On = Dec 7, 2010, at 1:27 PM, Andrew Voronkov drugdesign=3Dyandex.ru = wrote:

Sent to CCL by: Andrew Voronkov [drugdesign * = yandex.ru]
Thank you very much for the answer. Can also anyone = recommend me some way to describe the linearity of the molecule? Let's = say that I have 50 conformations for each compound and want to measure = the degree of linearity of the molecules. How is possible to do = that?

Best regards,
Andrew
24.11.10, 18:07, "Michel = Petitjean petitjean.chiral%x%gmail.com" = <owner-chemistry_._ccl.net>:

Sent to CCL = by: Michel Petitjean = [petitjean.chiral^gmail.com]
= Dear Andrew,
Please have a = look at the DIVCF freeware:
= http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#DIVCF=
Best = regards,
= Michel.

Michel = Petitjean
MTi, INSERM UMR-S = 973, University Paris 7
35 = rue Helene Brion, 75205 Paris Cedex 13, = France.
Phone: +331 5727 = 8434; Fax: +331 5727 8372
= E-mail: petitjean.chiral!^!gmail.com, = michel.petitjean!^!univ-paris-diderot.fr
htt= p://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html

2010/11/24 = Andrew Voronkov drugdesign||yandex.ru = <owner-chemistry!^!ccl.net>:

Sent to CCL by: Andrew Voronkov = [drugdesign[]yandex.ru]
Dear CCL users, I have the next = goal - to study multiple conformations of the compounds and check = the correlation with the biological activity. I'd like to cluster let's = say top 50 conformations and divide them into similarity clusters as = well as get representative and\or average structures for each of the = clusters.
Is there any software which can = help me with this? The conformations were generated using Frog2 = server.

Best = regards,
Andrew> =        http://www.ccl.ne= t/cgi-bin/ccl/send_ccl_message> =        http://www.ccl.ne= t/cgi-bin/ccl/send_ccl_message> =        http://www.ccl.net/c= hemistry/sub_unsub.shtml> =        http://www.ccl.net/spammers.txt>

-=3D This is automatically = added to each message by the mailing script =3D-
To recover the email = address of the author of the message, please change
the strange = characters on the top line to the || sign. You can also
look up the = X-Original-From: line in the mail header.

E-mail to subscribers: = CHEMISTRY||ccl.net or use:
=      http://www.ccl.ne= t/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST||ccl.net = or use
     http://www.ccl.ne= t/cgi-bin/ccl/send_ccl_message
=      http://www.ccl.net/c= hemistry/sub_unsub.shtml

Before posting, check wait time at: = http://www.ccl.net

Job: http://www.ccl.net/jobs =
Conferences: http:/= /server.ccl.net/chemistry/announcements/conferences/

Search = Messages: http://www.ccl= .net/chemistry/searchccl/index.shtml

If your mail bounces = > from CCL with 5.7.1 error, check:
     http://www.ccl.net/spammers.txt

RTFI: http://www.cc= l.net/chemistry/aboutccl/instructions/

<= /div>
= --Apple-Mail-2294--23930466-- From owner-chemistry@ccl.net Wed Dec 8 14:03:00 2010 From: "Utpal Sarkar utpalchemiitkgp[-]gmail.com" To: CCL Subject: CCL:G: Help for cluster Message-Id: <-43303-101208114813-505-qnFGuHQYivgPpzzCA9hPVQ-.-server.ccl.net> X-Original-From: Utpal Sarkar Content-Type: multipart/alternative; boundary=0015174c3d929edc070496e8e272 Date: Wed, 8 Dec 2010 17:48:05 +0100 MIME-Version: 1.0 Sent to CCL by: Utpal Sarkar [utpalchemiitkgp|-|gmail.com] --0015174c3d929edc070496e8e272 Content-Type: text/plain; charset=ISO-8859-1 Dear CCL users, We are planning to purchase a 16 node (or even 32 node depending upon the price needed) cluser in which we will run softwares like Gaussian, VASP, DLPOLY . So may I request you to kindly give your valuable suggestion about: a) which type of specification is better ? b) How much does it cost (we can spent upto $10K to $11K) ? c) does the company/ provider (ie, HP, Dell, SGI ets) will install the cluster in the lab or we have to install ourself? We are starting from the begining and have no idel of purchasing clusters, so asking so many questions. I am waiting for your vauable suggestions With best regards Utpal --0015174c3d929edc070496e8e272 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Dear CCL users,

=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0 We are planning to purchase a 16 node (or even 32 nod= e depending upon the price needed) cluser in which we will run softwares li= ke Gaussian, VASP, DLPOLY . So may I request you to kindly give your valuab= le suggestion about:

a) which type of specification is better ?

b) How much does it cost (we can spent upto $10K to $11K) ?

c) does the company/ provider (ie, HP, Dell, SGI ets) will install the= cluster in the lab or we have to install ourself?

=A0

We are starting =A0from the begining and have no idel of purchasing cl= usters, so asking so many questions.

=A0

I am waiting for your vauable suggestions

With best regards

Utpal

=A0

--0015174c3d929edc070496e8e272-- From owner-chemistry@ccl.net Wed Dec 8 15:34:00 2010 From: "servaas servaas.michielssens() student.kuleuven.be" To: CCL Subject: CCL: UFF - Simulated annealing Message-Id: <-43304-101208151440-17316-hdN1LSKqVTWH+277rHtkfQ-x-server.ccl.net> X-Original-From: servaas Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="UTF-8" Date: Wed, 08 Dec 2010 21:14:28 +0100 Mime-Version: 1.0 Sent to CCL by: servaas [servaas.michielssens%a%student.kuleuven.be] Dear, Can anyone give me a suggestion for a free package that can use the UFF force field and that can do simulated annealing? kind regards, Servaas Michielssens From owner-chemistry@ccl.net Wed Dec 8 16:58:00 2010 From: "jaleel uc jaleel.uc-#-gmail.com" To: CCL Subject: CCL:G: Help for cluster Message-Id: <-43305-101208142940-2250-iA0gUcbe9Ggzkc2J7w6ojg-x-server.ccl.net> X-Original-From: jaleel uc Content-Type: multipart/alternative; boundary=001636c5a8a4eda9a40496eb230e Date: Thu, 9 Dec 2010 00:59:31 +0530 MIME-Version: 1.0 Sent to CCL by: jaleel uc [jaleel.uc*o*gmail.com] --001636c5a8a4eda9a40496eb230e Content-Type: text/plain; charset=ISO-8859-1 Dear sir If you are form accedmic my suggsetion is to think about volunteer grid , eg 1. CDAC garuda grid http://www.garudaindia.in/html/messages.aspx 2, World community grid http://www.worldcommunitygrid.org/ with regards On Wed, Dec 8, 2010 at 10:18 PM, Utpal Sarkar utpalchemiitkgp[-]gmail.com < owner-chemistry[a]ccl.net> wrote: > Dear CCL users, > We are planning to purchase a 16 node (or > even 32 node depending upon the price needed) cluser in which we will run > softwares like Gaussian, VASP, DLPOLY . So may I request you to kindly give > your valuable suggestion about: > a) which type of specification is better ? > b) How much does it cost (we can spent upto $10K to $11K) ? > c) does the company/ provider (ie, HP, Dell, SGI ets) will install the > cluster in the lab or we have to install ourself? > > We are starting from the begining and have no idel of purchasing clusters, > so asking so many questions. > > I am waiting for your vauable suggestions > With best regards > Utpal > > > -- Dr U.C.A.Jaleel. Asst Professor in cheminformatics Cheminformatics Division( UGC) Malabar Christian College Calicut University --001636c5a8a4eda9a40496eb230e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable =A0=A0=A0=A0 Dear sir

=A0 If you are form accedmic =A0 my suggsetion= is to think=A0 about volunteer grid ,=A0 eg 1. =A0 CDAC garuda grid http://www.garudaindia.i= n/html/messages.aspx
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0 2, World community grid=A0
http://www.worldcommunitygrid.org/

= =A0with regards

On Wed, Dec 8, 2010 at 1= 0:18 PM, Utpal Sarkar utpalchemiitkgp[-]gmail.= com <ow= ner-chemistry[a]ccl.net> wrote:

Dear CCL use= rs,

=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0 We are planning to purchase a 16 node (or even 32 nod= e depending upon the price needed) cluser in which we will run softwares li= ke Gaussian, VASP, DLPOLY . So may I request you to kindly give your valuab= le suggestion about:

a) which type of specification is better ?

b) How much does it cost (we can spent upto $10K to $11K) ?

c) does the company/ provider (ie, HP, Dell, SGI ets) will install the= cluster in the lab or we have to install ourself?

=A0

We are starting =A0from the begining and have no idel of purchasing cl= usters, so asking so many questions.

=A0

I am waiting for your vauable suggestions

With best regards

Utpal

=A0

=A0

--
Dr U.C.A.Jaleel.=
Asst Professor in cheminformatics
Cheminformatics Division( UGC)Malabar Christian College
Calicut University
--001636c5a8a4eda9a40496eb230e-- From owner-chemistry@ccl.net Wed Dec 8 21:33:01 2010 From: "jjsu jjsu+*+ciac.jl.cn" To: CCL Subject: CCL:G: solvent Message-Id: <-43306-101208205801-12654-a5ebg9yxaCUSXIcCCWfCcQ(a)server.ccl.net> X-Original-From: "jjsu" Content-Type: multipart/alternative; boundary="=====003_Dragon376203076581_=====" Date: Thu, 9 Dec 2010 09:57:36 +0800 Mime-Version: 1.0 Sent to CCL by: "jjsu" [jjsu#,#ciac.jl.cn] This is a multi-part message in MIME format. --=====003_Dragon376203076581_===== Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear all friends, I am calculating emission spectra with TDDFT together with PCM. But I meet a problem that is the solvent {2-methyl-tetrahydrofunran(2-MeTHF)} I used can not be successfully run in Gaussian09. I have no idea about this problem. Can anyone know what shall I do? Thanks in advance. Juanjuan Su 2010-12-09 jjsu --=====003_Dragon376203076581_===== Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: 7bit

Dear all friends,

I am calculating emission spectra with TDDFT together with PCM. But I meet a problem that is the solvent {2-methyl-tetrahydrofunran(2-MeTHF)} I used can not be successfully run in Gaussian09. I have no idea about this problem. Can anyone know what shall I do?

Thanks in advance.

Juanjuan Su

2010-12-09

jjsu

--=====003_Dragon376203076581_=====-- From owner-chemistry@ccl.net Wed Dec 8 22:08:01 2010 From: "David Mannock dmannock%ualberta.ca" To: CCL Subject: CCL: I am applying to Phys Phd program at USA, need your advice. Message-Id: <-43307-101208061333-12708-070kFbdsCnN5V6NYnQ5SvQ ~ server.ccl.net> X-Original-From: David Mannock Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 08 Dec 2010 04:13:05 -0700 MIME-Version: 1.0 Sent to CCL by: David Mannock [dmannock^ualberta.ca] Tsung-Wen, Looking for someone in exactly the same area as your own studies is not always a good thing to do. This is playing safe. If you must work in this area search on the web of science using appropriate search terms. My advice is to look 10 years into the future of your intended area and ask yourself, where will this area be? Will it still be fundable and sexy? What marketable skills will I have at the end of my PhD studies? I should also mention to you that you should take care in deciding on a lab to work in. Will there be someone to guide and direct the project in the early stages? Are you capable of working on a project independently without guidance from day 1? If so, this is a big responsibility. With the cut throat state of funding at the moment in many western countries, you need to know that you will be funded at the full studentship level for your full PhD term. Competition will be intense and you should beware of the sharks in the water. You should be looking for a positive, supportive learning environment, both within a lab and a department. Whenever money becomes tight, there is a lot of back stabbing that goes on at both levels. You do not want to be in a pressure cooker with nothing to show for 5 years work. Make sure that the PI has some relevant skills. Is he/she a good paper/grant writer? Are the names of lab workers present as co-authors in grants? Are students permitted to be the corresponding authors on some papers? Where are the former students and postdoctoral fellows that have been through the lab? How many have faculty positions? Will you be able to talk to them or students in the department about their experiences locally. If the answers to these questions is negative, I would urge caution. Be wary of people with too many awards. Some people like to pad their CVs with other peoples accomplishments! Remember, the prospective employer wants to interview you, but you also need to interview them. You must not be shy in asking these questions. When you are finishing your thesis, you should be able to write a paper or a grant independently. This ultimately is what the western academic systems want to see at the end of a PhD studentship and this is what you must aim for yourself. That is my 10 cents worth. David Mannock On 12/7/2010 7:43 PM, Tsung-Wen Yen peter308~~gmail.com wrote: > Sent to CCL by: "Tsung-Wen Yen" [peter308%a%gmail.com] > Dear CCLers: > My research is about Metallic clusters, I studied its geometry, thermal properties,dynamics and time-correlation properties. Recently, I am studying its magnetism using DFT and I have discovered how cluster's symmetry induce its magnetism. I planned to apply for PHD in the phyics department in USA. However, I searched over the universities and find several groups which has the same research topic as mine. For example, Prof Landman in GIT and Prof.Bloomfield in U of Virgina, and many others. I just want to consult you that are there other research groups in USA that are well-knowed for their research in metallic clusters?( theory and simulation). Appreciated if you could give me some suggestions. I spend a lot of time searching on google and scholar google. I just want to confirm if I missed any researchers in this field. Please give me feedbacks if you think I am asking a dumb question. Many thanks! > > > > > > With Best Regards > Tsung-Wen Yen> > > From owner-chemistry@ccl.net Wed Dec 8 22:42:00 2010 From: "Geoffrey Hutchison geoffh++pitt.edu" To: CCL Subject: CCL: UFF - Simulated annealing Message-Id: <-43308-101208221244-18985-7lXsYbiiytIt9iVxJYPwiQ.@.server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=us-ascii Date: Wed, 08 Dec 2010 22:12:36 -0500 MIME-version: 1.0 (Apple Message framework v1082) Sent to CCL by: Geoffrey Hutchison [geoffh]-[pitt.edu] On Dec 8, 2010, at 3:14 PM, servaas servaas.michielssens() student.kuleuven.be wrote: > Can anyone give me a suggestion for a free package that can use the UFF > force field and that can do simulated annealing? You would have to write the simulated annealing code yourself, but the Open Babel library has a full implementation of UFF. It's free, open source software. http://openbabel.org/ Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Assistant Professor, Department of Chemistry University of Pittsburgh http://hutchison.chem.pitt.edu/ Office: (412) 648-0492 From owner-chemistry@ccl.net Wed Dec 8 23:24:00 2010 From: "Joe Leonard jleonard42^^^gmail.com" To: CCL Subject: CCL: Problem printing from Macbook Air 13" Message-Id: <-43309-101208232306-12217-MpwXBd0KjV+GnmR/KE8sCw(!)server.ccl.net> X-Original-From: Joe Leonard Content-Type: multipart/alternative; boundary=Apple-Mail-2-28752286 Date: Wed, 8 Dec 2010 23:22:44 -0500 Mime-Version: 1.0 (Apple Message framework v1082) Sent to CCL by: Joe Leonard [jleonard42++gmail.com] --Apple-Mail-2-28752286 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Folks, anybody have a new Macbook Air (13", but either might do)? We = have one, and it's unable to set up or use either our old or new Airport = Express - both look like they time out, so we're unable to print to the = printer attached to the Express. My older Macbook Pro has no = difficulty, nor did an older Macbook. Is there some magical new setting that has to be changed on the MBA? = The new Airport Express is from earlier this year, so (hopefully) that's = not an issue? Help appreciated! Joe Leonard jleonard42*o*gmail.com PS Yeah, off to find a Support rep at the Apple Store, and hopefully = they know what I'm talking about. Figured I'd asked the CCL folks, too. -- "This isn't right. This isn't even wrong." -- Wolfgang Pauli --Apple-Mail-2-28752286 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii