.fr/itoweb.petitjean.html


---------- Forwarde= d message ----------
> From: Yun Wang wangyun22{=3D}yahoo.com <own= er-chemistry : ccl.net>
Date: 2009/9/21
Subject: CCL: surface area calculator
To: "Petitjean, Michel " <petitjean.chiral : gmail.com>= ;


Dear Madam/Sir,

  Do you know whether there is a p= rogram to calculate the surface area
with 3D coordinates? Thank you for = your help.

Best wishes.
Yun


__________________________= ______
Get more done like never before with Yahoo!7 Mail. Learn more.


-=3D This is automatically added to each message by the mailin= g script =3D-
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=0A=0A= =0A=0A
=0AGet more done like never before with Yahoo!7 Ma= il. Learn more. --0-1390094685-1253611906=:38931-- From owner-chemistry@ccl.net Tue Sep 22 08:15:01 2009 From: "Didier Rognan didier.rognan||pharma.u-strasbg.fr" To: CCL Subject: CCL: sc-PDB 2009 release Message-Id: <-40317-090922071533-30699-PkAWw4B4jCRhVRzVEDNddQ*server.ccl.net> X-Original-From: Didier Rognan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 22 Sep 2009 12:31:51 +0200 MIME-Version: 1.0 Sent to CCL by: Didier Rognan [didier.rognan..*..pharma.u-strasbg.fr] Dear CCLers We are happy to announce the last release of the sc-PDB database (http://bioinfo-pharma.u-strasbg.fr/scPDB) archiving 7079 druggable protein-ligand binding sites. The database stores chemical, biological and structural data on 2378 unique proteins and 3688 unique ligands from the Protein Data Bank. The database can be queried from different viewpoints (Ligand, Protein, Binding mode) and structural data can be downloaded in standard structural file formats. In addition to the last PDB entries which are now registered, all binding sites of all proteins have been clustered and aligned by our in-house 3-D alignment tool. Dendograms of binding sites and pre-aligned PDB entries can now be visualized and downloaded. Hope you will have fun with the sc-PDB Kind regards -- From owner-chemistry@ccl.net Tue Sep 22 08:50:01 2009 From: "Close, David M. CLOSED^-^mail.etsu.edu" To: CCL Subject: CCL: Frequency Calculations at MP2(full)/6-311+G(2df,2pd) Message-Id: <-40318-090922081412-19952-bFQrZCGGMdMn51hbM5GiaQ#,#server.ccl.net> X-Original-From: "Close, David M." Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01CA3B7E.29366D12" Date: Tue, 22 Sep 2009 08:13:56 -0400 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_01CA3B7E.29366D12 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Arindam: You can find the disk space requirements in the output. A few pages down from the top there will be a print out saying SCF done. Next there is S**2=3D. A few lines below this it says Estimated scratch disk usage ************** words. These are 8 bit words. Regards, Dave. =20 > From: owner-chemistry+closed=3D=3Detsu.edu-,-ccl.net [mailto:owner-chemistry+closed=3D=3Detsu.edu-,-ccl.net] On Behalf Of = Arindam Ganguly arindamganguly###gmail.com Sent: Monday, September 21, 2009 6:17 PM To: Close, David M. Subject: CCL: Frequency Calculations at MP2(full)/6-311+G(2df,2pd) =20 Respected Dr. Close, Thank you very much for the prompt response. Yes, i have indeed reached this limit. By the way, if i can get access to a cluster, then how much more memory is required in order to finish this job? Sincerely, arindam On Mon, Sep 21, 2009 at 12:03 PM, Close, David M. CLOSED,mail.etsu.edu > wrote: Sent to CCL by: "Close, David M." [CLOSED]![mail.etsu.edu] Arindam: You have done all that is possible with a 32 bit machine. But did you look at the size of the scratch files you have set aside for the rwf's? Are there actually 8 files that are completely full? If so then you have reached the limit of a 32 bit machine. 2^^32 is 16 gbytes. That's all the addresses a 32 bit machine can write. If you have indeed exceeded this limit there is not much you can with the code you are using. Regards, Dave Close. -----Original Message----- > From: owner-chemistry+closed=3D=3Detsu.edu()ccl.net [mailto:owner-chemistry+closed =3D=3Detsu.edu()ccl.net] On Behalf Of Arindam Ganguly arindamganguly**gmail.com Sent: Monday, September 21, 2009 11:55 AM To: Close, David M. Subject: CCL: Frequency Calculations at MP2(full)/6-311+G(2df,2pd) Sent to CCL by: "Arindam Ganguly" [arindamganguly++gmail.com] Dear CCL users, I am trying to perform a frequency calculation on 14 atom molecule using the 6-311+G(2df,2pd) basis set. When I use the B3LYP method, the calculation finishes with its intended output. However, using the MP2(full) method the calculation keeps crashing asking for more memory. I am working on a 32bit Winxp system. This is how my input file looks like ------------------------------------------------------------------------ -------------------------------------------------------------- %mem=3D500MB %rwf=3Dc:\scratch\gxx,1970MB,c:\scr1\gxx,1970MB,c:\scr2\gxx,1970MB,c:\scr= 3 \gxx,1970MB,c:\scr4\gxx,1970MB,c:\scr5\gxx,1970MB,c:\scr6\gxx,1970MB,c:\ scr7\gxx,1970MB #p MP2=3DFull/6-311+G(2df,2pd) scf=3Ddirect opt=3Dz-matrix freq=3D(restart,raman) Any suggestions would be really helpful. Thank you all in advance. Sincerely, arindam -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=http://www.ccl.net/spammers.txt - This is automatically added to each message by the mailing script -
or use:E-mail to administrators: CHEMISTRY-REQUEST{=3Dcl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtml = http://www.linkedin.com/in/arindamganguly ------_=_NextPart_001_01CA3B7E.29366D12 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Arindam:

  You can find the disk space requirements in the = output.  A few pages down from the top there will be a print out saying SCF done.  = Next there is S**2=3D.  A few lines below this it says

Estimated scratch disk usage   = **************  words.  These are 8 bit words.

Regards, Dave.

 

From:= = owner-chemistry+closed=3D=3Detsu.edu-,-ccl.net [mailto:owner-chemistry+closed=3D=3Detsu.edu-,-ccl.net] On Behalf Of = Arindam Ganguly arindamganguly###gmail.com
Sent: Monday, September 21, 2009 6:17 PM
To: Close, David M.
Subject: CCL: Frequency Calculations at = MP2(full)/6-311+G(2df,2pd)

 

Respected Dr. = Close,
Thank you very much for the prompt response. Yes, i have indeed reached = this limit. By the way, if i can get access to a cluster, then how much more = memory is required in order to finish this job?
Sincerely,
arindam

On Mon, Sep 21, 2009 at 12:03 PM, Close, David M. = CLOSED,mail.etsu.edu <owner-chemistry{=3Dcl.net= > wrote:


Sent to CCL by: "Close, David M." [CLOSED]![mail.etsu.edu]
Arindam:
 You have done all that is possible with a 32 bit machine. =  But did you
look at the size of the scratch files you have set aside for the = rwf's?
Are there actually 8 files that are completely full?  If so then = you
have reached the limit of a 32 bit machine.  2^^32 is 16 gbytes.  That's
all the addresses a 32 bit machine can write.  If you have = indeed
exceeded this limit there is not much you can with the code you are
using.
 Regards, Dave Close.



-----Original Message-----
> From: owner-chemistry+closed=3D=3Detsu.edu()ccl.net
[mailto:owner-chemistry+closed=3D=3D= etsu.edu()ccl.net] On Behalf Of Arindam
Ganguly arindamganguly**gmail.com

Sent: Monday, = September 21, 2009 11:55 AM
To: Close, David M.
Subject: CCL: Frequency Calculations at MP2(full)/6-311+G(2df,2pd)


Sent to CCL by: "Arindam  Ganguly" [arindamganguly++gmail.com]
Dear CCL users,
I am trying to perform a frequency calculation on 14 atom molecule = using
the 6-311+G(2df,2pd) basis set. When I use the B3LYP method, the
calculation finishes with its intended output. However, using the
MP2(full) method the calculation keeps crashing asking for more = memory.
I am working on a 32bit Winxp system.
 This is how my input file looks like
------------------------------------------------------------------------<= br> --------------------------------------------------------------
%mem=3D500MB
%rwf=3Dc:\scratch\gxx,1970MB,c:\scr1\gxx,1970MB,c:\scr2\gxx,1970MB,c:\scr= 3
\gxx,1970MB,c:\scr4\gxx,1970MB,c:\scr5\gxx,1970MB,c:\scr6\gxx,1970MB,c:\<= br> scr7\gxx,1970MB
#p MP2=3DFull/6-311+G(2df,2pd) scf=3Ddirect  opt=3Dz-matrix
freq=3D(restart,raman)


Any suggestions would be really helpful. Thank you all in advance.

Sincerely,
arindam


-=3D This is automatically added to each message by = the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscrib= e/Unsubscribe: Job: http://www.ccl.net/jobs http://www.ccl.net/spammers.txt



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     http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/=




--
Arindam Ganguly
Graduate Student
VP(Chemistry Graduate Student Association-CGSA)
Dept. of Chemistry, UMKC
Phone:-816-419-1806
Email:- ArindamGanguly{=3Dmail.com
http://www.linkedin.co= m/in/arindamganguly

------_=_NextPart_001_01CA3B7E.29366D12-- From owner-chemistry@ccl.net Tue Sep 22 09:49:01 2009 From: "Yangsoo Kim vsmember()gmail.com" To: CCL Subject: CCL:G: Software for Intermolecular Forces Calculation Message-Id: <-40319-090922094425-9890-cISwCrpdtj1+sFWQsg6kXg(0)server.ccl.net> X-Original-From: "Yangsoo Kim" Content-Type: multipart/alternative; boundary="----=_NextPart_000_004A_01CA3BD5.119216A0" Date: Tue, 22 Sep 2009 22:36:00 +0900 MIME-Version: 1.0 Sent to CCL by: "Yangsoo Kim" [vsmember ~~ gmail.com] This is a multi-part message in MIME format. ------=_NextPart_000_004A_01CA3BD5.119216A0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear All, I'm wondering if anyone of you knows any software (commercial or free) that can calculate the values related to intermolecular forces (many body interactions) such as van der Waals forces, dipole-dipole interactions, and hydrogen bonding for a pure compound, under the conditions that only the 3D-structure of the single molecule is available, which is determined from quantum optimization calculations by GAMESS or Gaussian. Any suggestion or advice is greatly appreciated. Many thanks in advance, Yangsoo Kim ------=_NextPart_000_004A_01CA3BD5.119216A0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear = All,

 

I’m = wondering if anyone of you knows any software (commercial or free) that can calculate = the values related to intermolecular forces (many body interactions) such as = van der Waals forces, dipole-dipole interactions, and hydrogen bonding for a = pure compound, under the conditions that only the 3D-structure of the single molecule = is available, which is determined from quantum optimization calculations by = GAMESS or Gaussian.

 

Any suggestion = or advice is greatly appreciated.

 

Many thanks in = advance,

 

Yangsoo = Kim

 

 

------=_NextPart_000_004A_01CA3BD5.119216A0-- From owner-chemistry@ccl.net Tue Sep 22 10:22:01 2009 From: "Morad El-Hendawy M80elhendawy(!)yahoo.com" To: CCL Subject: CCL:G: Gaussian 03/09 + Material Studio + PDOS Message-Id: <-40320-090922095623-16358-BRink3/013M4xDPeIkHXUg]=[server.ccl.net> X-Original-From: "Morad El-Hendawy" Date: Tue, 22 Sep 2009 09:56:20 -0400 Sent to CCL by: "Morad El-Hendawy" [M80elhendawy*|*yahoo.com] Hello CCLers, I have two questions regarding Material studio: 1- Is Material studio able to read Gaussian 03/09 output file (*.out)? 2- Is Material studio able to calculate PDOS (Projected density of state) for molecular groups as well as individual atoms? My best regards, Morad El-Hendawy, IRELAND From owner-chemistry@ccl.net Tue Sep 22 10:57:01 2009 From: "donna-,-dbkonline.com" To: CCL Subject: CCL: MACCS Message-Id: <-40321-090922100537-20344-EtCAPjz+f9WC7hfUeBdJ7w++server.ccl.net> X-Original-From: donna()dbkonline.com Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Tue, 22 Sep 2009 08:05:25 -0500 MIME-Version: 1.0 Sent to CCL by: donna\a/dbkonline.com > From: donna .. dbkonline.com To: CCL Subscribers Subject: Middle Altantic Computational Chemists MIME-Version: 1.0 Content-Type: text/plain; =09charset=3DISO-8859-1; =09DelSp=3D"Yes"; =09format=3D"flowed" Content-Disposition: inline Content-Transfer-Encoding: quoted-printable User-Agent: Internet Messaging Program (IMP) H3 (4.1.6) X-AntiAbuse: This header was added to track abuse, please include it =20 with any abuse report X-AntiAbuse: Primary Hostname - eos.websitewelcome.com X-AntiAbuse: Original Domain - ccl.net X-AntiAbuse: Originator/Caller UID/GID - [47 12] / [47 12] X-AntiAbuse: Sender Address Domain - dbkonline.com I don't know how many of you are in the NJ/NY/PA area - but there will =3D20 be a meeting of the Middle Altantic Computational Chemists group =3D20 hosted by the Trenton American Chemical SOciety - in October. Info below - also a link to join our LinkedIn Group Donna DBK Web Development, lLC http://www.DBKWebDevelopment.com web development, custom programming, custom solutions =3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D= =3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D =3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D= =3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D =3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D=3D3D Dear Members, Fall is in the air and we have an exciting talk ?Going from Big to Small: What happens when you leave big Pharma?? scheduled for the Tuesday, Oct 13, 2009, 6.00 PM at the Rider University, 2083 Lawrenceville Road, Lawrenceville, NJ 08648. The talk is going to be presented by Ralph T. Mosley, Head, Computational Chemistry, Pharmasset, Inc., Princeton NJ. This is a timely topic in this era of mergers and acquisition and everybody should be able to gain something out of the talk. Please see below for the details. We would also like to invite you to join our MidAtlantic Computational Chemists (MACC) group on LinkedIn. Below is the link. If you have already joined the group then thank you, if not please join the group at your earliest convenience. http://www.linkedin.com/groups?gid=3D3D2310941&goback=3D3D.anb_2310941_*2 Please feel free to forward this to your colleagues and co-workers who might be interested but are not on our list. We look forward seeing you at the meeting! Sincerely, MACC Organizers Please see also: http://www.TrentonACS.org *Title* Going from Big to Small: What happens when you leave big Pharma? *Speaker* Ralph T. Mosley, PhD Head, Computational Chemistry, Pharmasset, Inc., Princeton NJ *Abstract* Whether the result of ?cost savings initiatives? or career development decisions, movement of personnel within the pharmaceutical industry seems to be increasing. One side effect is that ?best practices? in knowledge management are migrating or being re-defined as a consequence of the new reality and the new job description in which the practitioner finds him/her-self. The goal of this presentation will be to focus on the transition one may make in going from a large, multi-national pharmaceutical company to a much smaller pharmaceutical company. To be clear: even though there is a difference in size, each of these companies is dedicated to discovering and developing disease therapies and has the same need to turn data into knowledge to help achieve those goals. Even so, there will be disparities between the amount of data available (and subsequently archived), human and financial resources that can be used to tackle the problem, and the speed with which those can be brought to bear. Relative to the number of targets each company may focus upon, these differences may actually not be so large at the end of the day. Having been a molecular modeler for almost two decades at one of the top ten pharmaceutical companies with nearly sixty thousand employees and for the past two years heading up computational chemistry at a company of about sixty, I have been making that transition between big and small Pharma. During the course of this presentation, I will reflect on what impact that thousand fold difference in headcount has by trying to answer these questions: What are the similarities between these two companies in terms of data and knowledge management? What are the differences between them? How does one know what should be brought forward and what gets left behind? How does all of this impact one?s career? Also, some of the decision making process with regard to data and tools to access it that had preceded my arrival at Pharmasset will be touched upon. And finally, our ongoing effort to turn data into knowledge to help discover and develop new antiviral therapies at Pharmasset will be described. *Time and Location* Tuesday, October 13 at 6.00 PM Fireside Lounge - The Bart Luedeke Center (Student Center) Follow the building number 39 on the map, http://www.rider.edu/files/map-lville-full.pdf Rider University 2083 Lawrenceville Road Lawrenceville, NJ 08648-3001 Directions: http://www.rider.edu/139_1306.htm#car *Reservations* Dinner is at 6:00 pm. Lecture immediately following dinner. The lecture is free and open to the public. Reservations are required for dinner and usually must be made by Noon the Day Before the meeting. Early Reservations Appreciated! Exceptions will be noted in the meeting notice. Cancellation deadline is also Noon the Day Before. Contact Prof. Bruce at bburnham .. rider.edu (phone: 609-896-5207) or contact Bill McCarroll at mccarroll .. rider.edu Pizza Dinner - $5.00 payable at the meeting. Please note that no shows will be billed for dinner so please cancel reservations if you cannot attend. *About Ralph T. Mosley* Ralph T. Mosley knew in grade school that he wanted to be a chemist. After receiving a B.S. in chemistry from the University of Missouri-Columbia and an M.S. in organic chemistry from Purdue University-West Lafayette, IN, he joined Merck & Co, Inc., Rahway, NJ, in 1989. As a project scientist in Molecular Systems, Ralph provided computational chemistry input for discovery programs focused on a variety of targets including enzymes (HIV1P, HDAC, FAAH), G-protein coupled receptors (SSTR?s, GnRHR, MCHR), and nuclear hormone receptors (PPAR?s, ER?s, ERR?s), among others. His skills in lead identification, pharmacophore generation, homology modeling and =3D20 structure-based drug design were critical to the advancement of these medicinal chemistry programs. More recently, Ralph has drawn on his interest in 2D/3D pharmacophoric approaches to design and help develop the synthon analysis tool used in combinatorial library design and the visual property analysis tool used to triage HTS results.In late 2007, Ralph joined the team of scientists working at Pharmasset, Inc., to direct the computational chemistry group. There, he is leveraging his skills in molecular modeling and chemoinformatics to help Pharmasset discover and develop oral therapeutics to treat viral infections. Ralph is a co-inventor on five patents and co-author on more than fifty publications. ----- End forwarded message ----- From owner-chemistry@ccl.net Tue Sep 22 11:32:01 2009 From: "ilke ugur ilke_ugur-#-yahoo.com" To: CCL Subject: CCL: atomicfluct Message-Id: <-40322-090922103057-4621-+cTVjn++Y9EWoRNvyJjFpw!A!server.ccl.net> X-Original-From: ilke ugur Content-Type: multipart/alternative; boundary="0-1560093653-1253626244=:20970" Date: Tue, 22 Sep 2009 06:30:44 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: ilke ugur [ilke_ugur:+:yahoo.com] --0-1560093653-1253626244=:20970 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear All, =A0 Do you know how to calculate the atomicfluct by residue with ptraj by using= the first structure as a reference. (not calculating by using an average p= db) =A0 Thank you very much, =A0 Ilke Ugur=0A=0A__________________________________________________=0ADo You = Yahoo!?=0ATired of spam? Yahoo! Mail has the best spam protection around = =0Ahttp://mail.yahoo.com --0-1560093653-1253626244=:20970 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear All,
 
Do you know how to calculate the atomicfluct by residue with ptraj by = using the first structure as a reference. (not calculating by using = an average pdb)
 
Thank you very much,
 
Ilke Ugur

_________________________________= _________________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the = best spam protection around
http://mail.yahoo.com --0-1560093653-1253626244=:20970-- From owner-chemistry@ccl.net Tue Sep 22 12:07:01 2009 From: "Bahareh honarparvar bahareh_honarparvar]~[yahoo.com" To: CCL Subject: CCL: problem with PDB content Message-Id: <-40323-090922112227-15431-LE9VlaKwUYUrgKq2h2tAXg-,-server.ccl.net> X-Original-From: Bahareh honarparvar Content-Type: multipart/alternative; boundary="0-1035039673-1253632932=:36824" Date: Tue, 22 Sep 2009 08:22:12 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Bahareh honarparvar [bahareh_honarparvar,yahoo.com] --0-1035039673-1253632932=:36824 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear all, I am a chemist who is intersted in working with protein's structures but I = am not familiar with protein content (PDB). For instance in papers I saw th= at the resiadue 206 is TYR but in PDB=A0 there is no 206 for TYR=A0 or I sa= w Glu67 (in paper) but in PDB the residue for 67 is ARG 67. any comment and= help is appriciated. Regards Honarparvar =0A=0A=0A --0-1035039673-1253632932=:36824 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear all,
I am a chemist who is intersted = in working with protein's structures but I am not familiar with protein con= tent (PDB). For instance in papers I saw that the resiadue 206 is TYR but i= n PDB  there is no 206 for TYR  or I saw Glu67 (in paper) but in = PDB the residue for 67 is ARG 67. any comment and help is appriciated.
R= egards
Honarparvar

=0A=0A --0-1035039673-1253632932=:36824-- From owner-chemistry@ccl.net Tue Sep 22 13:37:00 2009 From: "Rajagopala Reddy Seelam rajagopalaseelam..gmail.com" To: CCL Subject: CCL: splitting of c6v geometry to lower symetry in JT distortions reg Message-Id: <-40324-090922133109-1810-7ldbAYvcmsK+aRKauHrZAA!A!server.ccl.net> X-Original-From: "Rajagopala Reddy Seelam" Date: Tue, 22 Sep 2009 13:31:05 -0400 Sent to CCL by: "Rajagopala Reddy Seelam" [rajagopalaseelam(a)gmail.com] Dear all, We knew that the Jahn -Teller Theorem causes splitting of highly symmetric open shell molecule to lower symmetry to attain stability.I have a molecule with C6V geometry which is prone to JT effect.Now this has two modes (E1 and E2 ) which can split c6v to lower symmetry.Is there is a way to know which symmetry does the distorted geometry belongs to. Thank you, S.Rajagopala Reddy Prof.Mahapatra lab School of Chemistry University of Hyderabad From owner-chemistry@ccl.net Tue Sep 22 14:59:00 2009 From: "Mahmoud A. A. Ibrahim m.ibrahim1982=yahoo.com" To: CCL Subject: CCL: problem with PDB content Message-Id: <-40325-090922145841-3164-tQhlV0G4U8YjCAzABbsooA%x%server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary="0-14653582-1253645886=:95236" Date: Tue, 22 Sep 2009 11:58:06 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim1982,,yahoo.com] --0-14653582-1253645886=:95236 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Honarparvar I don't know what the exact answer for your enquiry, because you didn't giv= e us enough information about your problem. But, I would like to pay your a= ttention to one important hint you may miss. There are two residue numberin= g system, one is the PDB residue number, and the another one is the sequent= ial numbering system, They are different, becuase there are always some res= idues missing. I hope this hint be helpful. Sincerely; M.Ibrahim Mahmoud A. A. Ibrahim Current Address School of Chemistry, University of Manchester,=20 Oxford Road, Manchester, M13 9PL, United Kingdom. Mahmoud.Ibrahim-2() postgrad.manchester.ac.uk=20 =20 Home Address =20 Chemistry Department, Faculty of Science,=20 Minia University,=20 Minia 61519,Egypt.=20 M.Ibrahim1982() yahoo.com=20 Mobile Phone No.: +20102554083 =20 Land Phone No.: +20226635916=20 Fax No.: +20862342601 --- On Tue, 9/22/09, Bahareh honarparvar bahareh_honarparvar]~[yahoo.com wrote: > From: Bahareh honarparvar bahareh_honarparvar]~[yahoo.com Subject: CCL: problem with PDB content To: "Ibrahim, Mahmoud A. A. " Date: Tuesday, September 22, 2009, 4:22 PM Dear all, I am a chemist who is intersted in working with protein's structures but I = am not familiar with protein content (PDB). For instance in papers I saw th= at the resiadue 206 is TYR but in PDB=A0 there is no 206 for TYR=A0 or I sa= w Glu67 (in paper) but in PDB the residue for 67 is ARG 67. any comment and= help is appriciated. Regards Honarparvar =0A=0A =0A=0A=0A --0-14653582-1253645886=:95236 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
=0A=0A=0A=0A --0-14653582-1253645886=:95236-- From owner-chemistry@ccl.net Tue Sep 22 15:53:00 2009 From: "Isaac B Bersuker bersuker*cm.utexas.edu" To: CCL Subject: CCL: splitting of c6v geometry to lower symetry in JT distortions reg Message-Id: <-40326-090922143754-31569-bGPL7hcygXq72fXhx+mVww__server.ccl.net> X-Original-From: Isaac B Bersuker Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8 Date: Tue, 22 Sep 2009 18:37:35 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: Isaac B Bersuker [bersuker_+_cm.utexas.edu] Dear S.Rajagopala Reddy, You have a simple (in the sense of traditional) two-mode JT problem; see any recent book on the JTE and find out how to reduce the two-mode problem to the ideal, one-mode one. There are a number of publications on this subject. Regards Dr. Isaac B. Bersuker Institute for Theoretical Chemistry The University of Texas at Austin Chem & Biochem Department 1 University Station A5300 Austin, TX 78712-0165 Phone: (512) 471-4671; Fax: (512) 471-8696 E-mail: bersuker\a/cm.utexas.edu http://www.cm.utexas.edu/isaac_bersuker ----- Original Message ----- > From: "Rajagopala Reddy Seelam rajagopalaseelam..gmail.com" To: "Isaac B. Bersuker" Sent: Tuesday, September 22, 2009 12:31:05 PM GMT -06:00 US/Canada Central Subject: CCL: splitting of c6v geometry to lower symetry in JT distortions reg Sent to CCL by: "Rajagopala Reddy Seelam" [rajagopalaseelam(a)gmail.com] Dear all, We knew that the Jahn -Teller Theorem causes splitting of highly symmetric open shell molecule to lower symmetry to attain stability.I have a molecule with C6V geometry which is prone to JT effect.Now this has two modes (E1 and E2 ) which can split c6v to lower symmetry.Is there is a way to know which symmetry does the distorted geometry belongs to. Thank you, S.Rajagopala Reddy Prof.Mahapatra lab School of Chemistry University of Hyderabadhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Sep 22 16:29:00 2009 From: "giorgio saladino g.saladino^_^fastwebnet.it" To: CCL Subject: CCL: problem with PDB content Message-Id: <-40327-090922141010-18620-uwJjxEtvE2mKvXIJ7Xrolw|a|server.ccl.net> X-Original-From: giorgio saladino Content-Type: multipart/alternative; boundary="=-t0qrG0j4dWA3D5ECFA54" Date: Tue, 22 Sep 2009 19:26:22 +0200 Mime-Version: 1.0 Sent to CCL by: giorgio saladino [g.saladino|*|fastwebnet.it] --=-t0qrG0j4dWA3D5ECFA54 Content-Type: text/plain Content-Transfer-Encoding: 7bit Honarparvar: PDB structures are obtained by X-ray diffraction and typically some residues in loop regions (or C-/N-terminal) are missing. You should check the beginning of the PDB file where informations are reported to control if any residue is missing. Hoping this will help, regard Giorgio S. On Tue, 2009-09-22 at 08:22 -0700, Bahareh honarparvar bahareh_honarparvar]~[yahoo.com wrote: > Dear all, > I am a chemist who is intersted in working with protein's structures > but I am not familiar with protein content (PDB). For instance in > papers I saw that the resiadue 206 is TYR but in PDB there is no 206 > for TYR or I saw Glu67 (in paper) but in PDB the residue for 67 is > ARG 67. any comment and help is appriciated. > Regards > Honarparvar > > --=-t0qrG0j4dWA3D5ECFA54 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: 7bit Honarparvar:
PDB structures are obtained by X-ray diffraction and typically some residues in loop regions (or C-/N-terminal) are missing. You should check the beginning of
the PDB file where informations are reported to control if any residue is missing.
Hoping this will help,
regard

Giorgio S.

On Tue, 2009-09-22 at 08:22 -0700, Bahareh honarparvar bahareh_honarparvar]~[yahoo.com wrote:
Dear Honarparvar
I don't know what the exa= ct answer for your enquiry, because you didn't give us enough information a= bout your problem. But, I would like to pay your attention to one important= hint you may miss. There are two residue numbering system, one is the PDB = residue number, and the another one is the sequential numbering system, The= y are different, becuase there are always some residues missin= g.
I hope this hint be helpful.
Sincerely;
M.Ibrahim
Mahmoud A. A. Ibrahim

Current Address
School of Chemistry, University of Manchester,
Oxfo= rd Road, Manchester, M13 9PL, United Kingdom.
Mahmoud.Ibrahim-2() postgrad.manches= ter.ac.uk

Home Address
Land Phone No.: +20226635916
Fax N= o.: +20862342601


--- On Tue, 9/22/09, Bahareh honarpa= rvar bahareh_honarparvar]~[yahoo.com <owner-chemistry() ccl.net>= wrote:

From: Bahareh honarparvar bahar= eh_honarparvar]~[yahoo.com <owner-chemistry() ccl.net>
Subject: CCL: problem with PDB content
To: "Ibrahim, Mahmoud A. A. " <m.ib= rahim1982() yahoo.com>
Date: Tuesday, September 22, 2009, 4:22 PM
Dear all,
I am a chemist who is intersted in working with protein's s= tructures but I am not familiar with protein content (PDB). For instance in= papers I saw that the resiadue 206 is TYR but in PDB  there is no 206= for TYR  or I saw Glu67 (in paper) but in PDB the residue for 67 is A= RG 67. any comment and help is appriciated.
Regards
Honarparvar

=0A=0A
Dear all,
I am a chemist who is intersted in working with protein's structures but I am not familiar with protein content (PDB). For instance in papers I saw that the resiadue 206 is TYR but in PDB  there is no 206 for TYR  or I saw Glu67 (in paper) but in PDB the residue for 67 is ARG 67. any comment and help is appriciated.
Regards
Honarparvar

--=-t0qrG0j4dWA3D5ECFA54-- From owner-chemistry@ccl.net Tue Sep 22 17:02:00 2009 From: "Francisco Hernandez-Guzman fhernand(~)accelrys.com" To: CCL Subject: CCL: problem with PDB content Message-Id: <-40328-090922153401-21442-NBZxECVtJgh6eQ7h2GwBpQ]=[server.ccl.net> X-Original-From: Francisco Hernandez-Guzman Content-Language: en-US Content-Type: multipart/related; boundary="_008_E05DB3B9FDB9D846B6C9E1875CD41A332EB7FA72exch1hiaccelrys_"; type="multipart/alternative" Date: Tue, 22 Sep 2009 14:33:39 -0400 MIME-Version: 1.0 Sent to CCL by: Francisco Hernandez-Guzman [fhernand.:.accelrys.com] --_008_E05DB3B9FDB9D846B6C9E1875CD41A332EB7FA72exch1hiaccelrys_ Content-Type: multipart/alternative; boundary="_000_E05DB3B9FDB9D846B6C9E1875CD41A332EB7FA72exch1hiaccelrys_" --_000_E05DB3B9FDB9D846B6C9E1875CD41A332EB7FA72exch1hiaccelrys_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Dear Honarpavar, Protein structures are models which are carefully crafted to match experime= ntal data provided by the X-ray diffraction experiment of protein crystals.= Sometimes the data is not complete, such is the case of missing side-chain= s or loops. In other cases the observed data (specially at high resolution)= may indicate a different identity for a particular residue than the known = identity determined by sequencing. There has been cases that a re-sequenci= ng effort corrects the identity of the residue in question. If a residue do= es not match what the published sequence is, in some lucky cases the experi= mental data may be available and you may be able to see what the experiment= alist saw when the initial interpretation of the data was made. So in all, structures deposited in structural databases like the PDB, are r= epresentations of experimental data. You should always be cautious of using= such and perform a proper assessment of what is important to your scientif= ic interest. I hope this helps. Francisco [cid:image001.gif]_[01CA3B78.86717FE0] [cid:image002.gif]_[01CA3B78.86717FE0] Francisco G. Hernandez-Guzman, Ph.D. Lead Solutions Scientist Accelrys, Inc. 10188 Telesis Court, Suite 100 San Diego, CA 92121, USA Ph: +1 858 799 5606 Cell: +1 858 361 3020 Fax: +1 858 799 5100 [cid:image003.gif]_[01CA3B78.86717FE0] [cid:im= age004.gif]_[01CA3B78.86717FE0] [cid:image005.gif]_[01CA3B78.86717FE0] Stay Connected with Accelrys and the Scientific & Engineering Community Blog | Forum | Web= site | Support > From: owner-chemistry+fhernandez=3D=3Daccelrys.com]_[ccl.net [mailto:owner-ch= emistry+fhernandez=3D=3Daccelrys.com]_[ccl.net] On Behalf Of Bahareh honarpar= var bahareh_honarparvar]~[yahoo.com Sent: Tuesday, September 22, 2009 8:22 AM To: Francisco Hernandez-Guzman Subject: CCL: problem with PDB content Dear all, I am a chemist who is intersted in working with protein's structures but I = am not familiar with protein content (PDB). For instance in papers I saw th= at the resiadue 206 is TYR but in PDB there is no 206 for TYR or I saw Gl= u67 (in paper) but in PDB the residue for 67 is ARG 67. any comment and hel= p is appriciated. Regards Honarparvar --_000_E05DB3B9FDB9D846B6C9E1875CD41A332EB7FA72exch1hiaccelrys_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear Honarpavar,

 

Protein structures are models which are carefully crafted to match experimental data provided by the X-ray diffraction experiment of pro= tein crystals. Sometimes the data is not complete, such is the case of missing side-chains or loops. In other cases the observed data (specially at high resolution) may indicate a different identity for a particular residue than= the known identity determined by sequencing.  There has been cases that a re-sequencing effort corrects the identity of the residue in question. If a residue does not match what the published sequence is, in some lucky cases = the experimental data may be available and you may be able to see what the experimentalist saw when the initial interpretation of the data was made.

 

So in all, structures deposited in structural databases like= the PDB, are representations of experimental data. You should always be cautiou= s of using such and perform a proper assessment of what is important to your scientific interest.

 

I hope this helps.

 

Francisco

 

 

3Dsig-accl-lo=

3Dsig-accl-e=

 =

Francisco G. Hernandez-Guzman, Ph.D.
Lead Solutions Scientist

Accelrys, Inc.
10188 Telesis Court, Suite 100
San Diego, CA 92121, USA
Ph:   +1 858 799 5606
Cell: +1 858 361 3020
Fax:  +1 858 799 5100

3Dtwitter   3D"Linked<= span style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497= D'>  

Stay Connected with Accelrys and the
Scientific & Engineering Community

Blog   | &nb= sp; Forum<= /a>   |   Website   | &nb= sp; Support

 

 

 

 

From: owner-chemistry+fhernandez=3D=3Daccelrys.com]_[ccl.net [mailto:owner-chemistry+fhernandez=3D=3Daccelrys.com]_[ccl.net] On Behalf = Of Bahareh honarparvar bahareh_honarparvar]~[yahoo.com
Sent: Tuesday, September 22, 2009 8:22 AM
To: Francisco Hernandez-Guzman
Subject: CCL: problem with PDB content

 

Dear all,
I am a chemist who is intersted in working with protein's structures but = I am not familiar with protein content (PDB). For instance in papers I saw tha= t the resiadue 206 is TYR but in PDB  there is no 206 for TYR  or= I saw Glu67 (in paper) but in PDB the residue for 67 is ARG 67. any comment= and help is appriciated.
Regards
Honarparvar

 

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filename="image005.gif"; size=547; creation-date="Tue, 22 Sep 2009 14:33:40 GMT"; modification-date="Tue, 22 Sep 2009 14:33:40 GMT" Content-ID: Content-Transfer-Encoding: base64 R0lGODlhFAAUANUAAJPC/qPL/////3qt7Gmc3Ex+vDhrq7TU/0J0tGGU063R/+ny/8Db/+Dt/9jp /1qNzFGEw+Xw//X5/8vh/vH3/1aJySpdnYK08u30/3Sn57vZ/y5hoH6x8U6BwXWo6B1QkHCh3tTn //j7/3Kl5TFkpBlMjD5wsCFUlEV4uBRHhyZZmRdKinCj4/v8/zZpqY/A/97s/9bo//39/9zr/4i7 +32v7meY1WWY2Gqb2Hiq6Xeo5S1gn5fE/3Kk4oe49WCS0SH5BAAAAAAALAAAAAAUABQAAAb/wAlh QywajyRdBKT6OJ/Q6MdyMaiuKhLNEVksYAETVmUpIIq/buCB6tRCFE6RBCkYDATKAXHvGy4CPHcm DxAIFRgHHQUVdRAPCA0CAhkIKD8PHQwCLQs5ABIyEgoFFJMYHRA4CQQRLQIRFRUHAjIPFTyTFAMP IDgvMAqTGQkjkwEJCSIiGgE3OiAKMxmTCgQEGAIL1xEzPBoEAwMHDSwLAhgsIxKTAywYAQEMGRc2 AQscwgIcATOvCgMoeJigwUOOHSgi0KAm4MAEHjMENFAAA1sOEggspDgQwsUEdA5uvODUIEONCB9W mNDoIgKADtVSlGC3wASFBClUakzxIEIAQHYFUqQY2WDBC6E6haaoEFFABRMoRkrIoTSpUgsDJsQI 4SAGABdKc5rocaKE2bNo05Y44SNCjQJw48qdWwCAgCAAOw== --_008_E05DB3B9FDB9D846B6C9E1875CD41A332EB7FA72exch1hiaccelrys_-- From owner-chemistry@ccl.net Tue Sep 22 17:44:01 2009 From: "Walter Ca on wcanon|,|ciq.uchile.cl" To: CCL Subject: CCL:G: Maximum Number of processors to run in parallel gaussian03 Message-Id: <-40329-090922170334-17295-KHIFoPfBwp2c13Y7XL4TnA(!)server.ccl.net> X-Original-From: "Walter Ca on" Date: Tue, 22 Sep 2009 17:03:30 -0400 Sent to CCL by: "Walter Ca on" [wcanon]-[ciq.uchile.cl] Dear CCL Subscribers; what is the maximum number of processors that can be use to run gaussian03 in paralel? thanks in advance. Walter From owner-chemistry@ccl.net Tue Sep 22 23:04:00 2009 From: "Anatoli Korkin a_korkin_._yahoo.com" To: CCL Subject: CCL: Web Tutorials for High and Middle School Students Message-Id: <-40330-090922230308-17194-K8wgSODFPx0usDUPH/zwoQ::server.ccl.net> X-Original-From: Anatoli Korkin Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 22 Sep 2009 20:02:52 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Anatoli Korkin [a_korkin*yahoo.com] Many Thanks Dr. Inbal Tuvi-Arad!=0A=0AFor your generous and kind support. I= added your references to the corresponding sections of the "NanoKids" web = page:=0A=0Ahttp://asdn.net/asdn/links/nanokids.shtml=0A=0Aas well as an Ack= nowledgement of Your contribution.=0A=0AYours Sincerely,=0AAnatoli Korkin = =0A=0A=0A=0A--- On Mon, 9/21/09, Inbal Tuvi-Arad inbaltu%a%openu.ac.il wrote:=0A=0A> From: Inbal Tuvi-Arad inbaltu%a%openu.a= c.il =0A> Subject: CCL: Web Tutorials for High and= Middle School Students=0A> To: "Korkin, Anatoli " =0A> Date: Monday, September 21, 2009, 11:52 PM=0A> =0A> Sent to CCL by= : "Inbal Tuvi-Arad" [inbaltu+*+openu.ac.il]=0A> Hi Anatoli,=0A> Here are f= ew links related to atomic structure and more:=0A> =0A> Physics 2000: http:= //www.colorado.edu/physics/2000/cover.html=0A> =0A> Miami museum of science= : The Atom Family:=0A> http://www.miamisci.org/af/sln/=0A> =0A> Chem4kids: = http://www.chem4kids.com/=0A> =0A> The Particle Adventure: http://particlea= dventure.org/=0A> =0A> A look inside the atom (history of physics from aip.= org=0A> with original=0A> recording of J. J. Thomson):=0A> http://www.aip.o= rg/history/electron/jjhome.htm=0A> =0A> Science is Fun!=A0 (Home experiment= s and much more):=0A> http://www.scifun.org/=0A> =0A> Molecule of the Month= : http://www.chm.bris.ac.uk/motm/motm.htm=0A> =0A> Webelements (a really go= od periodic table site):=0A> http://www.webelements.com/=0A> =0A> Merlot (m= ultimedia educational resources):=0A> http://www.merlot.org/merlot/index.ht= m=0A> =0A> There are plenty more excellent educational websites.=A0=0A> Per= haps you can=0A> try searching for a specific scientific topic.=A0 You=0A> = may also want to=0A> list other websites that list educational websites.=0A= > =0A> All the best,=0A> Inbal=0A> =0A> -----Original Message-----=0A> > Fr= om: owner-chemistry+inbaltu=3D=3Dopenu.ac.il]~[ccl.net=0A> [mailto:owner-ch= emistry+inbaltu=3D=3Dopenu.ac.il]~[ccl.net] On=0A> Behalf Of=0A> Anatoli Ko= rkin a_korkin%x%yahoo.com=0A> Sent: Monday, September 21, 2009 7:00 PM=0A> = To: Inbal Tuvi-Arad=0A> Subject: CCL: Web Tutorials for High and Middle Sch= ool=0A> Students=0A> =0A> =0A> Sent to CCL by: Anatoli Korkin [a_korkin]*[y= ahoo.com]=0A> Dear CCLers,=0A> =0A> I will appreciate if you could point on= web based tutorials=0A> in atomic=0A> scale science (physics, chemistry, b= iology) and related=0A> areas such as=0A> nanotechnology, which are made fo= r high and middle school=0A> students. =0A> =0A> I have started to collect = some on this web page:=0A> =0A> http://asdn.net/asdn/links/nanokids.shtml= =0A> =0A> Unfortunately, google search with the relevant key words=0A> are = dominated=0A> by irrelevant web pages promoted with help of "smart=0A> algo= rithms" and=0A> "cross farm" links.=0A> =0A> Thank you for your collaborati= on,=0A> Anatoli=A0 Korkin=0A> korkin-/at/-nanoandgiga-/dot/-com=0A> =0A> = =0A> =0A> -=3D This is automatically added to each message by the=0A> maili= ng script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsu= bscribe:=0Ahttp://www.ccl.net/spammers.txt= =0A> =0A> =0A> -=3D This is automatically added to each message by the=0A> = mailing script =3D-=0A> To recover the email address of the author of the m= essage,=0A> please change=0A> the strange characters on the top line to the= -x- sign. You=0A> can also=0A> look up the X-Original-From: line in the mail= header.=0A> =0A> E-mail to subscribers: CHEMISTRY-x-ccl.net=0A> or use:=0A> = =A0 =A0 =A0=0A> =0A> E-mail= to administrators: CHEMISTRY-REQUEST-x-ccl.net=0A> or use=0A> =A0 =A0 =A0 ht= tp://www.ccl.net/cgi-bin/ccl/send_ccl_message=0A> =0A> Subscribe/Unsubscrib= e:=0A> =A0 =A0 =A0=0A> =0A> Be= fore posting, check wait time at: http://www.ccl.net=0A> =0A> Job: http://w= ww.ccl.net/jobs=0A> Conferences: http://server.ccl.net/chemistry/announceme= nts/conferences/=0A> =0A> Search Messages: http://www.ccl.net/chemistry/sea= rchccl/index.shtml=0A> =0A> If your mail bounces from CCL with 5.7.1 error,= check:=0A> =A0 =A0 =A0=0A> =0A> RTFI: http= ://www.ccl.net/chemistry/aboutccl/instructions/=0A> =0A> =0A> =0A=0A=0A =