From owner-chemistry@ccl.net Tue Oct 7 00:31:00 2008 From: "Vlad vvv900[]anusf.anu.edu.au" To: CCL Subject: CCL: ADF Visualization Message-Id: <-37853-081006231348-8216-kDgDa0HPY2kbOaBmMA3mqw^^server.ccl.net> X-Original-From: Vlad Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 07 Oct 2008 12:53:15 +1100 MIME-Version: 1.0 Sent to CCL by: Vlad [vvv900|anusf.anu.edu.au] Hi Seth, > A colleague and I are working with ADF for the first time, and we are > curious about visualization options for the results. Jamberoo (http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html ) can parse and visualize ADF input and output files. In the case of output files, it can animate optimization pathway using interactive charting, animate vibrations, and show displacement vectors. Best wishes, Vlad -- Dr Vladislav Vassiliev Computational Chemist ANU Supercomputer Facility, 56 Leonard Huxley Building, The Australian National University, Canberra ACT 0200 Australia Telephone : +61 2 6125 9694 Fax : +61 2 6125 8199 WWW : http://sf.anu.edu.au/~vvv900/ From owner-chemistry@ccl.net Tue Oct 7 09:36:01 2008 From: "V ronique LEGRAND vflegrand a free.fr" To: CCL Subject: CCL:G: check the total number of molecular orbital Message-Id: <-37854-081007064401-18197-DQzx0McggNhffU1SgV3iQA%a%server.ccl.net> X-Original-From: "V ronique LEGRAND" Date: Tue, 7 Oct 2008 06:43:57 -0400 Sent to CCL by: "V ronique LEGRAND" [vflegrand- -free.fr] Hello everybody, I'm a french student in PHD, and I have a problem between 2 results of Gaussian calculation. To be clear : -First : I realised an NBO calculation and the generation of a WFN file with the syntax : #p UMP2/6-31G** GFPrint GFinput Scf=VeryTight Output=WFN Punch=Archive iop(5/14=2) Maxdisk=500000000 Pop=(Full,NBO) Test In this case I can't use density=current as it should be with MP2, otherwise I have not all the NBO description in the output (?). -So in a second time, to have the real energy of my molecule in MP2 I used: #p UMP2/6-31G** density=current GFPrint GFinput Output=WFN Punch=Archive iop(5/14=2) Maxdisk=500000000 Test There are no more NBO or scf calculation. When I compared the results of these 2 steps, I was very surprised to find 127 molecular orbitals in the first (NBO...) and 330 in the second. I don't know why it's so different, I used the same basis set, and method. Which one tell the truth !! Thank you so much for any explanation (please be sure), and help on this problem. LEGRAND Vronique at vflegrand:_:free.fr From owner-chemistry@ccl.net Tue Oct 7 10:11:00 2008 From: "Tim Holt tim.holt]*[royalsociety.org" To: CCL Subject: CCL: Biomolecular simulation - free to access Message-Id: <-37855-081007061727-14377-vE5vVC/jTzyqaj0QwLJVZQ(0)server.ccl.net> X-Original-From: "Tim Holt" Date: Tue, 7 Oct 2008 06:17:23 -0400 Sent to CCL by: "Tim Holt" [tim.holt^^^royalsociety.org] 'Biomolecular simulation' is a special theme issue of Journal of the Royal Society Interface. Organised by Adrian Mulholland, it consists of nine peer- reviewed articles all of which are free to access via the journal's homepage at: http://publishing.royalsociety.org/interface The issue contains: Introduction: Biomolecular simulation Biomolecular simulation and modelling: status, progress and prospects Destabilisation of DNA duplexes by oxidative damage at guanine: implications for lesion recognition and repair Dynamics of conserved waters in human HSP 90: implications for drug design Analysis of polarization in QM/MM modelling of biologically relevant hydrogen bonds Theoretical site-directed mutagenesis: Asp168Ala mutant of lactate dehydrogenase The enzyme aromatic amine dehydrogenase induces a substrate conformation crucial for a promoting vibration that significantly reduces the effective potential energy barrier to proton transfer Mapping protein electron transfer pathways with QM/MM methods DNA and lipid bilayers: self assembly and insertion Dr Tim Holt tim.holt(_)royalsociety.org The Royal Society 6-9 Carlton House Terrace London SW1Y 5AG From owner-chemistry@ccl.net Tue Oct 7 10:46:01 2008 From: "Alexander Kos software~~akosgmbh.eu" To: CCL Subject: CCL: Purchasing compounds Message-Id: <-37856-081007051716-4664-/8b5BvdJIlMk2i5UqiGWwg===server.ccl.net> X-Original-From: "Alexander Kos" Content-Language: de Content-Type: multipart/alternative; boundary="----=_NextPart_000_00B0_01C92868.E8F526E0" Date: Tue, 7 Oct 2008 10:39:00 +0200 MIME-Version: 1.0 Sent to CCL by: "Alexander Kos" [software\a/akosgmbh.eu] This is a multipart message in MIME format. ------=_NextPart_000_00B0_01C92868.E8F526E0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hi Ian Recently someone asked me the same question how he could find compounds that failed in late clinical testing. I have no good answer for this, but MDDR gives you at least the information in which phase the compounds are. If a compound is still in phase III after 5 years, I assume it was not a success. If you approach the question by knowing the structure and you want to know what happened to the compound we recommend CWM Global Search. This is a Google like search for chemists. You find information for both system on my home page. With best regards, Alex AKos Consulting & Solutions Deutschland GmbH (AKos GmbH) Dr. Alexander Kos Austr. 26 D-79585 Steinen Germany Phone: +49 7627 970068 Fax: +49 7627 970067 Fax (to mail): +49 1805 744743 8318 Mobile +49 171 526 9392 E-mail: software!^!akosgmbh.eu Homepage: www.akosgmbh.de Registered at Amtsgericht Freiburg HRB 700872, Ust-ID DE253131617, General Manager: Greta Auf der Maur, Alexander Kos Authorized agent for Symyx Technologies, Inc. ( www.symyx.com), DIMENSION 5, Ltd. ( www.miner3d.com), CompuDrug International ( www.compudrug.com), Molecular Networks GmbH ( www.mol-net.de), and others. > From: owner-chemistry!^!ccl.net [mailto:owner-chemistry!^!ccl.net] Sent: Dienstag, 7. Oktober 2008 02:54 To: Kos, Alexander J. Subject: CCL: Purchasing compounds Hi Iain, ZINC (http://zinc.docking.org/) has collected vendor information under the "Subsets' menu. You may check if the failed compounds of your inerest are included there. Best regards, Vincent ----- Original Message ---- > From: Iain Wallace iain.m.wallace/./gmail.com To: "Wang, Xianlong " Sent: Tuesday, October 7, 2008 5:45:48 AM Subject: CCL: Purchasing compounds Hi, A question slightly out of left field, but I was wondering if anybody knew a source of purchasing compounds that have either failed in Phase I,II or III or that have been withdrawn. Drugbank has a list of compounds that are withdrawn but it would be cool to know if there was a database that contained the information of compounds that failed Phase I-III Thanks Iain ------=_NextPart_000_00B0_01C92868.E8F526E0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi Ian

 

Recently someone asked me the same question how he could = find compounds that failed in late clinical testing. I have no good answer for this, = but MDDR gives you at least the information in which phase the compounds are. If a = compound is still in phase III after 5 years, I assume it was not a success. =

 

If you approach the question by knowing the structure and = you want to know what happened to the compound we recommend CWM Global Search. = This is a Google like search for chemists.

 

You find information for both system on my home = page.

 

With best regards,

Alex

 

 

AKos Consulting & Solutions Deutschland = GmbH

(AKos GmbH)
Dr. Alexander Kos
Austr. 26
D-79585 Steinen
Germany

Phone: +49 7627 970068

Fax: +49 7627 970067

Fax (to mail):   +49 1805 744743 8318
Mobile +49 171 526 9392

E-mail: software!^!akosgmbh.eu=
Homepage: www.akosgmbh.de

Registered at Amtsgericht Freiburg HRB 700872, Ust-ID DE253131617, General Manager: Greta Auf der Maur, Alexander = Kos

Authorized agent for Symyx Technologies, Inc. = = (= www.symyx.com= ), DIMENSION 5, Ltd. (www.miner3d.com= ), CompuDrug International (www.compudrug.com<= /a>= ), Molecular Networks GmbH (www.mol-net.de= = ), and others.

 

 

 

 

 

From: owner-chemistry!^!ccl.net [mailto:owner-chemistry!^!ccl.net]
Sent: Dienstag, 7. Oktober 2008 02:54
To: Kos, Alexander J.
Subject: CCL: Purchasing compounds

 

Hi Iain,

ZINC (http://zinc.docking.org/) has collected vendor information under = the "Subsets' menu.  You may check if the failed compounds of your inerest are included there. 

Best regards,
Vincent

 

----- Original = Message ----
> From: Iain Wallace iain.m.wallace/./gmail.com = <owner-chemistry[#]ccl.net>
To: "Wang, Xianlong " <xloongw[#]yahoo.com>
Sent: Tuesday, October 7, 2008 5:45:48 AM
Subject: CCL: Purchasing compounds

Hi,

A question slightly out of left field, but I was wondering if anybody = knew a source of purchasing compounds that have either failed in Phase I,II or = III or that have been withdrawn.
Drugbank has a list of compounds that are withdrawn but it would be cool = to know if there was a database that contained the information of compounds = that failed Phase I-III

Thanks

Iain

 

------=_NextPart_000_00B0_01C92868.E8F526E0-- From owner-chemistry@ccl.net Tue Oct 7 12:50:00 2008 From: "Curt M. Breneman brenec]_[rpi.edu" To: CCL Subject: CCL: Reminder: OASys deadline is coming for COMP Division Symposia! Invitation to submit to "Nanomaterials Modeling and Informatics" Message-Id: <-37857-081007124642-25909-qwC6cT1GXHL44L9zY69Sig[-]server.ccl.net> X-Original-From: "Curt M. Breneman" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 7 Oct 2008 12:45:36 -0400 MIME-Version: 1.0 Sent to CCL by: "Curt M. Breneman" [brenec#%#rpi.edu] Reminder: Please spread the word! The new "Nanomaterials Modeling and Informatics" symposium that will take place within the COMP Division program of the ACS National Meeting in Salt Lake City, UT March 22-29, 2009 is open for submissions through the ACS OASys system! Nanotube and nanomaterials modeling is a new program area for the COMP Division, but it is an emerging area and directly aligned with the "Nanoscience" theme of this ACS meeting. This is a rapidly developing field, so we at COMP are providing a venue for people to present their latest developmental work in this area. This announcement is deliberately broad because we envision the symposium to be rich in diverse methodologies and preliminary results, and will include discussions of current "Best" practices in all aspects of the computational modeling of nanotubes and nanocomposite materials. Sincerely, Curt Breneman Treasurer, ACS COMP Division RPI Chemistry Director, RECCR Center From owner-chemistry@ccl.net Tue Oct 7 14:02:00 2008 From: "Ol Ga eurisco1[]pochta.ru" To: CCL Subject: CCL:G: check the total number of molecular orbital Message-Id: <-37858-081007135832-28507-AYvsoL/LYXZJFtwM9modyA%%server.ccl.net> X-Original-From: "Ol Ga" Date: Tue, 7 Oct 2008 13:58:28 -0400 Sent to CCL by: "Ol Ga" [eurisco1*o*pochta.ru] Dear Legrand Vronique, I think that your two input sections are not correct. If you really want to do NBO analysis for MP2 you need to type DENSITY=CURRENT or DENSITY=ALL in the script, e.g. #p UMP2/6-31G** GFPrint GFinput DENSITY=CURRENT Scf=VeryTight Output=WFN # Punch=Archive iop(5/14=2) Maxdisk=500000000 Pop=(Full,NBO) Test You will get in .out ******************************Gaussian NBO Version Analyzing the MP2 density *********** Or you should use #p UMP2/6-31G** GFPrint GFinput DENSITY=ALL Scf=VeryTight Output=WFN # Punch=Archive iop(5/14=2) Maxdisk=500000000 Pop=(Full,NBO) Test In .out-file you will get both analysis of SCF and MP2 densities, i.e. You will get two sections of NBO analysis ******************************Gaussian NBO Version 3.1 Analyzing the SCF density ******************************Gaussian NBO Version 3.1 Analyzing the MP2 density --------------- I really dont understand why you see different numbers of orbitals (127 MO vs. 330). Obviously, scf(VeryTight) has not any influence for this type of calculations. I tried your two inputs I didnt see any difference in the number of orbitals. Sincerely, Ol Ga > Sent to CCL by: "V ronique LEGRAND" [vflegrand- -free.fr] > Hello everybody, > I'm a french student in PHD, and I have a problem between 2 results > of Gaussian calculation. To be clear : > -First : I realised an NBO calculation and the generation of a WFN file with the syntax : > #p UMP2/6-31G** GFPrint GFinput Scf=VeryTight Output=WFN Punch=Archive iop(5/14=2) > Maxdisk=500000000 Pop=(Full,NBO) Test > In this case I can't use density=current as it should be with MP2, > otherwise I have not all the NBO description in the output (?). > -So in a second time, to have the real energy of my molecule in MP2 I used: > #p UMP2/6-31G** density=current GFPrint GFinput Output=WFN Punch=Archive iop(5/14=2) > Maxdisk=500000000 Test > There are no more NBO or scf calculation. > When I compared the results of these 2 steps, I was very surprised > to find 127 molecular orbitals in the first (NBO...) and 330 in the second. > I don't know why it's so different, I used the same basis set, and > method. Which one tell the truth !! > Thank you so much for any explanation (please be sure), and help on this problem. > LEGRAND Vronique at vflegrand:+:free.fr From owner-chemistry@ccl.net Tue Oct 7 14:43:01 2008 From: "DIEGOI GOMEZ darkego21%a%yahoo.com" To: CCL Subject: CCL: Thomas Kuhn Paradigm Shift Award Message-Id: <-37859-081007143851-17778-VbnlrxofR0lpINGtJSnhRg__server.ccl.net> X-Original-From: DIEGOI GOMEZ Content-Type: multipart/alternative; boundary="0-806624480-1223394713=:85707" Date: Tue, 7 Oct 2008 08:51:53 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: DIEGOI GOMEZ [darkego21!^!yahoo.com] --0-806624480-1223394713=:85707 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi Sengen.=0A=0A(My english is bad, but I will do my best.=A0 I apologize f= or any mistake)=0A=0AI found really interesting your=A0concern about the "p= aradigm shift" and=A0its identification, so I am going to adventure to tell= something.=0A=0AFirstly, I don't remember=A0exactly all the theory about e= pistemology=A0and the parents=A0of the differents positions;=A0=A0but I hav= e present some additional concepts like "universal validity", "conceptual d= isequilibrium", "conceptual change",=A0"falsibility" and many others... whe= re each one could represent an position to evaluate the incidence of new th= eories and=A0hypothesis=A0or new knowledge on the society and on the indivi= dual.=0A=0ASecondly, I think that is important to rescue the idea that the = scientific knowledge (in general, the science)=A0is not something that is i= n the matter or into the object of study, but the scientific knowledge is a= social contruction where exist many positions.=0A=0ASince the above, I thi= nk that if one desire to give a valuation of the importance or the=A0trance= ndence of a new theory, one=A0would have to take different positions and to= interpret the conceptual phenomena from this. (and should be taken into ac= count=A0too the way through which the object or the real phenomena=A0is eva= luated an the=A0objective=A0of the evaluation.=A0the way=A0in which=A0a sol= id or crystal system is evaluated by a Physicist and by a Chemist, for exam= ple).=A0 So, as we cannot=A0do that (to take different positions or in othe= r words, we have a=A0"limited ability to judge") we have to wait till scien= tific society know, understand, use and apply the=A0new theory or new conce= pt from its particular positions (what induce a new independent variable, t= he time, and=A0this=A0do our discution a relative problem).=0A=0AAdditional= ly,=A0I think=A0that to live in a "highly civilized society" is synonymous= =A0of=A0better ways to exchange knowledge and so synonymous of highly knowl= edge state (but this is relative to our current knowledge state)=A0and this= doesn`t=A0affect the need =A0(relative to each scientist) to apply the new= theory in a particular interpretation process.=0A=0AWell,=A0no more...=0A= =0Athat is my humble opinion, I am not an expert in science or in epistemol= ogy, but the=A0issue is interesting for me.=0A=0AThanks=A0=0A=0ADiego Arman= do G=F3mez Hern=E1ndez.=0A=0A=0A=0A=0A=0A----- Original Message ----=0AFrom= : Sengen Sun sengensun*o*yahoo.com =0ATo: "Gomez, = Diego Armando " =0ASent: Monday, October 6, 20= 08 10:27:20 PM=0ASubject: CCL: Thomas Kuhn Paradigm Shift Award=0A=0A=0ASen= t to CCL by: Sengen Sun [sengensun(~)yahoo.com]=0AI am still concerned with= the AWARD that may cause philosophical =0Aconfusion in this human society.= =0A=0AAccording to Kuhn, a truly theoretical paradigm shift is often =0Aa l= ong-term struggle, induces confrontation, and eventually =0Achanges our ver= y fundamental view how human understands the nature.=0A=0AI'd like to give = an example what a Kuhn paradigm shift is really =0Aabout to me. During my g= raduate study for my PhD degree at =0AMcMaster University from 1989-1994, I= found that Professor =0ARichard Bader had been struggling for many years f= or his =0Arevolutionary philosophy about the role of electron density =0Ain= atoms and molecules. I did not work directly with Bader =0Abut was a close= spectator. Nowadays, Bader's theory is quite =0Apopular. But I don't think= the resistance is over until his =0Awork is awarded what it really deserve= s.=0A=0AThis case of Kuhn's paradigm shift leads me to think that =0Aeven i= n our highly civilized society today, it is very =0Adifficult to adjust our= minds to accept a fundamental revolution =0Aof scientific theory. At least= , there are two reasons for this =0Adifficulty. One is our limited ability = to judge no matter what =0Akind of experts we are; The other is the politic= al correctness as=0Arecognized by Kuhn. As soon as human is not free from t= hese two =0Afactors, awarding Kuhn paradigm shift is likely just a joke.=0A= =0AAlso imagine we are in an era when Kuhn paradigm shift happens =0Aevery = year! And recognized every year! After 50 years, we will =0Ahave a big list= . Is that really what Kuhn meant about theoretical =0Aparadigm shift?=0A=0A= The awarded works under this AWARD in the past are excellent works, =0Abut = no more than some technical changes, improvements or modifications in =0Aa = field. They do change things in a particular field, even very=0Asignificant= ly. To me, it is exaggerated and philosophically =0Amisleading to use the w= ords "Kuhn paradigm shift". They should =0Abe awarded in many other ways.= =0A=0AHow could you tell the difference between normal scientific progress = and truly a revolution?=0A=A0 =0AThanks for attention and welcome any comme= nts.=0A=0ASengen=0A=0A>=0A>=0A>=0A>=0A> From: "carlos simmerling" =0ASubject: CCL: Thomas Kuhn Paradigm Shift Award sy= mposium at Spring ACS meeting =0ADate: Wed, 1 Oct 2008 15:44:40 -0400 =0A= =0A------------------------------------------------------------------------= --------=0A=0ASent to CCL by: "carlos=A0 simmerling" [carlos.simmerling:-:g= mail.com]=0APlease forward this announcement of an award symposium to be he= ld in the COMP=0Adivision at the Spring ACS national meeting in Salt lake C= ity.=0AThe Thomas Kuhn Paradigm Shift Award is given each year to the talk = that most=0Acaptures the spirit of Kuhn's writings, exemplified in his land= mark book,=0A"The Structure of Scientific Revolutions". The symposium at ea= ch=0ASpring ACS is open to all and attempts to attract those whose work has= the=0Apotential to change the way we think about an aspect of science. Kuh= n's words=0Afor this, a "Paradigm Shift", have been much over used and as s= uch can=0Abe an intimidating standard to approach, but the intent is for ta= lks that=0Arepresent a fresh way of looking at an aspect of our field. As a= n example, the=0A2006 winner, Christopher Bayly of Merck-Frosst, proposed t= hat focused screening=0Awas a more efficient path to drug discovery than hi= gh throughput screening and=0Ain 2008 Derek Debe of Abbott Laboratories pre= sented the case for knowing=0Aconfidence intervals in molecular modeling. T= alks are usually within the=0Acomputational sphere. They are judged on nove= lty, potential impact and quality=0Aof presentation by a panel of independe= nt scientists with extensive=0Acomputational experience. It is hoped the Aw= ard, which carries a stipend of=A0 one=0Athousand dollars, can provide a pl= atform to researchers extending a mirror to=0Aour field and questioning the= scientific status quo.=0AAbstracts can be submitted on the OASYS web site = (oasys.acs.org) and four will=0Abe selected for 40 minute presentations to = take place during a half-day=0Asymposium at the national meeting.=A0 Abstra= cts not selected for the symposium=0Acompetition can be moved into consider= ation for the general symposia (which are=0Aalways well attended!) if desir= ed.=0AMore information on awards offered by the ACS COMP division can be fo= und on the=0Aweb site at http://www.acscomp.org/Awards/index.html=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=A0 =A0 =A0 http://www.ccl.net/cgi-bi= n/ccl/send_ccl_message=0A=0AE-mail to administrators: CHEMISTRY-REQUEST _ ccl= .net or use=0A=A0 =A0 =A0= =0A=0A=0A=A0 =A0 =A0 http://www.ccl.net/chemistry/su= b_unsub.shtml=0A=0A= =0A=0A=0AConferences: http://server.ccl.net/ch= emistry/announcements/conferences/=0A=0ASearch Messages: http://www.ccl.net= /htdig=A0 (login: ccl, Password: search)=0A=0AIf your mail bounces from CCL= with 5.7.1 error, check:=0A=A0 =A0 =A0=0A= =0A=0A=0A=0A --0-806624480-1223394713=:85707 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
=0A
Hi Sengen.
=0A
 
=0A
(My eng= lish is bad, but I will do my best.  I apologize for any mistake)=0A
 
=0A
I found really interesting your concern a= bout the "paradigm shift" and its identification, so I am going to adv= enture to tell something.
=0A
 
=0A
Firstly, I don't= remember exactly all the theory about epistemology and the paren= ts of the differents positions;  but I have present some add= itional concepts like "universal validity", "conceptual disequilibrium", "c= onceptual change", "falsibility" and many others... where each one cou= ld represent an position to evaluate the incidence of new theories and = ;hypothesis or new knowledge on the society and on the individual.=0A
 
=0A
Secondly, I think that is important to rescue= the idea that the scientific knowledge (in general, the science) is n= ot something that is in the matter or into the object of study, but the sci= entific knowledge is a social contruction where exist many positions.
= =0A
 
=0A
Since the above, I think that if one desire to = give a valuation of the importance or the trancendence of a new theory= , one would have to take different positions and to interpret the conc= eptual phenomena from this. (and should be taken into account too the = way through which the object or the real phenomena is evaluated an the=  objective of the evaluation. the way in which a s= olid or crystal system is evaluated by a Physicist and by a Chemist, for ex= ample).  So, as we cannot do that (to take different positions or= in other words, we have a "limited ability to judge") we have to wait= till scientific society know, understand, use and apply the new theor= y or new concept from its particular positions (what induce a new independe= nt variable, the time, and this do our discution a relative probl= em).
=0A
 
=0A
Additionally, I think that = to live in a "highly civilized society" is synonymous of better w= ays to exchange knowledge and so synonymous of highly knowledge state (but = this is relative to our current knowledge state) and this doesn`t = ;affect the need  (relative to each scientist) to apply the new theory= in a particular interpretation process.
=0A
 
=0A
W= ell, no more...
=0A
 
=0A
that is my humble opi= nion, I am not an expert in science or in epistemology, but the issue = is interesting for me.
=0A
 
=0A
Thanks 
= =0A
 
=0A
 
Diego Armando G=F3mez Hern=E1ndez.<= BR>
=0A

=0A

=0A
----- Original Message ----
From: Senge= n Sun sengensun*o*yahoo.com <owner-chemistry _ ccl.net>
To: "Gomez, = Diego Armando " <darkego21 _ yahoo.com>
Sent: Monday, Octobe= r 6, 2008 10:27:20 PM
Subject: CCL: Thomas Kuhn Paradigm Shift Award
=

Sent to CCL by: Sengen Sun [sengensun(~)yahoo.com]
I am still concerned with the AWARD th= at may cause philosophical
confusion in this human society.

Acco= rding to Kuhn, a truly theoretical paradigm shift is often
a long-term = struggle, induces confrontation, and eventually
changes our very fundam= ental view how human understands the nature.

I'd like to give an exa= mple what a Kuhn paradigm shift is really
about to me. During my gradua= te study for my PhD degree at
McMaster University from 1989-1994, I fou= nd that Professor
Richard Bader had been struggling for many years for his
revolutionary philoso= phy about the role of electron density
in atoms and molecules. I did no= t work directly with Bader
but was a close spectator. Nowadays, Bader's= theory is quite
popular. But I don't think the resistance is over unti= l his
work is awarded what it really deserves.

This case of Kuhn= 's paradigm shift leads me to think that
even in our highly civilized s= ociety today, it is very
difficult to adjust our minds to accept a fund= amental revolution
of scientific theory. At least, there are two reason= s for this
difficulty. One is our limited ability to judge no matter wh= at
kind of experts we are; The other is the political correctness asrecognized by Kuhn. As soon as human is not free from these two
factor= s, awarding Kuhn paradigm shift is likely just a joke.

Also imagine = we are in an era when Kuhn paradigm shift happens
every year! And recognized every year! After 50 years, we will
have a big list. Is= that really what Kuhn meant about theoretical
paradigm shift?

T= he awarded works under this AWARD in the past are excellent works,
but = no more than some technical changes, improvements or modifications in
a= field. They do change things in a particular field, even very
significa= ntly. To me, it is exaggerated and philosophically
misleading to use th= e words "Kuhn paradigm shift". They should
be awarded in many other way= s.

How could you tell the difference between normal scientific progr= ess and truly a revolution?
 
Thanks for attention and welcome = any comments.

Sengen

>
>
>
>
> Fro= m: "carlos simmerling" <carlos.simmerling ~ gmail.com>
Subject: CCL: Thomas Kuhn Paradigm = Shift Award symposium at Spring ACS meeting
Date: Wed, 1 Oct 2008 15:44:40 -0400

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

Sent to CCL by: "carlos  simmerli= ng" [carlos.simmerling:-:gmail.com]
Please forward this announcement of = an award symposium to be held in the COMP
division at the Spring ACS nat= ional meeting in Salt lake City.
The Thomas Kuhn Paradigm Shift Award is= given each year to the talk that most
captures the spirit of Kuhn's wri= tings, exemplified in his landmark book,
"The Structure of Scientific Re= volutions". The symposium at each
Spring ACS is open to all and attempts= to attract those whose work has the
potential to change the way we thin= k about an aspect of science. Kuhn's words
for this, a "Paradigm Shift",= have been much over used and as such can
be an intimidating standard to= approach, but the intent is for talks that
represent a fresh way of loo= king at an aspect of our field. As an example, the
2006 winner, Christopher Bayly of Merck-Frosst, proposed that focused screening
was = a more efficient path to drug discovery than high throughput screening and<= BR>in 2008 Derek Debe of Abbott Laboratories presented the case for knowing=
confidence intervals in molecular modeling. Talks are usually within th= e
computational sphere. They are judged on novelty, potential impact and= quality
of presentation by a panel of independent scientists with exten= sive
computational experience. It is hoped the Award, which carries a st= ipend of  one
thousand dollars, can provide a platform to researche= rs extending a mirror to
our field and questioning the scientific status= quo.
Abstracts can be submitted on the OASYS web site (oasys.acs.org) and four will
be se= lected for 40 minute presentations to take place during a half-day
sympo= sium at the national meeting.  Abstracts not selected for the symposium
competition can be moved into consideration for the general s= ymposia (which are
always well attended!) if desired.
More informatio= n on awards offered by the ACS COMP division can be found on the
web sit= e at h= ttp://www.acscomp.org/Awards/index.html



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=0A=0A --0-806624480-1223394713=:85707-- From owner-chemistry@ccl.net Tue Oct 7 16:05:00 2008 From: "javier mauricio vallejos javier33*o*vtr.net" To: CCL Subject: CCL:G: nbodel opt Message-Id: <-37860-081007141215-2415-7roQBTiN/qsjs2fl/pDAYw _ server.ccl.net> X-Original-From: "javier mauricio vallejos" Date: Tue, 7 Oct 2008 14:12:12 -0400 Sent to CCL by: "javier mauricio vallejos" [javier33-,-vtr.net] Dear All, With Gaussian03, I tried to do reoptimize the geometry after deleting some orbitals. This is the output %CHK=33DINITRO %MEM=128MB Default route: MaxDisk=2000MB --------------------------- # rhf/6-31g* pop=nbodel opt --------------------------- Warning: this job cannot use analytic gradients and so will do many energy evaluations. 1/29=20000,38=1/1,14; 2/17=6,18=5,29=3,40=1/2; 3/5=1,6=6,7=1,11=1,16=1,25=1,30=1/1,2,3; 4/7=1/1; 5/5=2,38=5/2; 6/7=2,8=2,9=2,10=2,28=1,40=11/1,7(2); 5/5=2,7=1,13=1,38=5/2; 6/7=2,8=2,9=2,10=2,28=1,40=3/7; 6/7=2,8=2,9=2,10=2,28=1,40=2/7(-2); 1//14(1); 99//99; 2/29=3/2; 3/5=1,6=6,7=1,11=1,16=1,25=1,30=1/1,2,3; 4/5=5,7=1,16=3/1; 5/5=2,38=5/2; 6/7=2,8=2,9=2,10=2,28=1,40=11/1,7(2); 5/5=2,7=1,13=1,38=5/2; 6/7=2,8=2,9=2,10=2,28=1,40=3/7; 6/7=2,8=2,9=2,10=2,28=1,40=2/7(-2); 1//14(-8); 2/29=3/2; 6/7=2,8=2,9=2,10=2,19=2,28=1,40=11/1,7; 99/9=1/99; --- fff --- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 S N 1 B1 C 2 B2 1 A1 C 3 B3 2 A2 1 D1 0 C 4 B4 3 A3 2 D2 0 C 5 B5 4 A4 3 D3 0 C 2 B6 1 A5 3 D4 0 S 1 B7 3 A6 2 D5 0 H 5 B8 4 A7 3 D6 0 H 7 B9 2 A8 1 D7 0 H 4 B10 3 A9 2 D8 0 N 6 B11 5 A10 4 D9 0 O 12 B12 6 A11 5 D10 0 O 12 B13 6 A12 5 D11 0 C 8 B14 1 A13 3 D12 0 N 15 B15 8 A14 1 D13 0 N 16 B16 15 A15 8 D14 0 N 17 B17 16 A16 15 D15 0 N 15 B18 8 A17 1 D16 0 C 19 B19 15 A18 8 D17 0 C 20 B20 19 A19 15 D18 0 C 20 B21 19 A20 15 D19 0 C 21 B22 20 A21 19 D20 0 H 21 B23 20 A22 19 D21 0 C 22 B24 20 A23 19 D22 0 H 22 B25 20 A24 19 D23 0 C 25 B26 22 A25 20 D24 0 H 23 B27 21 A26 20 D25 0 H 25 B28 22 A27 20 D26 0 H 27 B29 25 A28 22 D27 0 Variables: B1 2.67791 B2 1.34126 B3 1.41596 B4 1.39384 B5 1.3872 B6 1.33222 B7 2.0719 B8 1.0836 B9 1.08806 B10 1.07 B11 1.47 B12 1.19934 B13 1.19934 B14 1.78 B15 1.37723 B16 1.43212 B17 1.37719 B18 1.67217 B19 1.47 B20 1.39516 B21 1.39483 B22 1.39471 B23 1.09966 B24 1.39514 B25 1.0996 B26 1.39483 B27 1.09968 B28 1.09976 B29 1.09968 A1 35.78186 A2 119.69464 A3 120.20173 A4 118.90928 A5 155.67194 A6 95.13529 A7 118.52265 A8 115.48331 A9 119.89914 A10 121.45454 A11 118.39342 A12 118.39269 A13 109.47122 A14 125.6782 A15 111.52159 A16 111.52447 A17 122.76126 A18 133.08252 A19 119.99722 A20 120.00432 A21 120.00863 A22 119.98077 A23 120.00002 A24 120.008 A25 120.0047 A26 120.01279 A27 119.98395 A28 120.02486 D1 -180. D2 0. D3 0. D4 0. D5 -0.00981 D6 -180. D7 180. D8 180. D9 180. D10 0. D11 180. D12 180. D13 32.72787 D14 179.96688 D15 0.03622 D16 -147.27608 D17 0.01588 D18 -86.93855 D19 93.05617 D20 -179.97293 D21 -0.05203 D22 -179.97984 D23 -0.00555 D24 -0.03761 D25 179.96185 D26 179.97501 D27 -179.95633 1 tetrahedral angles replaced. 1 tetrahedral angles replaced. NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF- NUMERICAL EIGENVECTOR FOLLOWING MINIMUM SEARCH INITIALIZATION PASS ************************************************ ** ERROR IN INITNF. NUMBER OF VARIABLES ( 84) ** ** INCORRECT (SHOULD BE BETWEEN 1 AND 50) ** *********************************************** My question is: Is very big this moleule ? From owner-chemistry@ccl.net Tue Oct 7 17:39:01 2008 From: "Carlos Simmerling carlos.simmerling()gmail.com" To: CCL Subject: CCL: Thomas Kuhn Paradigm Shift Award Message-Id: <-37861-081007173341-1762-dM9ws74t6jBB00yOO4sZrQ,+,server.ccl.net> X-Original-From: "Carlos Simmerling" Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 7 Oct 2008 17:33:26 -0400 MIME-Version: 1.0 Sent to CCL by: "Carlos Simmerling" [carlos.simmerling**gmail.com] Anthony Nicholls of OpenEye created and sponsors these awards for ACS. He doesn't use CCL mail so I passed the original message to him, here is his reply: ---------- Forwarded message ---------- > From: Anthony Nicholls The comments by Sengun Sun reflect one of the main criticisms of Kuhn's work at the time it was first published. It was easy to see the shift in Newton-Einstein or Classical-Quantum as paradigm shifts but since these only happen every fifty years or so, what use is it? I believe the standard response is that Kuhn's insight into the difficulties new ideas face is exemplified by the "Epoch-making" changes in physics and other branches of Natural Science, but is widespread in humbler forms. If Sun had attended any of the Kuhn Symposia he would have heard my introduction wherein I give many examples of such and in particular champion the "Kuhn-lite" description by the great British geneticist J. B. S. Haldane (J. Genetics #58, 1963, p 464): Four stages of acceptance of a scientific theory: i) It is worthless nonsense. ii) This is an interesting, but perverse, point of view. iii) It is true, but quite unimportant. iv) I always said so. Every time I have given this introduction I have seen heads nod in rueful acknowledgement because most of us who have had original ideas have experienced just this process. We do not have to be suggesting the Earth revolve around the Sun or species arise from the fitness of inherited traits to know that new ideas always have a hard time. That is what the symposium is about. In defense of the "technical changes" that have won in previous years, the concept that large scale screening is an inefficient use of pharma resources (Bayly, 2006) is an excellent example of an idea weighing in against political correctness Sun states is a necessary characteristic of a paradigm shift. The concept of the importance of confidence limits in the field of computational chemistry (Debe, 2008) is a battle still being waged of immense importance, I believe, to the entire field. The degree to which it is not currently appreciated is again a necessary, if not sufficient characteristic. While neither may be the "Epoch-making" changes Sun is looking for, neither is Bader's work- by the strict definitions of a Kuhn Paradigm shift he suggests we ought to use. Kuhn's work arose from his reflections on his difficulties in comprehending how the pre-classical greats, for instance Aristotle, could have held views we now would think are ridiculous. It is this alteration in mindset that is almost impossible to reverse that is the hallmark of the 'Shift'. While Bader's work is interesting, clever, rigorous and "Haldane", it has not become a shift - there are plenty of other ways of considering bonds that are used everyday, i.e. Bader has not, nor may ever, become a de facto standard. Something like DFT, however, has undergone such a shift. These days many would find it inconceivable to not use DFT for small molecule calculations, while this view would have ridiculed 20 years ago. This is not to put down Bader, because for me his work is an example of a paradigm shift, but not of the type Sun believes defines the concept. Finally, while I accept that the concept of 'judging' a paradigm shift is hard, perhaps even logically tenuous, I would invite him to attend a symposium and see for himself. The last event, in addition to Debe's excellent talk on how to judge the value of predictions, featured a talk on a truly new way to include polarization in molecular mechanics, a way to account for correlations in large-scale simulations, and a proposal that chemistry as we know can is hopelessly hind-bound. I can not remember a better session at the ACS, or for that matter any other meeting. As with any good scientific idea, ultimate validity is measured by whether it is found useful. In my view, the Thomas Kuhn Paradigm Shift Award has already passed that test. Anthony Nicholls On Tue, Oct 7, 2008 at 11:51 AM, DIEGOI GOMEZ darkego21%a%yahoo.com wrote: > Hi Sengen. > > (My english is bad, but I will do my best. I apologize for any mistake) > > I found really interesting your concern about the "paradigm shift" and it= s > identification, so I am going to adventure to tell something. > > Firstly, I don't remember exactly all the theory about epistemology and t= he > parents of the differents positions; but I have present some additional > concepts like "universal validity", "conceptual disequilibrium", "concept= ual > change", "falsibility" and many others... where each one could represent = an > position to evaluate the incidence of new theories and hypothesis or new > knowledge on the society and on the individual. > > Secondly, I think that is important to rescue the idea that the scientifi= c > knowledge (in general, the science) is not something that is in the matte= r > or into the object of study, but the scientific knowledge is a social > contruction where exist many positions. > > Since the above, I think that if one desire to give a valuation of the > importance or the trancendence of a new theory, one would have to take > different positions and to interpret the conceptual phenomena from this. > (and should be taken into account too the way through which the object or > the real phenomena is evaluated an the objective of the evaluation. the > way in which a solid or crystal system is evaluated by a Physicist and by= a > Chemist, for example). So, as we cannot do that (to take different > positions or in other words, we have a "limited ability to judge") we hav= e > to wait till scientific society know, understand, use and apply the new > theory or new concept from its particular positions (what induce a new > independent variable, the time, and this do our discution a relative > problem). > > Additionally, I think that to live in a "highly civilized society" is > synonymous of better ways to exchange knowledge and so synonymous of high= ly > knowledge state (but this is relative to our current knowledge state) and > this doesn`t affect the need (relative to each scientist) to apply the n= ew > theory in a particular interpretation process. > > Well, no more... > > that is my humble opinion, I am not an expert in science or in epistemolo= gy, > but the issue is interesting for me. > > Thanks > > > Diego Armando G=F3mez Hern=E1ndez. > > > > ----- Original Message ---- > From: Sengen Sun sengensun*o*yahoo.com > To: "Gomez, Diego Armando " > Sent: Monday, October 6, 2008 10:27:20 PM > Subject: CCL: Thomas Kuhn Paradigm Shift Award > > > Sent to CCL by: Sengen Sun [sengensun(~)yahoo.com] > I am still concerned with the AWARD that may cause philosophical > confusion in this human society. > > According to Kuhn, a truly theoretical paradigm shift is often > a long-term struggle, induces confrontation, and eventually > changes our very fundamental view how human understands the nature. > > I'd like to give an example what a Kuhn paradigm shift is really > about to me. During my graduate study for my PhD degree at > McMaster University from 1989-1994, I found that Professor > Richard Bader had been struggling for many years for his > revolutionary philosophy about the role of electron density > in atoms and molecules. I did not work directly with Bader > but was a close spectator. Nowadays, Bader's theory is quite > popular. But I don't think the resistance is over until his > work is awarded what it really deserves. > > This case of Kuhn's paradigm shift leads me to think that > even in our highly civilized society today, it is very > difficult to adjust our minds to accept a fundamental revolution > of scientific theory. At least, there are two reasons for this > difficulty. One is our limited ability to judge no matter what > kind of experts we are; The other is the political correctness as > recognized by Kuhn. As soon as human is not free from these two > factors, awarding Kuhn paradigm shift is likely just a joke. > > Also imagine we are in an era when Kuhn paradigm shift happens > every year! And recognized every year! After 50 years, we will > have a big list. Is that really what Kuhn meant about theoretical > paradigm shift? > > The awarded works under this AWARD in the past are excellent works, > but no more than some technical changes, improvements or modifications in > a field. They do change things in a particular field, even very > significantly. To me, it is exaggerated and philosophically > misleading to use the words "Kuhn paradigm shift". They should > be awarded in many other ways. > > How could you tell the difference between normal scientific progress and > truly a revolution? > > Thanks for attention and welcome any comments. > > Sengen > >> >> >> >> >> From: "carlos simmerling" > Subject: CCL: Thomas Kuhn Paradigm Shift Award symposium at Spring ACS > meeting > Date: Wed, 1 Oct 2008 15:44:40 -0400 > > -------------------------------------------------------------------------= ------- > > Sent to CCL by: "carlos simmerling" [carlos.simmerling:-:gmail.com] > Please forward this announcement of an award symposium to be held in the > COMP > division at the Spring ACS national meeting in Salt lake City. > The Thomas Kuhn Paradigm Shift Award is given each year to the talk that > most > captures the spirit of Kuhn's writings, exemplified in his landmark book, > "The Structure of Scientific Revolutions". The symposium at each > Spring ACS is open to all and attempts to attract those whose work has th= e > potential to change the way we think about an aspect of science. Kuhn's > words > for this, a "Paradigm Shift", have been much over used and as such can > be an intimidating standard to approach, but the intent is for talks that > represent a fresh way of looking at an aspect of our field. As an example= , > the > 2006 winner, Christopher Bayly of Merck-Frosst, proposed that focused > screening > was a more efficient path to drug discovery than high throughput screenin= g > and > in 2008 Derek Debe of Abbott Laboratories presented the case for knowing > confidence intervals in molecular modeling. Talks are usually within the > computational sphere. They are judged on novelty, potential impact and > quality > of presentation by a panel of independent scientists with extensive > computational experience. It is hoped the Award, which carries a stipend = of > one > thousand dollars, can provide a platform to researchers extending a mirro= r > to > our field and questioning the scientific status quo. > Abstracts can be submitted on the OASYS web site (oasys.acs.org) and four > will > be selected for 40 minute presentations to take place during a half-day > symposium at the national meeting. Abstracts not selected for the sympos= ium > competition can be moved into consideration for the general symposia (whi= ch > are > always well attended!) if desired. > More information on awards offered by the ACS COMP division can be found = on > the > web site at http://www.acscomp.org/Awards/index.html > > > > -=3D This is automatically added to each message by the mailing script = =3D-> the strange characters on the top line to the :+: sign. You can also> > E-mail to subscribers: CHEMISTRY:+:ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST:+:ccl.net or use> > > > From owner-chemistry@ccl.net Tue Oct 7 20:49:00 2008 From: "feng zhu zhufengcc|,|gmail.com" To: CCL Subject: CCL:G: [g03] Format of basis set Message-Id: <-37862-081006204456-3171-LSgHu5CSEGxjSRrQl5kqzA++server.ccl.net> X-Original-From: "feng zhu" Content-Type: multipart/alternative; boundary="----=_Part_51519_30069850.1223340283583" Date: Tue, 7 Oct 2008 08:44:43 +0800 MIME-Version: 1.0 Sent to CCL by: "feng zhu" [zhufengcc,gmail.com] ------=_Part_51519_30069850.1223340283583 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear All CCLs, I download the basis set for Ke from https://bse.pnl.gov/bse/portal It looks like below: Kr 0 S 15 1.00 11713823.0080000 0.56915790360E-05 1755253.3979000 0.44214471278E-04 399717.4192400 0.23227813842E-03 113285.7926000 0.97973661050E-03 36977.2052930 0.35537627541E-02 13355.0365800 0.11468673282E-01 5210.9012988 0.33241627469E-01 2162.1137020 0.85620725674E-01 943.29291023 0.18708766876 429.20724331 0.31497583326 202.40720840 0.33406191042 3260.4985521 0.0000000 1011.1069716 0.0000000 392.44359273 0.0000000 173.21702132 0.0000000 S 15 1.00 11713823.0080000 0.0000000 1755253.3979000 0.0000000 399717.4192400 0.0000000 113285.7926000 0.0000000 36977.2052930 0.0000000 13355.0365800 0.0000000 5210.9012988 0.0000000 2162.1137020 0.0000000 943.29291023 0.0000000 429.20724331 0.0000000 202.40720840 0.0000000 3260.4985521 0.73091509287E-02 1011.1069716 0.74040355445E-01 392.44359273 0.35414962222 173.21702132 0.80188286115 ...... Please note that there are many lines containing 0.000000 in the basis set. I omit them (of course in the meantime changing "S 15" to "S 11" and "S 4" respectively), and find that all the results are the same, except that more "primitive gaussians" are used when these lines are in the basis set. My question is, what we will benifit from this format including these lines? Will we use more memory for this format because of more "primitive gaussians" are used? Or it is exactly the same for the two formats (with and without zero lines)? Thank you very much! Best regards, Zhu -- ------------------ Zhu feng Department of Physics, Anhui University, Hefei, China ------=_Part_51519_30069850.1223340283583 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Dear All CCLs,

I download the basis set for Ke from https://bse.pnl.gov/bse/portal
It looks like below:
Kr     0 
S   15   1.00
 11713823.0080000            0.56915790360E-05      
 1755253.3979000             0.44214471278E-04      
 399717.4192400              0.23227813842E-03      
 113285.7926000              0.97973661050E-03      


  36977.2052930              0.35537627541E-02      
  13355.0365800              0.11468673282E-01      
   5210.9012988              0.33241627469E-01      
   2162.1137020              0.85620725674E-01      


    943.29291023             0.18708766876    
    429.20724331             0.31497583326    
    202.40720840             0.33406191042    
   3260.4985521              0.0000000        
   1011.1069716              0.0000000        


    392.44359273             0.0000000        
    173.21702132             0.0000000        
S   15   1.00
 11713823.0080000            0.0000000        
 1755253.3979000             0.0000000        
 399717.4192400              0.0000000        


 113285.7926000              0.0000000        
  36977.2052930              0.0000000        
  13355.0365800              0.0000000        
   5210.9012988              0.0000000        
   2162.1137020              0.0000000        


    943.29291023             0.0000000        
    429.20724331             0.0000000        
    202.40720840             0.0000000        
   3260.4985521              0.73091509287E-02      
   1011.1069716              0.74040355445E-01      


    392.44359273             0.35414962222    
    173.21702132             0.80188286115
......

Please note that there are many lines containing 0.000000 in the basis set.
I omit them (of course in the meantime changing "S 15" to "S 11" and "S 4" respectively), and find that all the results are the same, except that more  "primitive gaussians" are used when these lines are in the basis set.

My question is, what we will benifit from this format including these lines?
Will we use more memory for this format because of more "primitive gaussians" are used?
Or it is exactly the same for the two formats (with and without zero lines)?

Thank you very much!

Best regards,
Zhu


--
------------------
Zhu feng
Department of Physics,
Anhui University, Hefei, China

------=_Part_51519_30069850.1223340283583-- From owner-chemistry@ccl.net Tue Oct 7 21:24:01 2008 From: "Geoffrey Hutchison geoffh+__pitt.edu" To: CCL Subject: CCL: Summary: Inverse Molecular Design Methods Message-Id: <-37863-081007200406-19670-IbHNnayGGD5WxZHRsL75lQ:server.ccl.net> X-Original-From: Geoffrey Hutchison Content-type: multipart/alternative; boundary=Apple-Mail-9-300289304 Date: Tue, 07 Oct 2008 19:03:45 -0400 MIME-version: 1.0 (Apple Message framework v929.2) Sent to CCL by: Geoffrey Hutchison [geoffh+-x-pitt.edu] --Apple-Mail-9-300289304 Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Content-Transfer-Encoding: 7bit I heard several responses to my request for some "inverse design" methods. I was particularly interested in so-called alchemical approaches, but I'm aware of the great work in fragment databases, "inverse QSAR," and some genetic algorithm approaches too. Work by Bruce Tidor and co-workers at MIT for designing "optimal" electrostatic binding to targets: * Optimization of Electrostatic Binding Free Energy. L.-P. Lee and B. Tidor. J. Chem. Phys. 106: 8681-8690 (1997). * Electrostatic Specificity in Molecular Ligand Design. E. Kangas and B. Tidor. J. Chem. Phys. 112: 9120-9131 (2000). * Charge Optimization Leads to Favorable Electrostatic Binding Free Energy.. E. Kangas and B. Tidor. Phys. Rev. E 59: 5958-5961 (1999). > This method has also applied by other groups including Purisima and > McCammon. > Secondly, the computational protein design field is a great example > of the inverse design paradigm. Look up papers by Steve Mayo, Homme > Hellinga, David Baker and Bruce Tidor among others, for interesting > applications here. If you look in the following paper, you should > be able to find most of the key references: > > Rational design of new binding specificity by simultaneous > mutagenesis of calmodulin and a target peptide. D. F. Green, A. T. > Dennis, P. S. Fam, B. Tidor, and A. Jasanoff. Biochemistry 45: > 12547-12559 (2006). Closer to my line of work (materials): * Anatole von Lilienfeld & Mark Tuckerman: J Chem. Theory Comput. (2007) 3, p. 1083 J. Chem. Phys. (2006) 125 p. 154104 PRL (2005) 95, 153002 * David Beratan and Weitao Yang JACS (2006) 128, 3228 JPC A (2007) 111, 176 I'm sure there are others... I'll continue to look and likely write something up on my website. Thanks so much to Shahar Keinan, David Green, and Jaydeep Bardhan who helped out with some pointers. Best regards, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh[-]pitt.edu web: http://hutchison.chem.pitt.edu/ --Apple-Mail-9-300289304 Content-Type: text/html; charset=US-ASCII Content-Transfer-Encoding: quoted-printable
I heard several responses = to my request for some "inverse design" methods. I was particularly = interested in so-called alchemical approaches, but I'm aware of the = great work in fragment databases, "inverse QSAR," and some genetic = algorithm approaches too.


Work = by Bruce Tidor and co-workers at MIT for designing "optimal" = electrostatic binding to targets:
* = Optimization of Electrostatic Binding Free Energy. L.-P. Lee and B. = Tidor.  J. Chem. Phys. 106: 8681-8690 = (1997).
* Electrostatic Specificity in Molecular = Ligand Design. E. Kangas and B. Tidor.  J. Chem. Phys. 112: = 9120-9131 (2000).
* Charge Optimization Leads to Favorable = Electrostatic Binding Free Energy.. E. Kangas and B. Tidor.  Phys. = Rev. E 59: 5958-5961 = (1999).

This method has also applied by other groups including Purisima = and McCammon.

Secondly, the = computational protein design field is a great example of the inverse = design paradigm.  Look up papers by Steve Mayo, Homme Hellinga, = David Baker and Bruce Tidor among others, for interesting applications = here.  If you look in the following paper, you should be able to = find most of the key references:

Rational design of new binding = specificity by simultaneous mutagenesis of calmodulin and a target = peptide. D. F. Green, A. T. Dennis, P. S. Fam, B. Tidor, and A. = Jasanoff.  Biochemistry 45: 12547-12559 = (2006).

Closer to my line = of work (materials):

* Anatole von = Lilienfeld & Mark Tuckerman:
   =  J Chem. Theory Comput. (2007) 3, p. 1083
   =  J. Chem. Phys. (2006) 125 p. 154104
   =  PRL (2005) 95, 153002
* = David Beratan and Weitao Yang
   JACS = (2006) 128, 3228
   JPC A (2007) 111, = 176

I'm sure there are = others... I'll continue to look and likely write something up on my = website.

Thanks so much to = Shahar Keinan, David Green, and Jaydeep Bardhan who helped out with some = pointers.

Best = regards,
-Geoff

geoffh[-]pitt.edu
web: http://hutchison.chem.pitt.edu/
=

= --Apple-Mail-9-300289304-- From owner-chemistry@ccl.net Tue Oct 7 22:35:01 2008 From: "Kirk Peterson kipeters-.-wsu.edu" To: CCL Subject: CCL:G: [g03] Format of basis set Message-Id: <-37864-081007220538-16639-+pru4QUvyy939xBuOOOiAQ^^^server.ccl.net> X-Original-From: Kirk Peterson Content-Type: multipart/alternative; boundary=Apple-Mail-20-308738093 Date: Tue, 7 Oct 2008 18:24:33 -0700 Mime-Version: 1.0 (Apple Message framework v929.2) Sent to CCL by: Kirk Peterson [kipeters(a)wsu.edu] --Apple-Mail-20-308738093 Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Content-Transfer-Encoding: 7bit Dear Zhu, it will definitely be advantageous to remove those lines with contraction coefficients of exactly zero as you mention. This looks like a bug in the EMSL basis set exchange where it is attempting to convert general contractions to segmented ones. The integral program probably will probably not recognize that some primitives in a contraction have zero coefficients, so it will calculate integrals over all these primitives. This will translate into a lot more CPU required (of course the final answers should be identical). You should report this problem on the EMSL basis set website. What basis is this? The exponents look very strange which makes think there's another (more severe) error going on here. regards, Kirk Peterson On Oct 6, 2008, at 5:44 PM, feng zhu zhufengcc|,|gmail.com wrote: > Dear All CCLs, > > I download the basis set for Ke from https://bse.pnl.gov/bse/portal > It looks like below: > Kr 0 > S 15 1.00 > 11713823.0080000 0.56915790360E-05 > 1755253.3979000 0.44214471278E-04 > 399717.4192400 0.23227813842E-03 > 113285.7926000 0.97973661050E-03 > > > 36977.2052930 0.35537627541E-02 > 13355.0365800 0.11468673282E-01 > 5210.9012988 0.33241627469E-01 > 2162.1137020 0.85620725674E-01 > > > 943.29291023 0.18708766876 > 429.20724331 0.31497583326 > 202.40720840 0.33406191042 > 3260.4985521 0.0000000 > 1011.1069716 0.0000000 > > > 392.44359273 0.0000000 > 173.21702132 0.0000000 > S 15 1.00 > 11713823.0080000 0.0000000 > 1755253.3979000 0.0000000 > 399717.4192400 0.0000000 > > > 113285.7926000 0.0000000 > 36977.2052930 0.0000000 > 13355.0365800 0.0000000 > 5210.9012988 0.0000000 > 2162.1137020 0.0000000 > > > 943.29291023 0.0000000 > 429.20724331 0.0000000 > 202.40720840 0.0000000 > 3260.4985521 0.73091509287E-02 > 1011.1069716 0.74040355445E-01 > > > 392.44359273 0.35414962222 > 173.21702132 0.80188286115 > ...... > > Please note that there are many lines containing 0.000000 in the > basis set. > I omit them (of course in the meantime changing "S 15" to "S 11" and > "S 4" respectively), and find that all the results are the same, > except that more "primitive gaussians" are used when these lines > are in the basis set. > > My question is, what we will benifit from this format including > these lines? > Will we use more memory for this format because of more "primitive > gaussians" are used? > Or it is exactly the same for the two formats (with and without zero > lines)? > > Thank you very much! > > Best regards, > Zhu > > > -- > ------------------ > Zhu feng > Department of Physics, > Anhui University, Hefei, China > --Apple-Mail-20-308738093 Content-Type: text/html; charset=US-ASCII Content-Transfer-Encoding: quoted-printable Dear Zhu,

it = will definitely be advantageous to remove those lines with contraction = coefficients of exactly zero as you mention.  This
looks = like a bug in the EMSL basis set exchange where it is attempting to = convert general contractions to
segmented ones.  The = integral program probably will probably not recognize that some = primitives in a
contraction have zero coefficients, so it will = calculate integrals over all these primitives. This = will
translate into a lot more CPU required (of course the = final answers should be identical).  You should = report
this problem on the EMSL basis set = website.

What basis is this?  The = exponents look very strange which makes think there's another (more = severe) error going on = here.

regards,

Kirk = Peterson


On Oct 6, = 2008, at 5:44 PM, feng zhu zhufengcc|,|gmail.com wrote:

Dear All = CCLs,

I download the basis set for Ke from https://bse.pnl.gov/bse/portal
It looks like = below:
Kr     0 
S   15   1.00
 11713823.0080000           =
 0.56915790360E-05      
 1755253.3979000             =
0.44214471278E-04      
 399717.4192400              =
0.23227813842E-03      
 113285.7926000              =
0.97973661050E-03      


  36977.2052930              0.35537627541E-02      
  13355.0365800  =
            0.11468673282E-01      
   5210.9012988              =
0.33241627469E-01      
   2162.1137020              =
0.85620725674E-01      


    943.29291023             0.18708766876    
    429.20724331       =
      0.31497583326    
    202.40720840             0.33406191042    =

   3260.4985521              0.0000000        
   1011.1069716    =
          0.0000000        


    392.44359273             0.0000000        
    173.21702132       =
      0.0000000        
S   15   1.00
 11713823.0080000            =
0.0000000        
 1755253.3979000             0.0000000        
 =
399717.4192400              0.0000000        


 113285.7926000              0.0000000        
  36977.2052930        =
      0.0000000        
  13355.0365800              0.0000000        =

   5210.9012988              0.0000000        
   2162.1137020    =
          0.0000000        


    943.29291023             0.0000000        
    429.20724331       =
      0.0000000        
    202.40720840             0.0000000        =

   3260.4985521              0.73091509287E-02      
   =
1011.1069716              0.74040355445E-01      


    392.44359273             0.35414962222    
    173.21702132       =
      0.80188286115
......

Please note that there are = many lines containing 0.000000 in the basis set.
I omit them (of = course in the meantime changing "S 15" to "S 11" and "S 4" = respectively), and find that all the results are the same, except that = more  "primitive gaussians" are used when these lines are in the = basis set.

My question is, what we will benifit from this format = including these lines?
Will we use more memory for this format = because of more "primitive gaussians" are used?
Or it is exactly the = same for the two formats (with and without zero lines)?

Thank = you very much!

Best regards,
Zhu


-- =
------------------
Zhu feng
Department of Physics,
Anhui = University, Hefei, = China


= --Apple-Mail-20-308738093--