From owner-chemistry@ccl.net Wed Jul 23 01:32:01 2008 From: "Alexander Hofmann ah:+:chemie.hu-berlin.de" To: CCL Subject: CCL: error in VASP polarization calculation using Berry phase Message-Id: <-37393-080723012905-32456-dZicJb6kW+/gv2ZuyZk5qw{:}server.ccl.net> X-Original-From: Alexander Hofmann Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 23 Jul 2008 07:28:53 +0200 MIME-Version: 1.0 Sent to CCL by: Alexander Hofmann [ah~~chemie.hu-berlin.de] Dear Ping Lin, have you checked the dedicated VASP forum for that? http://cms.mpi.univie.ac.at/vasp-forum/forum.php Best regards Alexander Ping Lin plin1112(a)gmail.com wrote: > Sent to CCL by: "Ping Lin" [plin1112^gmail.com] > Dear all, > > We try to use vasp to calculate polarization using berry phase as suggested in the manual. > > During the berry phase calculation, it always stops with an error in the OUTCAR: > > Error in subroutine BERRY: did not find all determinants > > Matrix CMK is not an nxn matrix for > ISTR = 1 j = 0 > > Can anyone tell us how to carry out the calculation, even for the example in vasp manual (NaF)? > > Thank you in advance.> > From owner-chemistry@ccl.net Wed Jul 23 03:08:00 2008 From: "Vincent Vivien vincent]|[eyesopen.com" To: CCL Subject: CCL: OpenEye EuroCUP III - Apr 22-24, 2009 - Toledo, Spain - 1st announcemt Message-Id: <-37394-080723030606-25790-pCM3kiOP07ZRWnqrsCr+yQ],[server.ccl.net> X-Original-From: "Vincent Vivien" Date: Wed, 23 Jul 2008 03:06:02 -0400 Sent to CCL by: "Vincent Vivien" [vincent^_^eyesopen.com] Dear Colleague, After Sheffield in 2007 and Strasbourg in 2008, the 3rd edition of OpenEye's annual European science meeting, EuroCUP III, will be held in Toledo, Spain, on April 22-24, 2009. The venue will be the Parador Toledo, a medium-sized hotel with local character: http://www.parador.es/en/tratarFichaParadorCabecera.do?parador=079 EuroCUP III topics are not yet finalized, but we are considering the following 4 sessions: - Shape and Electrostatics - QSAR: is it worth it? - Fragment design: good idea or the latest blind alley? - Simulations and Force-fields: are they any use in drug design? At all? If you find the above inspiring and would like to contribute, please let us know by emailing eurocup-,-eyesopen.com More details will be communicated in September, when we expect to open online registration. Have an excellent summer! With best regards, Vincent Vivien Director of European Accounts OpenEye Scientific Software vincent-,-eyesopen.com www.eyesopen.com From owner-chemistry@ccl.net Wed Jul 23 04:09:00 2008 From: "Antje Wolf antje.wolf.:.scai.fraunhofer.de" To: CCL Subject: CCL: Multiligand docking on AutoDock Tool Message-Id: <-37395-080723035430-18586-LVg2a8yAcMKE8iyWRbna/w() server.ccl.net> X-Original-From: Antje Wolf Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Wed, 23 Jul 2008 09:21:31 +0200 MIME-Version: 1.0 Sent to CCL by: Antje Wolf [antje.wolf+/-scai.fraunhofer.de] Have a look at the AutoDock website. There is a VS tutorial. http://autodock.scripps.edu/faqs-help/tutorial/using-autodock4-for-virtual-screening Antje sobia ahsan halim sobia_halim(0)yahoo.com schrieb: > Sent to CCL by: "sobia ahsan halim" [sobia_halim|,|yahoo.com] > Hi All > > I am using autodock tool (adt) for the docking purpose and I am looking for any option of multi ligand docking on adt. Can any one please suggest me how to run multiple ligand file simultaneously???? or is there any script available to perform virtual screening??? Kindly let me know...Thanks a lot in advance. > > Bye.> > > -- Antje Wolf Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI) Department Bioinformatics Schloss Birlinghoven D-53754 Sankt Augustin Tel.: +49 - 228 - 2699 - 318 E-mail: antje.wolf]![scai.fraunhofer.de Internet: http://www.scai.fraunhofer.de From owner-chemistry@ccl.net Wed Jul 23 08:33:00 2008 From: "gnli gnli(a)dicp.ac.cn" To: CCL Subject: CCL:G: a question about gaussian function Message-Id: <-37396-080723083105-6861-zJXZZYML/P27CJnjavTKag|*|server.ccl.net> X-Original-From: "gnli" Content-Type: multipart/related; boundary="----=_NextPart_000_000C_01C8ED03.2B91A830" Date: Wed, 23 Jul 2008 20:32:03 +0800 MIME-Version: 1.0 Sent to CCL by: "gnli" [gnli.:.dicp.ac.cn] This is a multi-part message in MIME format. ------=_NextPart_000_000C_01C8ED03.2B91A830 Content-Type: multipart/alternative; boundary="----=_NextPart_001_000D_01C8ED03.2B91A830" ------=_NextPart_001_000D_01C8ED03.2B91A830 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear CLLer I have read a paper (JPCA 2003 v107 2524-2539 ), Please allow me asking a question about the Gaussian function for CD spectrum. As we know, the Gaussian function is defined as follow : (1) But in the paper(page3), they said that "The CD spectra were simulated by overlapping Gaussian functions for each transition according to (2) Uing the width of the band at 1/e height " I will very appreciate if you can give a explanation how the equation (2) is got, because I don't quite understand. Besides, maybe, I guess these is a " ) " missing during the equation (2). I think the last part is (3) But it is just a guess. Please forgive me if I'm wrong. I will look forward to your response. Thank you very much ! best wishes Guanna Li gnli+*+dicp.ac.cn ------=_NextPart_001_000D_01C8ED03.2B91A830 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear = CLLer

I have read = a = paper (JPCA = 2003 v107 = 2524-2539 ), Please allow me asking a question about the Gaussian function for CD = spectrum.

As we know, the Gaussian = function is defined as follow :

 

(1)

 

But in the paper(page3), = they = said that “The CD spectra were = simulated by overlapping Gaussian functions for each transition according = to

(2)

 

Uing = the width of the band at 1/e height ”

 

I will very appreciate if = you can give a explanation how the equation (2) is got, because I don’t = quite understand.

Besides, maybe, I guess = these is a “ ) “ missing during the equation (2). I think the last part = is

 

(3)

 

But it is just a guess. = Please forgive me if I’m wrong.

 

I will look forward to your = response. Thank you very much !

best wishes
Guanna Li
gnli+*+dicp.ac.cn

 

 

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name="image002.gif" Content-Transfer-Encoding: base64 Content-ID: R0lGODlhpwBNAHcAMSH+GlNvZnR3YXJlOiBNaWNyb3NvZnQgT2ZmaWNlACH5BAEAAAAALAIAAgCi AEkAgAAAAAAAAAL/hI+py+0PTZgz2osjpbn7rwTgSFpiiabIqbZP1bDu3Mn0fdrrzV96P/tJgBqa 0EQEHJfJGMx1hEShi+g0efVkq82DTcTsMrYZcsKMkm1i4rFRG6o8NfIwsh1618Zo79TcF6R3tsHh 5UZY+HMFiJcnuMf1wYgRSAVZxhUI5vd453iIWfnYlzOkdDYKKjGXYqmWAxiLSnvqswr0ymMaeou7 C2IpZVv6Cxysx5upxNJqTKf83DnS3LyiKGzEmy2NeMqNZ13b7bozboKdrr6u/i1+zR4vP0+vo3bO rNht2Euedu2vCLGA5fp1qbcGnjlczkq8awNO0qpoaTg5iijxF0Y//xsjiapYrEVHOKwwdnw47NLE gQ5FLnyBj8TIZePAzTQYT6VIbBlfpks5iJnBoK5QppIkxxZQnV+IjGzKxlMoMjehDv3Y0qdRfFu9 qbB6VWfWhRa5IlX1VapSHC6PmgPbq1HaqdWw7Jx29B5dvEsdFuJ40ytIK1/+zmkomOCki4HDKkYL MddjmZOpVUZ2WUvCzHw2c/4MOrTo0aRLmz6NOrXq1axbu34NOwjC2e1iS7btujFuULp3X4TNM1++ OmCeGGrIrwxinxzVOuDXW+pDvedgEcIck2xcgAJrRWdObLpbodxJrs0L/rzXrpigWqSutCz5f97s ZIep/qfltaaigZktKx9liFjx1nzPvTSfSZ6h0l8inr2n3nALjkdKVIcch18/cC3G3xAB/vfNfTQN mJgyBI63oXlNNYigXhCOFdUiZ0UYk1ERLVEXhS6ypx+FBtpIYoRCACkgH3xVRxZF5jFYE07gbQVf jgZOklx6JQE2HC0TVvLXdhp2KWFx9oBZ2HK+HRhfE9+1RlF0a7JZYw9v5jbnmbe1VgAAOw== ------=_NextPart_000_000C_01C8ED03.2B91A830-- From owner-chemistry@ccl.net Wed Jul 23 09:29:01 2008 From: "Tsung-Wen Yen peter308- -gmail.com" To: CCL Subject: CCL: non-converging gradient force in geometry optimization(deMon2k users) Message-Id: <-37397-080723053111-22473-U8S5dE6NcecHXrJ3Sk0TsA%a%server.ccl.net> X-Original-From: "Tsung-Wen Yen" Date: Wed, 23 Jul 2008 05:31:07 -0400 Sent to CCL by: "Tsung-Wen Yen" [peter308:gmail.com] Dear CCL subscribers: I am currently using DeMon2k to do my geometric optimization on metallic clusters,say Ag13.I used serveal basis sets,some of them, for ex:DZVP,DZVP-GGA,ECPS could easily achieve convergence within 30 cycles.However, i get stuck in gradient force convergence when i use model-core potential basis(MCPS,RMCPS).I ran for more than 300 cycles.The gradient force seems to oscillate around some value instead of decreasing.I also look for solutions at other forums, uusually they suggest to increase the maximum cycles,decrease the optimization step size or change to a smaller basis set.I use this basis set is because i try to reproduce a paper's results, and that author uses MCP as basis set.I wonder if anyone who has experience in this technical issue would be so kind to offer me any suggestions.I 've stucked by this for more than a month. And I still can't find a permanent solution to it.It's really frustrating for a newcomer in this field.I sincerly appreciated for your help. P.S.I could provide my input and output files if anyone needs them!! I am a research assistant at N.C.U. Taiwan you could call me Yen and contact me at peter308]_[gmail.com Many thanks!! Best regards Yen From owner-chemistry@ccl.net Wed Jul 23 10:04:02 2008 From: "Michael Fernandez Llamosa michael_llamosa ~ yahoo.com" To: CCL Subject: CCL: Multiligand docking on AutoDock Tool Message-Id: <-37398-080722073456-23388-LM1VaWgNQZwlNH9NVfkMqA|,|server.ccl.net> X-Original-From: Michael Fernandez Llamosa Content-Type: multipart/alternative; boundary="0-368980066-1216722879=:51273" Date: Tue, 22 Jul 2008 03:34:39 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Michael Fernandez Llamosa [michael_llamosa..yahoo.com] --0-368980066-1216722879=:51273 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable here u can find it....=0Ahttp://autodock.scripps.edu/faqs-help/tutorial/usi= ng-autodock4-for-virtual-screening=0A=0A=0A----- Mensaje original ----=0ADe= : sobia ahsan halim sobia_halim(0)yahoo.com =0APar= a: "Fernandez, Michael " =0AEnviado: mar= tes, 22 de julio, 2008 19:06:32=0AAsunto: CCL: Multiligand docking on AutoD= ock Tool=0A=0A=0ASent to CCL by: "sobia ahsan halim" [sobia_halim|,|yahoo.c= om]=0AHi All=0A=0AI am using autodock tool (adt) for the docking purpose an= d I am looking for any option of multi ligand docking on adt. Can any one p= lease suggest me how to run multiple ligand file simultaneously???? or is t= here any script available to perform virtual screening??? Kindly let me kno= w...Thanks a lot in advance.=0A=0ABye.=0A=0A=0A=0A-=3D This is automaticall= y added to each message by the mailing script =3D-=0ATo recover the email a= ddress of the author of the message, please change=0Athe strange characters= on the top line to the ]![ sign. You can also=0Alook up the X-Original-From:= line in the mail header.=0A=0AE-mail to subscribers: CHEMISTRY]![ccl.net or = use:=0A=0A=0AE-mail to= administrators: CHEMISTRY-REQUEST]![ccl.net or use=0A http://www.ccl.ne= t/cgi-bin/ccl/send_ccl_message=0A=0A=0A http://= www.ccl.net/chemistry/sub_unsub.shtml=0A=0ABefore posting, check wait time = at: http://www.ccl.net=0A=0A=0AConferences: ht= tp://server.ccl.net/chemistry/announcements/conferences/=0A=0ASearch Messag= es: http://www.ccl.net/htdig (login: ccl, Password: search)=0A=0AIf your m= ail bounces from CCL with 5.7.1 error, check:=0A http://www.ccl.net/sp= ammers.txt=0A=0A= =0A=0A=0A ____________________________________________________________= ________________________=0AYahoo! MTV Blog & Rock >=C2=A1Cu=C3=A9ntanos = tu historia, inspira una canci=C3=B3n y g=C3=A1nate un viaje a los Premios = MTV! Participa aqu=C3=AD http://mtvla.yahoo.com/ --0-368980066-1216722879=:51273 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
here u can find it....
http://autodock.scripps.edu/faqs-hel= p/tutorial/using-autodock4-for-virtual-screening

----- Mensaje ori= ginal ----
De: sobia ahsan halim sobia_halim(0)yahoo.com <owner-chemi= stry]![ccl.net>
Para: "Fernandez, Michael " <michael_llamosa= ]![yahoo.com>
Enviado: martes, 22 de julio, 2008 19:06:32
Asunto: CC= L: Multiligand docking on AutoDock Tool


Sent to CCL by: "sobia a= hsan halim" [sobia_halim|,|yahoo.com]
Hi All

I am using autodock = tool (adt) for the docking purpose and I am looking for any option of multi= ligand docking on adt. Can any one please suggest me how to run multiple ligand file simultaneously???? or is there any script available to perform= virtual screening??? Kindly let me know...Thanks a lot in advance.

= Bye.



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Participa aqu=C3=AD http://mtvla.yahoo.com/ --0-368980066-1216722879=:51273-- From owner-chemistry@ccl.net Wed Jul 23 10:38:01 2008 From: "Alessandro Contini alessandro.contini],[unimi.it" To: CCL Subject: CCL: Multiligand docking on AutoDock Tool Message-Id: <-37399-080723102526-7959-omq1S9lBvWE7CUbkuSiEKA],[server.ccl.net> X-Original-From: Alessandro Contini Content-transfer-encoding: 8BIT Content-type: text/plain; charset=utf-8 Date: Wed, 23 Jul 2008 16:25:01 +0200 MIME-version: 1.0 Sent to CCL by: Alessandro Contini [alessandro.contini_-_unimi.it] Hi Michael, check this link http://autodock.scripps.edu/faqs-help/tutorial/using-autodock-for-virtual-screening/VSTutorial2.pdf Regards, Alessandro Contini Il giorno mar, 22/07/2008 alle 03.34 -0700, Michael Fernandez Llamosa michael_llamosa ~ yahoo.com ha scritto: > here u can find it.... > http://autodock.scripps.edu/faqs-help/tutorial/using-autodock4-for-virtual-screening > > ----- Mensaje original ---- > De: sobia ahsan halim sobia_halim(0)yahoo.com > > Para: "Fernandez, Michael " > Enviado: martes, 22 de julio, 2008 19:06:32 > Asunto: CCL: Multiligand docking on AutoDock Tool > > > Sent to CCL by: "sobia ahsan halim" [sobia_halim|,|yahoo.com] > Hi All > > I am using autodock tool (adt) for the docking purpose and I am > looking for any option of multi ligand docking on adt. Can any one > please suggest me how to run multiple ligand file simultaneously???? > or is there any script available to perform virtual screening??? > Kindly let me know...Thanks a lot in advance. > > Bye. > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change > the strange characters on the top line to the # sign. You can also > E-mail to subscribers: CHEMISTRY#ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST#ccl.net or use> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > > > > > ______________________________________________________________________ > > Yahoo! MTV Blog & Rock > ¡Cuéntanos tu historia, inspira una canción y gánate un viaje a los > Premios MTV! > Participa aquí http://mtvla.yahoo.com/ -- Dr. Alessandro Contini Istituto di Chimica Organica "Alessandro Marchesini" Universita' degli Studi di Milano, Facolta' di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini,unimi.it skype alessandrocontini From owner-chemistry@ccl.net Wed Jul 23 15:45:01 2008 From: "flavio forti fforti.:.fortisrl.com.ar" To: CCL Subject: CCL: Optimization with imaginary frequency Message-Id: <-37400-080723153907-13810-NfBFt+2i+74fPpFc5UFvPQ===server.ccl.net> X-Original-From: "flavio forti" Date: Wed, 23 Jul 2008 15:39:02 -0400 Sent to CCL by: "flavio forti" [fforti^_^fortisrl.com.ar] Hi everybody. I am trying to optimize a large set of histamine monocation conformers in solution (PCM) with B3LYP/6-31G*. I had some which converged to a saddle point (1 imaginary frequency) but finally, after several reoptimizations with CalcFC they arrived to a minimum. But there is one still resisting. CalcAll would be to expensive, what do you suggest? thanks flavio From owner-chemistry@ccl.net Wed Jul 23 17:41:01 2008 From: "Reinaldo Pis Diez reinaldo.pisdiez|-|gmail.com" To: CCL Subject: CCL:G: Optimization with imaginary frequency Message-Id: <-37401-080723173620-15603-Tixf4Kam84fPqpXBXzr6kg__server.ccl.net> X-Original-From: Reinaldo Pis Diez Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 23 Jul 2008 17:39:52 -0300 MIME-Version: 1.0 Sent to CCL by: Reinaldo Pis Diez [reinaldo.pisdiez..gmail.com] Hi Flavio, A possible approach to face the problem could be to take to cartesian coords of the normal mode associated to the imaginary frequency that you can find in the output (it is clear you're using gaussian from the keywords you're mentioning) and use them to perturb the geometry that leads to the saddle point. To make things clearer, if xi_old is the optimized cart coord of the i-th atom (taken from the standard orientation, not from the input one) and Xi is the corresponding cart coord of the imaginary normal mode, then the perturbed coord will be: xi_new <- xi_old + factor * Xi where factor could be 0.1 or 0.25, for example, a small value to make perturbation small. Then, the new, perturbed geometry is optimized at the same level of theory as before. Hope this helps. Regards, Reinaldo flavio forti fforti.:.fortisrl.com.ar escribió: > Sent to CCL by: "flavio forti" [fforti^_^fortisrl.com.ar] > Hi everybody. I am trying to optimize a large set of histamine monocation conformers in solution (PCM) with B3LYP/6-31G*. I had some which converged to a saddle point (1 imaginary frequency) but finally, after several reoptimizations with CalcFC they arrived to a minimum. But there is one still resisting. CalcAll would be to expensive, what do you suggest? > thanks > flavio> > > From owner-chemistry@ccl.net Wed Jul 23 20:55:00 2008 From: "Andrew Orry orry.molsoft=gmail.com" To: CCL Subject: CCL: ICM Desktop Modeling Version 3.6 Released Message-Id: <-37402-080723204644-30755-dCTgd9thkhghu+s8cjmZ7g(-)server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=ISO-8859-1 Date: Wed, 23 Jul 2008 16:42:21 -0700 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [orry.molsoft/a\gmail.com] MolSoft LLC  is pleased to announce the release of a major new upgrade (Version 3.6) of its ICM desktop modeling software for computational biology and chemistry. For more information please see our July 2008 newsletter. The new release contains many new and exciting tools for structure-based and ligand-based drug design including a state-of-the-art ligand editor; new ways to dock, on the fly, Markush libraries;  multiple receptor conformation docking; and much more... We have also released a new product called ActiveICM ,which enables fully-interactive 3D objects to be displayed inside Microsoft Office products and web browsers.

Here are some ways for you to find out how you can use the new features and products for your research:

1. You are invited join us at our  workshop entitled "Protein Structure and Drug Discovery" at our offices in La Jolla, CA. The workshop is presented by Prof. Ruben Abagyan (The Scripps Research Institute, Founder MolSoft LLC) and Dr. Maxim Totrov (Principal Scientist, MolSoft).

2. We provide free once a month web demonstrations focusing on different aspects of the software. The demo in September will focus on how to use the ligand editor for lead optimization.

3. Join the MolSoft ICM discussion forum and interact with the worldwide ICM user community.

Best regards,

Andrew Orry
Senior Research Scientist
MolSoft LLC
3366 North Torrey Pines Court
Suite 300
La Jolla, CA 92037
U S A

Phone: (858) 625-2000 (x108)
Fax: (858) 625-2888

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name="image001.gif" Content-Transfer-Encoding: base64 Content-ID: R0lGODlhpwBNAHcAMSH+GlNvZnR3YXJlOiBNaWNyb3NvZnQgT2ZmaWNlACH5BAEAAAAALAIAAgCi AEkAgAAAAAAAAAL/hI+py+0PTZgz2osjpbn7rwTgSFpiiabIqbZP1bDu3Mn0fdrrzV96P/tJgBqa 0EQEHJfJGMx1hEShi+g0efVkq82DTcTsMrYZcsKMkm1i4rFRG6o8NfIwsh1618Zo79TcF6R3tsHh 5UZY+HMFiJcnuMf1wYgRSAVZxhUI5vd453iIWfnYlzOkdDYKKjGXYqmWAxiLSnvqswr0ymMaeou7 C2IpZVv6Cxysx5upxNJqTKf83DnS3LyiKGzEmy2NeMqNZ13b7bozboKdrr6u/i1+zR4vP0+vo3bO rNht2Euedu2vCLGA5fp1qbcGnjlczkq8awNO0qpoaTg5iijxF0Y//xsjiapYrEVHOKwwdnw47NLE gQ5FLnyBj8TIZePAzTQYT6VIbBlfpks5iJnBoK5QppIkxxZQnV+IjGzKxlMoMjehDv3Y0qdRfFu9 qbB6VWfWhRa5IlX1VapSHC6PmgPbq1HaqdWw7Jx29B5dvEsdFuJ40ytIK1/+zmkomOCki4HDKkYL MddjmZOpVUZ2WUvCzHw2c/4MOrTo0aRLmz6NOrXq1axbu34NOwjC2e1iS7btujFuULp3X4TNM1++ OmCeGGrIrwxinxzVOuDXW+pDvedgEcIck2xcgAJrRWdObLpbodxJrs0L/rzXrpigWqSutCz5f97s ZIep/qfltaaigZktKx9liFjx1nzPvTSfSZ6h0l8inr2n3nALjkdKVIcch18/cC3G3xAB/vfNfTQN mJgyBI63oXlNNYigXhCOFdUiZ0UYk1ERLVEXhS6ypx+FBtpIYoRCACkgH3xVRxZF5jFYE07gbQVf jgZOklx6JQE2HC0TVvLXdhp2KWFx9oBZ2HK+HRhfE9+1RlF0a7JZYw9v5jbnmbe1VgAAOw== ------=_NextPart_000_000C_01C8ED77.8CA4C980-- From owner-chemistry@ccl.net Wed Jul 23 23:20:01 2008 From: "Aleksey Kuznetsov AlexKuznetsov2007^^^yandex.ru" To: CCL Subject: CCL: TM5.10: problems with constrained geometry optimization during a search for a transition state Message-Id: <-37404-080723230821-7982-JulwBGzs4E1ASkLE0T+sNw[*]server.ccl.net> X-Original-From: Aleksey Kuznetsov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Thu, 24 Jul 2008 06:24:27 +0400 MIME-Version: 1.0 Sent to CCL by: Aleksey Kuznetsov [AlexKuznetsov2007[#]yandex.ru] Dear Uwe, thanks a lot for your recommendation! I sent an email to the Turbomole support team and got a reply from them, too, but, unfortunately, that reply did not clarify much for me. :-( Do you think it would be useful to put this question of mine at the Turbomole forum? With best regards, Aleksey. 18.07.08, 12:30, UweHuniaruwe.huniar]=[cosmologic.de : > Sent to CCL by: Uwe Huniar [uwe.huniar^_^cosmologic.de] > Hello, > this does not look like a known problem, so I would like to ask you to send an > email to the Turbomole support (turbomole at cosmologic de - see > http://www.cosmologic.de/data/DOK_HTML/node3.html). > Regards, > Uwe ------------------------------------------- Dr. Aleksey Kuznetsov Cherry L. Emerson Center for Scientific Computation Emory University 1515 Dickey Drive Atlanta, GA 30322 USA Phone: (404)727-2381 Email: akuznets{:}euch4e.chem.emory.edu ------------------------------------------- From owner-chemistry@ccl.net Wed Jul 23 23:50:00 2008 From: "gnli gnli|*|dicp.ac.cn" To: CCL Subject: CCL:G: a question about gaussian function Message-Id: <-37405-080723232755-20310-8jw26Kxcgumhn/98xH6KSQ++server.ccl.net> X-Original-From: "gnli" Content-Type: multipart/related; boundary="----=_NextPart_000_0019_01C8ED80.71514F10" Date: Thu, 24 Jul 2008 11:28:46 +0800 MIME-Version: 1.0 Sent to CCL by: "gnli" [gnli[*]dicp.ac.cn] This is a multi-part message in MIME format. ------=_NextPart_000_0019_01C8ED80.71514F10 Content-Type: multipart/alternative; boundary="----=_NextPart_001_001A_01C8ED80.71514F10" ------=_NextPart_001_001A_01C8ED80.71514F10 Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit Dear CLLer, In the equation (2), they multiply a Ei before Ri, I want to know why ? the position of $B&R(B width factor are different between $B!J(B1$B!K(B and $B!J(B2$B!K(B, which formula is right? best wishes Guanna Li gnli[*]dicp.ac.cn _____ > From: owner-chemistry[*]ccl.net [mailto:owner-chemistry[*]ccl.net] Sent: Wednesday, July 23, 2008 8:32 PM To: Li, Guanna Subject: CCL:G: a question about gaussian function Dear CLLer I have read a paper (JPCA 2003 v107 2524-2539 ), Please allow me asking a question about the Gaussian function for CD spectrum. As we know, the Gaussian function is defined as follow : (1) But in the paper(page3), they said that $B!H(BThe CD spectra were simulated by overlapping Gaussian functions for each transition according to (2) Uing the width of the band at 1/e height $B!I(B I will very appreciate if you can give a explanation how the equation (2) is got, because I don$B!G(Bt quite understand. Besides, maybe, I guess these is a $B!H(B ) $B!H(B missing during the equation (2). I think the last part is (3) But it is just a guess. Please forgive me if I$B!G(Bm wrong. I will look forward to your response. Thank you very much ! best wishes Guanna Li gnli##dicp.ac.cn ------=_NextPart_001_001A_01C8ED80.71514F10 Content-Type: text/html; charset="iso-2022-jp" Content-Transfer-Encoding: quoted-printable

Dear = CLLer,

In = the equation (2), they multiply a Ei before Ri, I want to know why ? the position of = =1B$B&R=1B(J width factor are different between =1B$B!J=1B(J1=1B$B!K=1B(J and = =1B$B!J=1B(J2=1B$B!K=1B(J, which formula =  is right?

 <= /span>

best wishes
Guanna Li
gnli[*]dicp.ac.cn



From: = owner-chemistry[*]ccl.net = [mailto:owner-chemistry[*]ccl.net]
Sent: Wednesday, July 23, = 2008 8:32 PM
To: Li, Guanna =
Subject: CCL:G: a = question about gaussian function

 

Dear = CLLer

I have read a paper = (JPCA 2003 v107 2524-2539 = ), Please allow me asking a question about the Gaussian function for CD = spectrum.

As we know, the Gaussian = function is defined as follow :

 

(1)

 

But in the paper(page3), = they said that =1B$B!H=1B(JThe CD = spectra were simulated by overlapping Gaussian functions for each transition = according to

(2)

 

Uing = the width of the band at 1/e height =1B$B!I=1B(J

 

I will very appreciate if = you can give a explanation how the equation (2) is got, because I = don=1B$B!G=1B(Jt quite understand.

Besides, maybe, I guess = these is a =1B$B!H=1B(J ) =1B$B!H=1B(J missing during the equation (2). I think the = last part is

 

(3)<= /b>

 

But it is just a guess. = Please forgive me if I=1B$B!G=1B(Jm wrong.

 

I will look forward to your = response. Thank you very much !

best wishes
Guanna Li
gnli##dicp.ac.cn

 

 

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