From owner-chemistry@ccl.net Tue Sep 1 02:54:01 2009 From: "Dipl.-Ing. Thomas Mitterfellner thomas.mitterfellner^^^tugraz.at" To: CCL Subject: CCL: Generating enantiomers Message-Id: <-40135-090831120923-29896-j9VzQDQ0EKdLnWp51kBV4w||server.ccl.net> X-Original-From: "Dipl.-Ing. Thomas Mitterfellner" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Mon, 31 Aug 2009 17:32:54 +0200 MIME-Version: 1.0 Sent to CCL by: "Dipl.-Ing. Thomas Mitterfellner" [thomas.mitterfellner]*[tugraz.at] Hello! Does anyone know of a program/tool for generating an enantiomer of a given structure (xyz, mol2, etc.)? Thank you, Thomas From owner-chemistry@ccl.net Tue Sep 1 04:13:00 2009 From: "Ol Ga eurisco1]_[pochta.ru" To: CCL Subject: CCL:G: ERROR TRANSITION STATE CALCULATION Message-Id: <-40136-090901035950-25992-BpwcQ6LlZyfDMdTYWPo57g * server.ccl.net> X-Original-From: "Ol Ga" Date: Tue, 1 Sep 2009 03:59:46 -0400 Sent to CCL by: "Ol Ga" [eurisco1%%pochta.ru] Dear Carlos Pereira da Silva, I use similar input in many cases - it works very well. I can explain my choice: gdiis - very good optimisation method noeigen - if you have bad starting point for TS search, possible you will get more than one imaginary freq. Hence, the job will be aborted without keyword noeigen. Be carefull! xqc - it solves problem with bad SCF convergence. Sincerely, Ol Ga PS: I advice you to find in internet Gaussain 03 Manual. ***************************** Hello Eurisco. you can detail the commands? - gdiis - noeigen - xqc THANKs 2009/8/31 Ol Ga eurisco1]*[pochta.ru Sent to CCL by: "Ol Ga" [eurisco1() pochta.ru] Dear Carlos Pereira da Silva, It is better to use the following input section %chk=C:\Documents and Settings\Gaussian\Desktop\ET\3b-QST2-EMIN.chk %mem=900mb %nproc=1 #p opt=(calcfc,ts,maxcycle=100,gdiis,noeigen) rb3lyp/lanl2dz #geom=connectivity scf(xqc,maxcycle=450) Sincerely, Ol Ga PS: geom=connectivity with connectivity data after coordinates is not required for DFT calculations ************************** HELP-ME PLEASE... ERROR DETAILS ===================================================================== INPUT ===================================================================== %chk=C:\Documents and Settings\Gaussian\Desktop\ET\3b-QST2-EMIN.chk %mem=900mb %nproc=1 #p opt=(calcfc,ts) rb3lyp/lanl2dz geom=connectivity scf=maxcycle=450 test . ===================================================================== WINDOW IN WIN XP ===================================================================== Severe Error Message # 2070 The processing of the last link ended abnormally. All processing has been aborted. ===================================================================== OUTPUT ===================================================================== EVERY WORD THAT YOU WRITE IS A BLOW THAT SMITES THE DEVIL. -- ST. BERNARD OF CLAIRVAUX Error termination request processed by link 9999. Error termination via Lnk1e in C:\G03W\l9999.exe at Mon Aug 31 08:27:32 2009. Job cpu time: 0 days 7 hours 57 minutes 35.0 seconds. File lengths (MBytes): RWF= 605 Int= 0 D2E= 0 Chk= 16 Scr= 1 ===================================================================== NOW I'AM TESTING WITH... %chk=C:\Documents and Settings\Gaussian\Desktop\ET\3b-QST2-EMIN.chk %mem=900mb %rwf=a,245mw,b,245mw,c,245mw,d,245mw,e,245mw,f,245mw,g,245mw,h,245mw #p opt=(calcfc,ts) b3lyp/lanl2dz scf=(maxcycle=600) test MaxDisk=1960MW .IS OK ? -- Carlos Pereira da Silva http://Carlosps.110mb.com carlosps1985,+,gmail.com (86)99223852 -- Carlos Pereira da Silva http://Carlosps.110mb.com carlosps1985---gmail.com (86)99223852 From owner-chemistry@ccl.net Tue Sep 1 05:37:01 2009 From: "Fedor Goumans fedor.goumans]![googlemail.com" To: CCL Subject: CCL: Generating enantiomers Message-Id: <-40137-090901053458-14300-116502yWuftdgcGlQPaK1A]~[server.ccl.net> X-Original-From: Fedor Goumans Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 1 Sep 2009 10:37:10 +0200 MIME-Version: 1.0 Sent to CCL by: Fedor Goumans [fedor.goumans,,googlemail.com] Hi Thomas, For an enantiomer: it's the mirror image so just invert x,y,z. For instance for an xyz-file: awk '{ if (NF =3D=3D 4) {print $1, -$2, -$3, -$4} else {print} }' HTH, Fedor 2009/8/31 Dipl.-Ing. Thomas Mitterfellner thomas.mitterfellner^^^tugraz.at : > > Sent to CCL by: "Dipl.-Ing. Thomas Mitterfellner" > [thomas.mitterfellner]*[tugraz.at] > > Hello! > > Does anyone know of a program/tool for generating an enantiomer of a give= n > structure (xyz, mol2, etc.)? > > Thank you, > > Thomas > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0> =A0 =A0=A0 =A0 http://www.ccl.net/chemistry/sub_unsub.sht= mlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> =A0 =A0> > > From owner-chemistry@ccl.net Tue Sep 1 06:15:00 2009 From: "Ralf Tonner ralf.tonner]*[googlemail.com" To: CCL Subject: CCL: Generating enantiomers Message-Id: <-40138-090901042219-15510-ZpeyRKOH5aCGNWmIKGZCDg%%server.ccl.net> X-Original-From: Ralf Tonner Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 1 Sep 2009 20:01:32 +1200 MIME-Version: 1.0 Sent to CCL by: Ralf Tonner [ralf.tonner*googlemail.com] Hi Thomas, if you simply invert an xyz-file by changing the sign of every (x-, y-, z-)coordinate, the resulting structure is the enantiomer . Hope this helps Ralf. 2009/9/1 Dipl.-Ing. Thomas Mitterfellner thomas.mitterfellner^^^tugraz.at : > > Sent to CCL by: "Dipl.-Ing. Thomas Mitterfellner" > [thomas.mitterfellner]*[tugraz.at] > > Hello! > > Does anyone know of a program/tool for generating an enantiomer of a give= n > structure (xyz, mol2, etc.)? > > Thank you, > > Thomas > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0> =A0 =A0=A0 =A0 http://www.ccl.net/chemistry/sub_unsub.sht= mlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> =A0 =A0> > > --=20 Dr. Ralf Tonner Centre of Theoretical Chemistry and Physics New Zealand Institute for Advanced Study Massey University Auckland NEW ZEALAND Phone (64) 09 414 0800 extn 9894 Fax (64) 09 443 9779 ---- From owner-chemistry@ccl.net Tue Sep 1 06:46:00 2009 From: "Dipl.-Ing. Thomas Mitterfellner thomas.mitterfellner|a|tugraz.at" To: CCL Subject: CCL: Generating enantiomers Message-Id: <-40139-090901054044-15973-BoQz8J5iIohQeFWNDFjUyg-x-server.ccl.net> X-Original-From: "Dipl.-Ing. Thomas Mitterfellner" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Tue, 01 Sep 2009 11:39:07 +0200 MIME-Version: 1.0 Sent to CCL by: "Dipl.-Ing. Thomas Mitterfellner" [thomas.mitterfellner!=!tugraz.at] > For an enantiomer: it's the mirror image so just invert x,y,z. For > instance for an xyz-file: > > awk '{ if (NF == 4) {print $1, -$2, -$3, -$4} else {print} }' Thanks a lot! Why didn't I think of awk myself? ;o) I modified the line somewhat to give a cleaner formatting: awk '{ if (NF == 4) {printf("%2s %12.6f %12.6f %12.6f\n", $1, -$2, -$3, -$4)} else {print} }' file.xyz > file_enantiomer.xyz Thomas From owner-chemistry@ccl.net Tue Sep 1 07:28:01 2009 From: "Val Gillet v.gillet!^!sheffield.ac.uk" To: CCL Subject: CCL: Sheffield Chemoinformatics Conference July 2010 Message-Id: <-40140-090901072614-24485-Aw0BmKX4DQecFfjav4bQsA%server.ccl.net> X-Original-From: "Val Gillet" Date: Tue, 1 Sep 2009 07:26:10 -0400 Sent to CCL by: "Val Gillet" [v.gillet-.-sheffield.ac.uk] First announcement for: The Fifth Joint Sheffield Conference on Chemoinformatics, 13-15 July 2010. The conference will be held at The University of Sheffield, UK. The meeting is being sponsored by the Chemical Structure Association Trust and the Molecular Graphics and Modelling Society. The call for papers will be announced in the autumn and further details will be placed at http://cisrg.shef.ac.uk/shef2010/ Val Gillet (v.gillet * sheffield.ac.uk) From owner-chemistry@ccl.net Tue Sep 1 08:04:01 2009 From: "Peter Bladon p.bladon**strath.ac.uk" To: CCL Subject: CCL: Generating enantiomers Message-Id: <-40141-090901072044-20676-ov8zyDGw+p7SJkV9dgawtA^_^server.ccl.net> X-Original-From: Peter Bladon Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Tue, 1 Sep 2009 11:38:41 +0100 MIME-Version: 1.0 Sent to CCL by: Peter Bladon [p.bladon_._strath.ac.uk] Dear Thomas, Any good modelling package will have a tool for converting a structure into= its enantiomer. But in the absence a of such a tool you can use an editor to change the sig= ns of all of the (say) x coordinates. This operation will cause the structure to be reflecte= d in the YZ plane Similarly changing the signs of the y coordinates will cause reflection in = the XZ plane, and changing the signs of all the z coordinates will cause reflection in the XY= plane. If you change the signs of ALL the coordinates, this gives you inversion of= the structure about the origin. All this is easy. If what what you want is the generation of diastereoisom= ers, that is another matter. I do not know of a general method for doing this. I can think of s= ituations, where if you were to invert one chiral centre in a structure with two (or more) chir= al centres, you could end up with a sterically crowded structure. In these circumstances you woul= d need to follow the inversion with some form of energy minimization process. One way of app= roaching this problem, is to cut the structure into separate parts, each with one chiral = center, work on the parts to effect inversion as needed, and then to join them up again. The program INTERCHEM (http://www.interprobe.co.uk) has all the simple inve= rsion methods built in, as well as a lot of other useful tools for investigating stereoch= emistry. Hope this helps Cheers Peter Bladon ________________________________________ > From: owner-chemistry+cbas25=3D=3Dstrath.ac.uk- -ccl.net [owner-chemistry+cba= s25=3D=3Dstrath.ac.uk- -ccl.net] On Behalf Of Dipl.-Ing. Thomas Mitterfellner= thomas.mitterfellner^^^tugraz.at [owner-chemistry- -ccl.net] Sent: Monday, August 31, 2009 4:32 PM To: Bladon, Peter Subject: CCL: Generating enantiomers Sent to CCL by: "Dipl.-Ing. Thomas Mitterfellner" [thomas.mitterfellner]*[t= ugraz.at] Hello! Does anyone know of a program/tool for generating an enantiomer of a given structure (xyz, mol2, etc.)? Thank you, Thomas -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Sep 1 08:49:00 2009 From: "Carlos Pereira carlosps1985[*]gmail.com" To: CCL Subject: CCL: Transition State Calculation, METHOD - THANKs for all help Message-Id: <-40142-090901082311-5723-rgdtRW78hppdn7FkVAd1QQ(0)server.ccl.net> X-Original-From: Carlos Pereira Content-Type: multipart/alternative; boundary=001636eee39e39bfc90472831f58 Date: Tue, 1 Sep 2009 09:16:36 -0300 MIME-Version: 1.0 Sent to CCL by: Carlos Pereira [carlosps1985%a%gmail.com] --001636eee39e39bfc90472831f58 Content-Type: text/plain; charset=ISO-8859-1 Thanks for all I am calculation transition states in four steps: *FIRST - CALCULATION THE POSSIBLE TRANSITION STRUCTURE* #p opt=(qst2,ts,calcfc) b3lyp/lanl2dz geom=connectivity scf=maxcycle=450 test (*) INPUT WITH REACT AND PRODUCT (**) REACT AND PRODUCT WITH SAME NUMERATION AND CONNECTIVITY (IT'S DIFFICULT TO MAKE) *SECOND - OPTIMIZATION THE STRUCTURE FROM STEP ONE, AS TRANSITION STRUCTURE* #p opt=(ts,calcfc) b3lyp/lanl2dz geom=connectivity scf=maxcycle=450 test *THIRD - FREQUENCY CALCULATIONS (STRUCTURE FROM STEP TWO)* #p freq b3lyp/lanl2dz geom=connectivity scf=maxcycle=450 test *FOURTH - IRC CALCULATION * #p irc=calcfc rb3lyp/lanl2dz geom=connectivity scf=maxcycle=450 test (***) *INFORMATIONS FOUND IN *"DOI: 10.1590/S0100-40422008000500055" * (****) IN ALL STEPS ADD:* %rwf=a,245mw,b,245mw,c,245mw,d,245mw,e,245mw,f,245mw,g,245mw,h,245mw OR %mem= OR MaxDisk=2000MB *TO ASSIST IN ERROR CALCULATION*S (*****) *NOW WITH YOUR'S HELP: *- DELL: geom=connectivity - ADD: noigen OR noigentest; gdiis, xqc * * -- Carlos Pereira da Silva http://Carlosps.110mb.com carlosps1985-x-gmail.com (86)99223852 --001636eee39e39bfc90472831f58 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Thanks for all

=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 I am= calculation transition states in four steps:

FIRST - CALCU= LATION THE POSSIBLE TRANSITION STRUCTURE

#p opt=3D(qst2,= ts,calcfc) b3lyp/lanl2dz geom=3Dconnectivity scf=3Dmaxcycle=3D450 test

(*) INPUT WITH REACT AND PRODUCT
(**) REACT AND PRODUCT WITH SAME NU= MERATION AND CONNECTIVITY (IT'S DIFFICULT TO MAKE)

SECOND = - OPTIMIZATION THE STRUCTURE FROM STEP ONE, AS TRANSITION STRUCTURE<= /b>

#p opt=3D(ts,calcfc) b3lyp/lanl2dz geom=3Dconnectivity scf=3Dmaxcycle= =3D450 test

THIRD - FREQUENCY CALCULATIONS (STRUCTURE FROM = STEP TWO)

#p freq b3lyp/lanl2dz geom=3Dconnectivity scf= =3Dmaxcycle=3D450 test

FOURTH - IRC CALCULATION

#p irc=3Dcalcfc r= b3lyp/lanl2dz geom=3Dconnectivity scf=3Dmaxcycle=3D450 test

(***) INFORMATIONS FOUND IN "DOI: 10.1590/S0100-40422008000500055"=

(****) IN ALL STEPS ADD:

%rwf=3Da,245mw,b,245mw,c,245mw,d= ,245mw,e,245mw,f,245mw,g,245mw,h,245mw
OR
%mem=3D
OR
MaxDisk=3D= 2000MB

TO ASSIST IN ERROR CALCULATIONS

(*****) NOW WITH YOUR'S HELP:

- DELL: geom=3Dconnectivity
- ADD: noigen OR noigentest; gdiis, = xqc



--
Carlos Pereira da Silva
http://Carlosps.110mb.com
carlosps1985-x-gmail.com
(86)99223852
--001636eee39e39bfc90472831f58-- From owner-chemistry@ccl.net Tue Sep 1 09:23:01 2009 From: "Jan Labanowski janl.:.speakeasy.net" To: CCL Subject: CCL: Environmental Toxicity Challenge -- new deadline is September 10 Message-Id: <-40143-090901085233-24250-l5oLo9itXFejfOI0sVxG8w : server.ccl.net> X-Original-From: Jan Labanowski Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 01 Sep 2009 08:52:18 EDT MIME-Version: 1.0 Sent to CCL by: Jan Labanowski [janl(-)speakeasy.net] [I was ask to repost it, Jan] Environmental Toxicity Challenge Following requests of participants we extended the submission deadline to September 10th. This challenge is co-organized by ICANN'09: International Conference on Artificial Neural Networks, European Neural Network Society (ENNS) and CAD= ASTER project. Goals of this study: Develop in silico models to predict environmental toxi= city of molecules against T. pyriformis using data from [1]. Estimate the predi= ction intervals for new compounds. Further information can be found at http://www.cadaster.eu. Five datasets of descriptors are available:=20 Quantum Chemistry, E-state, DRAGON, SimulationsPlus and MOE descriptors Important key dates New deadline to submit: September 10 September 14-17 2009 The winner will be announced at the ICANN'09 conference (there is no requirement to participate to this conference) The winner will be identified according to the criteria defined below. It is expected that the winner as well as other participants will submit articles describing their methodological approaches for publication in a peer-revie= wed journal (under discussion).=20 Criteria for success Firstly, methods with Root Mean Squared Error (RMSE) non-significantly dif= ferent to the method with lowest RMSE (according to the bootstrap test, p<0.05) w= ill be identified as the first-pass winners.=20 Secondly, the method providing the best likelihood criteria between estimat= ed and observed confidences for the blind test set as described in [2] will be=20 identified amid the first-pass winners.=20 Igor V. Tetko, Terry W. Schultz and Wlodzislaw Duch=20 [1] Zhu, H.; Tropsha, A.; Fourches, D.; Varnek, A.; Papa, E.; Gramatica, P.; Oberg, T.; Dao, P.; Cherkasov, A.; Tetko, I. V. Combinatorial QSAR Modeling= =20 of Chemical Toxicants Tested against Tetrahymena pyriformis J. Chem. Inf. M= odel. 2008, 48 (4), 766-784. [2] Tetko, I. V.; Sushko, I.; Pandey, A. K.; Zhu, H.; Tropsha, A.; Papa, E.= ;=20 Oberg, T.; Todeschini, R.; Fourches, D.; Varnek, A., Critical assessment of= =20 QSAR models of environmental toxicity against Tetrahymena pyriformis: focu= sing on applicability domain and overfitting by variable selection J.=20 Chem. Inf. Model. 2008, 48 (9), 1733-46. Dr. Igor V. Tetko Institute of Bioinformatics and Systems Biology Helmholtz Zentrum Muenchen=20 German Research Center for Environmental Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany Tel./Fax: +49-89-3187-3575/x85 e-mail: itetko|*|vcclab.org, itetko|*|gmail.com http://www.vcclab.org http://www.cadaster.eu -- see prediction challenge! From owner-chemistry@ccl.net Tue Sep 1 09:59:00 2009 From: "errol lewars elewars!=!trentu.ca" To: CCL Subject: CCL:G: ERROR TRANSITION STATE CALCULATION Message-Id: <-40144-090831144344-30983-a2w7CLyZGNSYvIJ4aplLeg . server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 31 Aug 2009 14:43:36 -0400 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars(0)trentu.ca] 2009 Aug 31 Gaussian TS optimizations need the keyword NoEigenTest: e.g. Opt(TS, NoEigenTest, CalcFC) or Opt(TS, NoEigenTest, MNDOFC), unless your input TS is close enough to the final geometry so that every test for eigenvalues will give one negative one force constant (one imaginary frequency). This happens about once every million tries. E. Lewars === Carlos Pereira carlosps1985,,gmail.com wrote: > HELP-ME PLEASE... > > > *ERROR DETAILS * > > ===================================================================== > */INPUT/* > ===================================================================== > %chk=C:\Documents and Settings\Gaussian\Desktop\ET\3b-QST2-EMIN.chk > %mem=900mb > %nproc=1 > #p opt=(calcfc,ts) rb3lyp/lanl2dz geom=connectivity scf=maxcycle=450 test > ... > ===================================================================== > /*WINDOW IN WIN XP*/ > ===================================================================== > > Severe Error Message # 2070 > The processing of the last link ended abnormally. > All processing has been aborted. > > ===================================================================== > /*OUTPUT*/ > ===================================================================== > EVERY WORD THAT YOU WRITE IS A BLOW THAT SMITES THE DEVIL. > -- ST. BERNARD OF CLAIRVAUX > Error termination request processed by link 9999. > Error termination via Lnk1e in C:\G03W\l9999.exe at Mon Aug 31 > 08:27:32 2009. > Job cpu time: 0 days 7 hours 57 minutes 35.0 seconds. > File lengths (MBytes): RWF= 605 Int= 0 D2E= 0 Chk= > 16 Scr= 1 > ===================================================================== > > > NOW I'AM TESTING WITH... > > %chk=C:\Documents and Settings\Gaussian\Desktop\ET\3b-QST2-EMIN.chk > %mem=900mb > %rwf=a,245mw,b,245mw,c,245mw,d,245mw,e,245mw,f,245mw,g,245mw,h,245mw > #p opt=(calcfc,ts) b3lyp/lanl2dz scf=(maxcycle=600) test MaxDisk=1960MW > > ...IS OK ? > > -- > Carlos Pereira da Silva > http://Carlosps.110mb.com > carlosps1985 * gmail.com > (86)99223852 From owner-chemistry@ccl.net Tue Sep 1 16:29:00 2009 From: "Nicola Zonta nicola.zonta-x-gmail.com" To: CCL Subject: CCL: Zem release Message-Id: <-40145-090901162632-19511-vuRGkFisi0kNuf9WBM6Ngg*server.ccl.net> X-Original-From: Nicola Zonta Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Tue, 1 Sep 2009 21:38:37 +0200 Mime-Version: 1.0 (Apple Message framework v930.3) Sent to CCL by: Nicola Zonta [nicola.zonta|gmail.com] Dear fellow CCLers, I'm proud to announce the first release of Zem (ZedeN's Editor of Molecules). Based on the Molsketch project, Zem is a 2D molecular editor capable of reading and saving more than 80 chemical formats, and several graphical formats (image files can be scanned for molecules thanks to OSRA). Starting with version 0.7 (which should be released before the end of september) Zodiac will feature Zem as 2D editor and display for ligand- protein interaction plots. Zem 0.3 beta is now ready for download. Info and download links, as usual, on our new website: www.zeden.org please vote on our polls ;) Many thanks to Harm van Eersel and Tim van der Meersch for their invaluable contributions Nicola Zonta