From owner-chemistry@ccl.net Fri May 20 03:01:00 2011 From: "Kunal Roy kunalroy_in[A]yahoo.com" To: CCL Subject: CCL: New review article on metrics of validation of QSAR models Message-Id: <-44709-110520025841-7808-k3+WSptwuVJkeLT9rOkTpw/./server.ccl.net> X-Original-From: Kunal Roy Content-Type: multipart/alternative; boundary="0-848361760-1305874709=:3930" Date: Fri, 20 May 2011 12:28:29 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: Kunal Roy [kunalroy_in/./yahoo.com] --0-848361760-1305874709=:3930 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable ****Apology for multiple posting**** =A0 New review article on metrics of validation of QSAR models:=20 =A0 Roy K, Mitra I, On various metrics used for validation of predictive QSAR m= odels with applications in virtual screening and focused library design. Co= mb Chem High Throughput Screen, 14, 2011, 450-474,=20 http://www.benthamdirect.org/pages/content.php?CCHTS/2011/00000014/00000006= /0003A.SGM =A0 =A0 This review focuses on various metrics used for validation of predictive QS= AR models with an overview of application of QSARs in virtual screening and= focused library design Kunal Roy, Ph.D.=20 Associate Professor, Drug Theoretics and Cheminformatics Lab, Department of= Pharmaceutical Technology,=20 JADAVPUR UNIVERSITY, Kolkata 700 032 (INDIA) Email : kroy|pharma.jdvu.ac.in , kunalroy_in|yahoo.com=A0=A0 URL :=A0=A0 http://sites.google.com/site/kunalroyindia/=A0, http://www.jadu= niv.edu.in/profile.php?uid=3D550=A0=A0 =A0 =A0 --0-848361760-1305874709=:3930 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
****Apology for multi= ple posting****
 
New review article on metrics of validation of QSAR models:<= /STRONG>
 
Roy K, Mitra I, On various metrics used for validation of predicti= ve QSAR models with applications in virtual screening and focused library d= esign. Comb Chem High Throughput Screen, 14, 2011= , 450-474,

http://www.benthamdirect.org/pages/content.php?CCHTS/2011/000= 00014/00000006/0003A.SGM  

 
This r= eview focuses on various metrics used for validation of predictive QSAR mod= els with an overview of application of QSARs in virtual screening and focus= ed library design

Kunal Roy, Ph.D.
<= EM>Associate Professor, Drug Theoretics and Cheminformatics Lab, Depar= tment of Pharmaceutical Technology,
JADAVPUR UNIVERSITY, Kolkata 700 032 (INDIA)
<= /B> 
 
--0-848361760-1305874709=:3930-- From owner-chemistry@ccl.net Fri May 20 05:12:00 2011 From: "Pedro Silva pedros%a%ufp.edu.pt" To: CCL Subject: CCL: New review article on metrics of validation of QSAR models Message-Id: <-44710-110520045918-24239-g2Rn+p48ILQb8jVRdekmoQ=server.ccl.net> X-Original-From: Pedro Silva Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 20 May 2011 09:59:10 +0100 MIME-Version: 1.0 Sent to CCL by: Pedro Silva [pedros(a)ufp.edu.pt] Dear Dr. Kunal Roy, Ten days ago, you already "advertised" a new paper of yours on CCL. I did not speak out then, considering it "a rookie's mistake". Today's posting establishes an unwelcome pattern. If every member posted such a "message" every time they get a new paper out, CCL would soon be drowned in manuscript advertising. I do not intend to start a flame war, but I believe these "messages" should be considered spam and not posted to CCL subscribers, unless they describe new releases of commonly used programs/servers. Unfortunately, I am sure the workload of the good people who run CCL is already too heavy, and an increase in their moderation burden would be unworkable. Maybe banning would be more workable. Pedro Silva PS: If you think you should "Apologize for multiple posting", then refrain from multiple posting. -- Pedro J. Silva Associate Professor Universidade Fernando Pessoa Porto - Portugal http://www2.ufp.pt/~pedros/science/science.htm From owner-chemistry@ccl.net Fri May 20 06:33:00 2011 From: "zborowsk-.-chemia.uj.edu.pl" To: CCL Subject: CCL: New review article on metrics of validation of QSAR models Message-Id: <-44711-110520063045-24075-DPZiv7JIofsr63Ied2eyNQ%a%server.ccl.net> X-Original-From: zborowsk*chemia.uj.edu.pl Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Fri, 20 May 2011 12:30:29 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: zborowsk++chemia.uj.edu.pl I wanted to write that when I publish something I inform you too But now I want only support prof Silva > > Sent to CCL by: Pedro Silva [pedros(a)ufp.edu.pt] > Dear Dr. Kunal Roy, > > Ten days ago, you already "advertised" a new paper of yours on CCL. I > did not speak out then, considering it "a rookie's mistake". Today's > posting establishes an unwelcome pattern. If every member posted such > a "message" every time they get a new paper out, CCL would soon be > drowned in manuscript advertising. I do not intend to start a flame > war, but I believe these "messages" should be considered spam and not > posted to CCL subscribers, unless they describe new releases of > commonly used programs/servers. Unfortunately, I am sure the workload > of the good people who run CCL is already too heavy, and an increase > in their moderation burden would be unworkable. Maybe banning would be > more workable. > > Pedro Silva > > PS: If you think you should "Apologize for multiple posting", then > refrain from multiple posting. > > > > -- > Pedro J. Silva > Associate Professor > Universidade Fernando Pessoa > Porto - Portugal > http://www2.ufp.pt/~pedros/science/science.htm> > > -- http://www.youtube.com/watch?v=EXh0PT2lovk&feature=channel Krzysztof K. Zborowski Faculty of Chemistry Jagiellonian University 3 Ingardena Street 30-060 Krakow Poland phone: +48(12)632-4888 ext. 2064 or 2067 fax: +48(12)634-05-15 email: zborowsk%chemia.uj.edu.pl gg 3817259 skype kzys70 www.chemia.uj.edu.pl/~zborowsk From owner-chemistry@ccl.net Fri May 20 08:18:00 2011 From: "Gerard Pujadas gerard.pujadas#,#gmail.com" To: CCL Subject: CCL: New review article on metrics of validation of QSAR models Message-Id: <-44712-110520081646-20403-MctfRSDE1MLE+QRot1W6wg]![server.ccl.net> X-Original-From: Gerard Pujadas Content-Type: multipart/alternative; boundary=00151750e4d0eaba3104a3b4175f Date: Fri, 20 May 2011 14:16:37 +0200 MIME-Version: 1.0 Sent to CCL by: Gerard Pujadas [gerard.pujadas*gmail.com] --00151750e4d0eaba3104a3b4175f Content-Type: text/plain; charset=ISO-8859-1 Dear Prof. Silva, Ten days ago, you already "advertised" a new paper of yours on CCL. I > did not speak out then, considering it "a rookie's mistake". Today's > posting establishes an unwelcome pattern. If every member posted such > a "message" every time they get a new paper out, CCL would soon be > drowned in manuscript advertising. I do not intend to start a flame > war, but I believe these "messages" should be considered spam and not > posted to CCL subscribers, unless they describe new releases of > commonly used programs/servers. Unfortunately, I am sure the workload > of the good people who run CCL is already too heavy, and an increase > in their moderation burden would be unworkable. Maybe banning would be > more workable. > > Prof. Kunal Roy is a recognized expert in the field of QSAR with significant contributions to the QSAR validation topic. According to his web page ( http://www.jaduniv.edu.in/viewAllDataPopUpProfile.php?page=1&uid=552&pageName=Journalpaperspublished) he has been the corresponding author of 23 scientific papers since 2010 and only a significant part of them has been announced by the author to the CCL list: Partha Pratim Roy , Somnath Paul , Indrani Mitra and Kunal Roy * Article: On Two Novel Parameters for Validation of Predictive QSAR Models Molecules 2009, 14(5), 1660-1701 On further application of rm2 as a metric for validation of QSAR models Mitra I, Roy PP, Kar S, Ojha P, Roy K J Chemometrics, 24, 2010, 22-33 Roy K, Mitra I, On various metrics used for validation of predictive QSAR models with applications in virtual screening and focused library design. Comb Chem High Throughput Screen, 14, 2011, 450-474 In my opinion, these three contributions are of enough general interest to be announced at CCL but, in any case, we are always free to decide if we want to read or not one e-mail. In any case, I would like to encourage CCL readers to use the list to inform of publications they consider of general interest because this way is, usually, faster for disseminating the information than advertisements from PubMed or Current Contents. Best Gerard -- Gerard Pujadas http://bioquimica.urv.cat/eng/fitxa.jsp?id=22 Nutrigenomics Research Group phone +34 977 55 (9565) Biochemistry and Biotechnology Department Office 106, Building N4, Campus Sescelades Universitat Rovira i Virgili Tarragona, Catalonia --00151750e4d0eaba3104a3b4175f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Prof. Silva,


Ten days ago, you already "advertised" a new paper of yours on CC= L. I
did not speak out then, considering it "a rookie's mistake". = Today's
posting establishes an unwelcome pattern. If every member posted such
a "message" every time they get a new paper out, CCL would soon b= e
drowned in manuscript advertising. I do not intend to start a flame
war, but I believe these "messages" should be considered spam and= not
posted to CCL subscribers, unless they describe new releases of
commonly used programs/servers. Unfortunately, I am sure the workload
of the good people who run CCL is already too heavy, and an increase
in their moderation burden would be unworkable. Maybe banning would be
more workable.


Prof. Kunal Roy is a recognized ex= pert in the field of QSAR with significant contributions to the QSAR valida= tion topic. According to his web page (http://www.jaduniv.edu.in/viewAllDataPopU= pProfile.php?page=3D1&uid=3D552&pageName=3DJournalpaperspublished) he has been the corresponding author of 23 scientific papers since 2010= and only a significant part of them has been announced by the author to th= e CCL list:

Partha Pratim Roy , Somnath Paul , In= drani Mitra=A0 and Kunal Roy * Article: On Two Novel Parameters for Validat= ion of Predictive QSAR Models Molecules 2009, 14(5), 1660-1701

On fu= rther application of rm2 as a metric for validation of QSAR models=A0 Mitra= I, Roy PP, Kar S, Ojha P, Roy K=A0 J Chemometrics, 24, 2010, 22-33

Roy K, Mitra I, On various metrics used for validation of predictive QS= AR models with applications in virtual screening and focused library design= . Comb Chem High Throughput Screen, 14, 2011, 450-474

In my opinion, these three contributions are of enough general interest= to be announced at CCL but, in any case, we are always free to decide if w= e want to read or not one e-mail. In any case, I would like to encourage CC= L readers to use the list to inform of publications they consider of genera= l interest because this way is, usually, faster for disseminating the infor= mation than advertisements from PubMed or Current Contents.


Best

Gerard

--
Gerard Pujadas
http://bioqui= mica.urv.cat/eng/fitxa.jsp?id=3D22
Nutrigenomics Research Group
p= hone +34 977 55 (9565)
Biochemistry and Biotechnology Department
Office 106, Building N4, Campus Sescelades
Universitat Rovira i Virgili<= br>Tarragona, Catalonia
--00151750e4d0eaba3104a3b4175f-- From owner-chemistry@ccl.net Fri May 20 09:44:00 2011 From: "Steen Hammerum steen.:.kiku.dk" To: CCL Subject: CCL: New review article on metrics of validation of QSAR models Message-Id: <-44713-110520092903-1796-R6JHXCXeuJQIGKrTkF2gdg++server.ccl.net> X-Original-From: Steen Hammerum Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Fri, 20 May 2011 15:28:45 +0200 (METDST) MIME-Version: 1.0 Sent to CCL by: Steen Hammerum [steen^_^kiku.dk] Dear Professor Silva - thank you for voicing these sentiments. We all consider our work significant, maybe even important, but to advertise our papers on CCL is completely inappropriate, if for no other reason because of the volume it would generate. Most papers are of interest to a select subgroup of CCL readers, and without much interest to most. That applies also to the paper that started this thread, no matter how towering figures the authors may be within their speciality. Steen Hammerum Department of Chemistry University of Copenhagen > > > Sent to CCL by: Pedro Silva [pedros(a)ufp.edu.pt] > Dear Dr. Kunal Roy, > > Ten days ago, you already "advertised" a new paper of yours on CCL. I > did not speak out then, considering it "a rookie's mistake". Today's > posting establishes an unwelcome pattern. If every member posted such > a "message" every time they get a new paper out, CCL would soon be > drowned in manuscript advertising. I do not intend to start a flame > war, but I believe these "messages" should be considered spam and not > posted to CCL subscribers, unless they describe new releases of > commonly used programs/servers. Unfortunately, I am sure the workload > of the good people who run CCL is already too heavy, and an increase > in their moderation burden would be unworkable. Maybe banning would be > more workable. > > Pedro Silva > > PS: If you think you should "Apologize for multiple posting", then > refrain from multiple posting. > > > > -- > Pedro J. Silva > Associate Professor > Universidade Fernando Pessoa > Porto - Portugal > http://www2.ufp.pt/~pedros/science/science.htm> > > -- Steen Hammerum steen**kiku.dk Department of Chemistry (+45) 35 32 02 08 University of Copenhagen, Denmark fax: (+45) 35 32 02 12 From owner-chemistry@ccl.net Fri May 20 10:18:00 2011 From: "Chido chido.mpamhanga*_*gmail.com" To: CCL Subject: CCL: Senior Data Curator: IUPHAR Database Message-Id: <-44714-110520094932-22875-EtCAPjz+f9WC7hfUeBdJ7w!=!server.ccl.net> X-Original-From: Chido Content-Type: multipart/alternative; boundary=20cf3054a46152351904a3b562d6 Date: Fri, 20 May 2011 14:49:00 +0100 MIME-Version: 1.0 Sent to CCL by: Chido [chido.mpamhanga_+_gmail.com] --20cf3054a46152351904a3b562d6 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Centre for Cardiovascular Science, University of Edinburgh Senior Data Curator: IUPHAR Database We wish to recruit a senior data curator to assist with the development of the IUPHAR Database (http://www.iuphar-db.org) and the British Pharmacological Society =1CGuide to Receptors and Channels=1D (http://www.brjpharmacol.org/view/0/GRAC.html). You should hold a PhD or equivalent in Pharmacology, Medicinal Chemistry or a related discipline together with relevant experience in bioinformatics or chemoinformatics. Based in the Queen's Medical Research Institute, you will work independently on a day-to-day basis but in close contact with Professor Tony Harmar, with the database developer and in liaison with IUPHAR and BPS. Informal enquiries should be made to Prof Harmar (Email tony.harmar at ed.ac.uk Tel. 0131 242 6693). For further information and to apply, see http://bit.ly/kDl7mu). Closing date is 22nd June. This post is fixed term until 31st July 2012 with possibility of extension should further funding be obtained. --20cf3054a46152351904a3b562d6 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable 
Centre for Cardiovascular Science, University of Edinburgh
Senior D=
ata Curator: IUPHAR Database

We wish to recruit a senior data curato=
r to assist with the development of the IUPHAR Database (http://www.iuphar-db.org) and the British Pharmacol=
ogical Society =1CGuide to Receptors and Channels=1D (http://www.brjpharmacol.org/view/0/GRAC=
.html). You should hold a PhD or equivalent in Pharmacology, Medicinal =
Chemistry or a related discipline together with relevant experience in bioi=
nformatics or chemoinformatics. Based in the Queen's Medical Research I=
nstitute, you will work independently on a day-to-day basis but in close co=
ntact with Professor Tony Harmar, with the database developer and in liaiso=
n with IUPHAR and BPS. Informal enquiries should be made to Prof Harmar (Em=
ail tony.harmar at ed.ac.uk Tel. 0131 242 6693).


For further information and to apply, see http://bit.ly/kDl7mu). 

Closing date is 22nd June.

Th=
is post is fixed term until 31st July 2012 with possibility of extension sh=
ould further funding be obtained.
--20cf3054a46152351904a3b562d6-- From owner-chemistry@ccl.net Fri May 20 11:36:00 2011 From: "Sanjay Bharathwaj computationalchemist()gmail.com" To: CCL Subject: CCL: Software to Cleave a specified Surface from the Unit Cell Message-Id: <-44715-110520113451-15628-Shx9bntbhqPTdUCEgjUKdg],[server.ccl.net> X-Original-From: Sanjay Bharathwaj Content-Type: multipart/alternative; boundary=485b397dcccd746b1904a3b6dc25 Date: Fri, 20 May 2011 17:34:44 +0200 MIME-Version: 1.0 Sent to CCL by: Sanjay Bharathwaj [computationalchemist-#-gmail.com] --485b397dcccd746b1904a3b6dc25 Content-Type: text/plain; charset=ISO-8859-1 Dear Collegues, I wish to ask you about the free wares that could help me in cleaving the surface from the given unit cell. I know about material studio, but that's not free. Does any one know about the softwares that can do this job and get it for free. Thanks in advance. Dr. Sanjay -- Regards, Dr. Sanjay Bharathwaj Kumar, Dharmendra Institute of Technology, India. --485b397dcccd746b1904a3b6dc25 Content-Type: text/html; charset=ISO-8859-1 Dear Collegues,

I wish to ask you about the free wares that could
help me in cleaving the surface from the given unit cell.

I know about material studio, but that's not free.
Does any one know about the softwares that can do this job
and get it for free.

Thanks in advance.
Dr. Sanjay


--
Regards,
Dr. Sanjay Bharathwaj Kumar,
Dharmendra Institute of Technology,
India.
--485b397dcccd746b1904a3b6dc25-- From owner-chemistry@ccl.net Fri May 20 12:10:01 2011 From: "Tristan Youngs t.youngs++qub.ac.uk" To: CCL Subject: CCL: Software to Cleave a specified Surface from the Unit Cell Message-Id: <-44716-110520120913-1599-bi6kzTj9cLRdb47oYRBG3w^_^server.ccl.net> X-Original-From: Tristan Youngs Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 20 May 2011 17:10:34 +0100 MIME-Version: 1.0 Sent to CCL by: Tristan Youngs [t.youngs{:}qub.ac.uk] You may try out Aten (www.projectaten.net). As well as offering standard select/cut tools, there is also the ability to select along Miller planes in order to cleave periodic models. Cheers, Tris. On 20/05/11 16:34, Sanjay Bharathwaj computationalchemist()gmail.com wrote: > Dear Collegues, > > I wish to ask you about the free wares that could > help me in cleaving the surface from the given unit cell. > > I know about material studio, but that's not free. > Does any one know about the softwares that can do this job > and get it for free. > > Thanks in advance. > Dr. Sanjay > > > -- > Regards, > Dr. Sanjay Bharathwaj Kumar, > Dharmendra Institute of Technology, > India. -- Dr. T. Youngs (t.youngs()qub.ac.uk) Atomistic Simulation Centre Old Physics Building Queen's University Belfast Belfast, BT7 1NN, N.I. From owner-chemistry@ccl.net Fri May 20 13:46:00 2011 From: "Steven Trohalaki steven.trohalaki-*-wpafb.af.mil" To: CCL Subject: CCL: voronoi tessellation method for free volume in polymers Message-Id: <-44717-110520134245-29844-/g4lbIUpJUNpwVImvZRD1Q * server.ccl.net> X-Original-From: "Steven Trohalaki" Date: Fri, 20 May 2011 13:42:44 -0400 Sent to CCL by: "Steven Trohalaki" [steven.trohalaki*wpafb.af.mil] Years ago when Accelrys was Biosym/MSI, one could determine the free volume distribution in bulk polymer models using the Voronoi Tessellation method (developed by Suter, et al., at MIT and ETH) within Insight. This method is not available in Materials Studio (Accelrys), so I wonder if anyone still has it, and would be willing to make it available. Thanks. From owner-chemistry@ccl.net Fri May 20 16:10:01 2011 From: "Close, David M. CLOSED^^^mail.etsu.edu" To: CCL Subject: CCL: CCL policy on announcing new publication Message-Id: <-44718-110520133125-31638-g+bOJAsHUFZje39bJoPcpg%x%server.ccl.net> X-Original-From: "Close, David M." Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_9D6140C35ABD534F9C463F41FC3A9CC141FE78BBetsums2etsuedu_" Date: Fri, 20 May 2011 17:31:25 +0000 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED_-_mail.etsu.edu] --_000_9D6140C35ABD534F9C463F41FC3A9CC141FE78BBetsums2etsuedu_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable To CCL: Yes I agree that the CCL discussion group is no place to announce new pub= lications. I expect that most subscribers are already on ASAP journal page= s, so this seems entirely redundant. I see one downside here however. If = it is agreed not to do this, then there is still the burden on Jon to act a= s a moderator. This is not fair, and so I think the group should agree to = this, and then announce that this is CCL policy. Afterwards anyone who sen= ds in such a post should be banned. Regards, Dave Close. --_000_9D6140C35ABD534F9C463F41FC3A9CC141FE78BBetsums2etsuedu_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

To CCL:

  Yes I agree that the= CCL discussion group is no place to announce new publications.  I exp= ect that most subscribers are already on ASAP journal pages, so this seems = entirely redundant.  I see one downside here however.  If it is a= greed not to do this, then there is still the burden on Jon to act as a mod= erator.  This is not fair, and so I think the group should agree to th= is, and then announce that this is CCL policy.  Afterwards anyone who = sends in such a post should be banned.

  Regards, Dave Close.

 

 

= --_000_9D6140C35ABD534F9C463F41FC3A9CC141FE78BBetsums2etsuedu_-- From owner-chemistry@ccl.net Fri May 20 16:45:00 2011 From: "Igor Filippov Contr igorf*_*helix.nih.gov" To: CCL Subject: CCL: New review article on metrics of validation of QSAR models Message-Id: <-44719-110520105047-14725-4VcqPwsuMzSIxtRy8SKCoQ---server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="UTF-8" Date: Fri, 20 May 2011 10:44:32 -0400 MIME-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf~~helix.nih.gov] > In any case, I would like to encourage CCL readers to use the list to > inform of publications they consider of general interest because this > way is, usually, faster for disseminating the information than > advertisements from PubMed or Current Contents. Please oh, please I hope nobody will take you up on that offer. I get so many "informative" announcements during a single day already that a significant portion of my time is spent hitting "Delete" key. Make your paper easy to find, publish it in an open access journal - absolutely yes. If I want it, I will find it. Posting announcements on multiple mail lists (CCL, QSAR, etc.) - thanks but no thanks. I personally think this is just very presumptuous to feel that your paper warrants a general announcement to everyone. Best, Igor From owner-chemistry@ccl.net Fri May 20 17:20:00 2011 From: "Zhen liuzhencc-.-gmail.com" To: CCL Subject: CCL:G: a strange error encountered in the QST3 calculations. Message-Id: <-44720-110520105751-20186-gJ86XGl4Y+BYEU28mnDFiA++server.ccl.net> X-Original-From: "Zhen" Content-Language: zh-cn Content-Type: multipart/alternative; boundary="----=_NextPart_000_000D_01CC1741.5698F680" Date: Fri, 20 May 2011 22:57:42 +0800 MIME-Version: 1.0 Sent to CCL by: "Zhen" [liuzhencc.:.gmail.com] This is a multipart message in MIME format. ------=_NextPart_000_000D_01CC1741.5698F680 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear CCLers, I encountered a strange error in searching transition states with QST3 methodology. In order to investigate the catalytic behavior of the Z-N catalysts. I set up a cluster model with the active center supported on a surface. The support part was set to frozen during the optimizations. Everything goes fine except for the section of "Modifications to 3rd set of coordinates" in the QST3 calculations. The job terminated with the error messages, " WANTED AN INTEGER AS INPUT. FOUND A STRING AS INPUT. 1 f" Part of the input is shown below and the full input and output file are also attached. ----- %chk=test3.chk %mem=6gb %nprocshared=8 #P ub3lyp/lanl2dz SCF=(MaxCycle=200) OPT=(ModRedundant,QST3,NoOptReactant,NoOptProduct) guess=always gfinput Reactant 0 2 Cartesian coordinates of the reactant (43 atoms) 1 f . 22 f Product 0 2 Cartesian coordinates of the product (43 atoms) 1 f . 22 f transition state 0 2 Cartesian coordinates of transition state (43 atoms) 1 f . 22f ---- Am I missed some basic points in my calculations? Or this is a bug in the Gaussian package? Please show me some points on this problem. Your suggestions would greatly appreciated. Thank you in advance! Sincerely yours, ZHEN from East China University of Science and technology. liuzhencc * gmail.com ------=_NextPart_000_000D_01CC1741.5698F680 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear CCLers,

 

I = encountered a strange error in searching transition states with QST3 = methodology.

In order to investigate = the catalytic behavior of the Z-N catalysts.

I set = up a cluster model with the active center supported on a surface. =

The support part was set to frozen = during the optimizations.

Everything = goes fine except for the section of “Modifications to 3rd set of = coordinates” in the QST3 calculations.

The job terminated with the error messages,

 

“ WANTED AN INTEGER AS = INPUT.

    FOUND A STRING AS = INPUT.

    1  = f”

 

Part of the input is shown below and the full input = and output file are also attached.

-----

%chk=3Dtest3.chk

%mem=3D6gb

%nprocshared=3D8

#P = ub3lyp/lanl2dz SCF=3D(MaxCycle=3D200) = OPT=3D(ModRedundant,QST3,NoOptReactant,NoOptProduct) guess=3Dalways = gfinput

 

Reactant

 

0 = 2

Cartesian coordinates of the = reactant (43 atoms)

 

1 = f

…

22 f

 

Product

 

0 = 2

Cartesian coordinates of the = product (43 atoms)

 

1 = f

…

22 f

 

transition = state

 

0 2

Cartesian = coordinates of transition state (43 atoms)

 

1 = f

…

22f

 

----

 

Am I missed = some basic points in my calculations? Or this is a bug in the Gaussian = package?

Please show me some = points on this problem. Your = suggestions would greatly appreciated.

 

Thank you in = advance!

 

Sincerely yours,

 

ZHEN from = East China University of Science and technology.

liuzhencc * gmail.com

 

 

------=_NextPart_000_000D_01CC1741.5698F680-- From owner-chemistry@ccl.net Fri May 20 17:56:00 2011 From: "Shirley Peng speng.:.chemcomp.com" To: CCL Subject: CCL: QuantumBio and CCG Release the DivCon Discovery Suite for MOE Message-Id: <-44721-110520113339-14503-eu1NsLLR5OVtozQ9HU8dmg : server.ccl.net> X-Original-From: "Shirley Peng" Date: Fri, 20 May 2011 11:33:38 -0400 Sent to CCL by: "Shirley Peng" [speng!=!chemcomp.com] QuantumBio Inc. and Chemical Computing Group, Inc. Announce the Release of the DivCon Discovery Suite for the Molecular Operating Environment (MOE) State College, PA, May 20, 2011 QuantumBio Inc., a leader in Structure-based and Fragment-based Drug Discovery solutions, based upon their next-generation linear-scaling quantum mechanics (QM) methods, has announced the release of DivCon Discovery Suite 5.0 for the Molecular Operating Environment (MOE) platform from Chemical Computing Group, Inc. (CCG). QuantumBio's DivCon Discovery Suite provides pharmaceutical and biotechnology companies, contract research organizations, and academic groups with the ability to significantly improve accuracy during the virtual screening and lead optimization stages of the drug discovery process, leading to higher quality predictions of candidate lead molecules. Scientists can harness the power of QuantumBios linear-scaling semi-empirical QM algorithms in the Suite to accurately analyze the atomic interactions of large biomolecular complexes consisting of hundreds or even thousands of atoms. These methods are routinely applied to protein/ligand complexes, and recently it has even been successfully applied to more challenging protein/protein systems. Using a combination of CCGs Scientific Vector Language and QuantumBio's proprietary QM toolkit, these methods can now be available within the familiar MOE environment. This collaboration also enhances CCGs product line by adding linear scaling QM methods applicable to NMR chemical shift perturbation prediction, and protein/ligand and protein/protein complex characterization. Lance Westerhoff, General Manager of QuantumBio says, "The MOE environment provides a powerful scientific and visualization toolbox that has the right combination of efficiency, design and raw power necessary to intuitively prepare, monitor, and analyze the large scale QM simulations used by our customers to solve their everyday problems. We feel that the tools provided by MOE and available to our software through this integration significantly increase the accessibility of these highly accurate methods methods that were once only available within specialized academic laboratories. Paul Labute, President and CEO of CCG, added that "We are pleased with the results of our collaboration to combine the strengths of MOE with QuantumBios unique toolkit. The DivCon Discovery Suite provides a technology for protein:ligand scoring using semi-empirical quantum mechanical methods and we feel that the combination with MOE's protein preparation, structural and statistical analysis capabilities will be of great benefit to our customers." He went on to say that We feel that this collaboration with QuantumBio provides an important technological expansion to our product offering and we look forward to collaborating further to maximize the potential of the integration" With the integration in place, QuantumBios QMScore, QM-based Pairwise Energy Decomposition, and Nuclear Magnetic Resonance (NMR) results are easier to analyze and visualize using a mixture of standard MOE graphical user interface elements and new elements added by QuantumBios scientists. Today, a structure can be correctly prepared using familiar MOE tools and plug-ins, visualized using intuitive structure visualization facilities, and QM-characterized in either an interactive or a batch mode. The results of these characterizations can then be analyzed and visualized through the same MOE interface. Please visit http://www.quantumbioinc.com for more information on this integration, on purchasing the MOE plug-ins, and for cited literature involving QuantumBios technologies. About QuantumBio Inc. QuantumBio is a leader in Computer Assisted Drug Design (CADD) and Computer Assisted Molecular Modeling (CAMM), providing a new generation of quantum mechanics solutions to Pharmaceutical, Biotech, Materials and Nanotechnology companies. QuantumBio works with leading pharmaceutical and biotech companies as well as government and academic research organizations to solve problems. About Chemical Computing Group Chemical Computing Group (CCG) is a leading supplier of software solutions for life sciences. From its inception in 1994, CCG has provided state of the art drug discovery applications for pharmaceutical, biotech, and academic research. CCG has a proven track record in scientific innovation, consistently producing releases and upgrades for all their products. CCG's products and services are used by biologists, medicinal chemists and computational chemists throughout the world. CCG is known for its strong collaborative scientific support, maintaining support offices in both Europe and North America. CCG headquarters is in Montreal, Canada. For additional information please contact: QuantumBio Inc. Lance M. Westerhoff, PhD lance- -quantumbioinc.com www.QuantumBioInc.com Chemical Computing Group Inc. Raul Alvarez ralvarez- -chemcomp.com www.chemcomp.com From owner-chemistry@ccl.net Fri May 20 18:45:01 2011 From: "Jim Kress ccl_nospam ~~ kressworks.com" To: CCL Subject: CCL: New review article on metrics of validation of QSAR models Message-Id: <-44722-110520184350-14831-pjuh/hyP8WupL6/v5iqeiA(0)server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 20 May 2011 18:43:24 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam..kressworks.com] Although this will probably result in an avalanche of "publication announcements", I must agree, in toto, with Pedro. Jim Kress > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com/a\ccl.net [mailto:owner- > chemistry+ccl_nospam==kressworks.com/a\ccl.net] On Behalf Of Pedro Silva > pedros%a%ufp.edu.pt > Sent: Friday, May 20, 2011 4:59 AM > To: Kress, Jim > Subject: CCL: New review article on metrics of validation of QSAR > models > > > Sent to CCL by: Pedro Silva [pedros(a)ufp.edu.pt] > Dear Dr. Kunal Roy, > > Ten days ago, you already "advertised" a new paper of yours on CCL. I > did not speak out then, considering it "a rookie's mistake". Today's > posting establishes an unwelcome pattern. If every member posted such > a "message" every time they get a new paper out, CCL would soon be > drowned in manuscript advertising. I do not intend to start a flame > war, but I believe these "messages" should be considered spam and not > posted to CCL subscribers, unless they describe new releases of > commonly used programs/servers. Unfortunately, I am sure the workload > of the good people who run CCL is already too heavy, and an increase > in their moderation burden would be unworkable. Maybe banning would be > more workable. > > Pedro Silva > > PS: If you think you should "Apologize for multiple posting", then > refrain from multiple posting. > > > > -- > Pedro J. Silva > Associate Professor > Universidade Fernando Pessoa > Porto - Portugal > http://www2.ufp.pt/~pedros/science/science.htm> To recover the email address of the author of the message, please > change> From owner-chemistry@ccl.net Fri May 20 23:13:00 2011 From: "richard bonar-law bonarlaw_-_liv.ac.uk" To: CCL Subject: CCL: DFT-D for DZP basis sets Message-Id: <-44723-110520192534-16102-xSl1GVrk6CPe9aOl34LCPw~~server.ccl.net> X-Original-From: "richard bonar-law" Date: Fri, 20 May 2011 19:25:32 -0400 Sent to CCL by: "richard bonar-law" [bonarlaw###liv.ac.uk] Anybody know if DFT-D dispersion parameters for def2_SV(P) have been published, or indeed if its sensible/possible to allow for short range attraction due to BSSE with the DFT-D approach and small basis sets. Thanks Richard From owner-chemistry@ccl.net Fri May 20 23:48:00 2011 From: "Jan Labanowski janl[A]speakeasy.net" To: CCL Subject: CCL: CCL policy on announcing new publication Message-Id: <-44724-110520230051-32645-70BBs2rRWWfr8XfrM1JYMw~~server.ccl.net> X-Original-From: Jan Labanowski Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 20 May 2011 23:00:40 EDT MIME-Version: 1.0 Sent to CCL by: Jan Labanowski [janl.:.speakeasy.net] On Fri May 20 13:31 , 'Close, David M. CLOSED^^^mail.etsu.edu' sent: > To CCL: Yes I agree that the CCL discussion group is no place > to announce new publications. > I expect that most subscribers are already on ASAP journal pages, > so this seems entirely redundant. I see one downside here > however. If it is agreed not to do this, then there is still > the burden on Jon to act as a moderator. This is not fair, > and so I think the group should agree to this, and then > announce that this is CCL policy. Afterwards anyone > who sends in such a post should be banned. Regards, Dave Close. Dave, I picked to answer your message, but I could answer any of the many... Just your bad luck {:-)}. First, I encourage everyone to read the instructions for the list: http://www.ccl.net/instructions/ Yes... It is too long, but it is also "kind of" legal document to protect my butt. 1) Why I am weary to "moderate the CCL". The burden is a small portion of this, but obviously it it would be bigger if I did. The real reason is that by approving" messages I become legally responsible for their content. And believe me, I was several times about to be sued (for legal reasons, I will not tell you who and why). What got me out was a simple statement: "I do not moderate the list... I am a phone company... Sue the author!". And in a similar manner I am answering the "Cease and desist" messages. 2) The other reason is that I know many people on the list. I do not want to have enemies... I already have plenty of them. 3) On the other hand, note that posting to the list is not restricted to the list of subscribers. Many years ago, I realized that it is not practical. Most of us get their email forwarded from one of many email accounts to some common email account that we have, and forcing people to post from some "unique" address is just not practical for many of us. Moreover, the email addresses change constantly, sometimes without even our knowledge, like the sysadmins change institutional emails by adding some sub-domain, when they change mail gateway, or protect the UNIX ids by converting short user names to schemas like: first_name.last_name:something.somewhere.org. I decided long time ago that subscription to CCL is for RECEIVING the CCL messages, while posting from a given address is an independent mechanism, where I just approve the address for posting the first time the message is sent to CCL > from a given address, and then only confirmation is required from the user, and I do not participate in it. Hence, in this mode there is no way to block someone > from posting, since even if I blocked a particular email address, the person may have a dozen other emails. So, essentially, after I approve the sender's address the first time, since the email message seems legit (yes, I review first messages), I do not have a chance to monitor this address, unless I explicitly block it (yes, I can). But then, the person can get another address on some free email service, like abc1234:some.free.emaildomain.com, and post the legit message again, and then post spam. The system works in a great majority of cases, and if you see inappropriate messages on CCL THEY ARE INTENTIONAL and THEY COME FROM A REAL EMAIL ADDRESS (they require confirmation). So, for this reason you do not see random SPAM on CCL. Now... What can be done? Without false modesty, I am an expert in email and web, and I do my living off it (not of computational chemistry, for quite some time). I could devise some gizmo that allows CCL subscribers to block the email address > from posting if say, 100 people will click on the button. The problem is, this will not work (if you read the pt. 3 above). Moreover, most people will just click on delete when seeing scrap, since, anyhow, I am sure that only few people read all messages on CCL, and most sort the messages to read by Subject:. BUT YOU ARE MANY!!! Note that you have an unalienable right to respond to the message PRIVATELY (please, do not do flame wars on CCL, it does not serve and purpose). You can send a message PRIVATELY to the sender of the inappropriate message and vent... Or you can kindly, like in this particular case, send a message to the person with 20 attachments with PDFs of your papers, saying: "Thank you for a pointer to your paper, I am sending you my papers since I am a kind soul and what to share may papers with you". If enough people gets "pissed off" like this, I am sure, the person will stop sending inappropriate messages to CCL. Note, their email address is REAL and verified. I would like to stress that Internet is not what it once was (yes, I was on Internet in 1980-ties). And email is one of the most popular and most vulnerable protocols on the Internet. Many times I was advised to change the CCL to the blog. But emails have interactivity and CCL in current form is a community. CCL without email WILL DIE. If you want it to die, send me 1000 messages: "Jan, convert CCL to blog only", and I will comply. By the way, CCL is also a kind of BLOG. Go to the archives: http://www.ccl.net/chemistry/resources/messages/index.shtml and click on some recent message, say http://www.ccl.net/cgi-bin/ccl/message-new?2011+05+20+001 and you will notice in the upper left corner a link: [Respond to the message]. So yes, you do not have to be subscribed to CCL to participate. But for those of you who are subscribers, my big THANK YOU for being real members of the community for good and for worse. You suffer, but hopefully you also gain. Jan -- Jan Labanowski jkl:ccl.net