From owner-chemistry@ccl.net Tue Oct 17 03:36:01 2006 From: "Stan van Gisbergen vangisbergen/a\scm.com" To: CCL Subject: CCL:G: Morokuma energy decomposition Message-Id: <-32815-061017033205-12645-ShQ4AqgMEs482NVYDkxPDA : server.ccl.net> X-Original-From: Stan van Gisbergen Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Date: Tue, 17 Oct 2006 09:31:26 +0200 Mime-Version: 1.0 (Apple Message framework v619.2) Sent to CCL by: Stan van Gisbergen [vangisbergen::scm.com] Dear Adlane, The Amsterdam Density Functional (ADF) software package supports fragment calculations and energy decomposition analysis within DFT. I quote from our brochure: "Bond energy analysis ADF calculates various chemically meaningful terms that add up to the bond energy, with an adaptation of Morokuma's bond energy decomposition to the Kohn-Sham MO method. The individual terms are chemically intuitive quantities such as electrostatic energy, Pauli repulsion, and orbital interactions. The latter are symmetry decomposed according to the Ziegler transition state method." Our online tutorial number 8 for the ADF Graphical User Interface explains how fragment calculations and the associated energy decomposition are now simplified drastically in the ADF2006 release: http://www.scm.com/Doc/Doc2006.01/ADFGUI/ADFGUI_tutorial/page124.html Another example explains how to analyze bonding of the PCCP molecule in terms of the open-shell PC fragments: http://www.scm.com/Doc/Doc2006.01/ADF/Examples/page29.html A free trial is available from our web site if you want to give this a try. Best regards, Stan van Gisbergen On Oct 16, 2006, at 12:14 AM, Sergio Emanuel Galembeck segalemb]~[usp.br wrote: > Sent to CCL by: Sergio Emanuel Galembeck [segalemb%a%usp.br] > Adlane, > > Gaussian don't do Morokuma analysis. The best alternative > is Gamess. > > Hope this help you, > > Sergio > > ============================================================== > Sergio Emanuel Galembeck > Assistant Professor in Physical Chemistry > Laboratorio de Quimica Quantica Computacional > Departamento de Quimica > Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto > Universidade de Sao Paulo > Av Bandeirantes, 3900 > Ribeirao Preto, SP > Brasil > > phone: +55-16-602-37-65 > fax: +55-16-633-81-51 > e-mail: segalemb : usp.br > ============================================================== > > > Citando "Adlane sayede adlane.sayede_._gmail.com" ccl.net>: > >> Sent to CCL by: "Adlane sayede" [adlane.sayede]^[gmail.com] >> ------=_Part_169462_26340894.1160940038555 >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> Content-Transfer-Encoding: 7bit >> Content-Disposition: inline >> >> Dear CCL users, I am looking for the g03 keyword to perform Morokuma >> energy >> decomposition. >> >> Somebody can indicate to me how to do it?? >> >> Thank you in advance for your help, >> >> Adlane** >> >> ------=_Part_169462_26340894.1160940038555 >> Content-Type: text/html; charset=ISO-8859-1 >> Content-Transfer-Encoding: 7bit >> Content-Disposition: inline >> >> >> >>

Dear CCL >> users, I >> am looking for the g03 keyword to perform Morokuma energy >> decomposition.

>> >> >> >>

> lang="EN-US">Somebody can >> indicate to me how to do it??

>> >> >> >>

> lang="EN-US">Thank you in >> advance for your help,

>> >> >> >>

> lang="EN-US">Adlane> lang="EN-US">

>> >> >> ------=_Part_169462_26340894.1160940038555--> To recover the email address of the author of the message, please > change> > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > > Dr. S.J.A. van Gisbergen       Scientific Computing & Modelling NV Theoretical Chemistry, Vrije Universiteit De Boelelaan 1083 1081 HV Amsterdam The Netherlands                                 vangisbergen{}scm.com   http://www.scm.com T: +31-20-5987626     F: +31-20-5987629       From owner-chemistry@ccl.net Tue Oct 17 08:36:00 2006 From: "matthew tassell mjt22]_[sussex.ac.uk" To: CCL Subject: CCL:G: sdd basis sets Message-Id: <-32816-061017053142-32239-IL2YnwvD7VMXRnKlS2CzCA:+:server.ccl.net> X-Original-From: "matthew tassell" Date: Tue, 17 Oct 2006 05:31:42 -0400 Sent to CCL by: "matthew tassell" [mjt22{=}sussex.ac.uk] dear all, ive just started a project in computational chemistry and hope to study a gold xenon system. part of the project involves using ecp's and basis sets that are relativistic. i went to the Stuttgart site to look at their ecp's but found it quite technical. and have also searched the ccl database for information about this,as well as how i add them to gaussian input files. below is a list of questions that if perhaps anybody could help me with i would be really gratefull. exactly what type of ecp's are there on the Stuttgart site? are they only ecp's or do they contain the valence basis set as well? How would i go about adding a ecp that consists of exponants and coeficents to a gaussian input gile?( perhaps you may be able to donate an example of one you have). How do i make sence of the format that the ecp's are written in? any surgestions about the above questions would be really grate, or just if you have any comments that might help me out when using gold or xenon in calculations. thank you in advance, matt From owner-chemistry@ccl.net Tue Oct 17 09:10:00 2006 From: "Axel Mathieu AMathieu^^tranzyme.com" To: CCL Subject: CCL: influence of ionic strength on beta sheets Message-Id: <-32817-061016173908-8683-Ts7fJkuPpuvMN/5OmZw3qw[#]server.ccl.net> X-Original-From: "Axel Mathieu" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 16 Oct 2006 16:55:07 -0400 MIME-Version: 1.0 Sent to CCL by: "Axel Mathieu" [AMathieu:+:tranzyme.com] Hello everyone, A colleague of mine asked what would be the best way to study the effect of ionic strength on beta sheets structures using molecular modeling. I in turn, ask you this as an open question and discussion. My belief is that molecular modeling will not be any good unless used in "very long" explicit solvent (with ions) MD simulations - and even there. What do you think? Have you ever tried this? References would be appreciated ... Thanks, Axel From owner-chemistry@ccl.net Tue Oct 17 09:46:00 2006 From: "zborowsk#chemia.uj.edu.pl" To: CCL Subject: CCL:G: optimizations in gaussian break symmetry Message-Id: <-32818-061017072905-15977-D5iGlpK55rsIYwKNzII0YA++server.ccl.net> X-Original-From: zborowsk-*-chemia.uj.edu.pl Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Tue, 17 Oct 2006 12:46:39 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: zborowsk_-_chemia.uj.edu.pl Dear Ben Are you sure it is symmetry breaking It will be very strange Probably Gaussian did not break symmetry of your system but opposite process occured For me you should take the last coordinates and restart calculations with the new symmetry group If you want to avoid this next time (and if you do not want to be informed that your system changed symmetry) you should probably use the "NoSymm "command > Sent to CCL by: "Ben Vastine" [vastinator===gmail.com] > ------=_Part_54217_32474097.1161011524714 > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > Content-Transfer-Encoding: 7bit > Content-Disposition: inline > > does anyone know how to avoid breaking the symmetry in optimizations in > Gaussian? for example, here is the end of one my files: > > Leave Link 103 at Fri Oct 13 02:55:01 2006, MaxMem= 73400320 cpu: > 10.1 > (Enter /home/chem1/g03_dir/g03/l202.exe) > Stoichiometry C34H53P2Rh > Framework group C2[C2(RhH),X(C34H52P2)] > Deg. of freedom 132 > Full point group C2 NOp 2 > Omega: Change in point group or standard orientation. > > Old FWG=C02 [C2(H1Rh1),X(C34H52P2)] > New FWG=C02 [C2(Rh1H1),X(C34H52P2)] > Error termination via Lnk1e in /home/chem1/g03_dir/g03/l202.exe at Fri > Oct > 13 02:55:03 2006. > > I've tried to change the grid, but I've had no success with that idea. > What > about step size? > > Thanks. > > ------=_Part_54217_32474097.1161011524714 > Content-Type: text/html; charset=ISO-8859-1 > Content-Transfer-Encoding: 7bit > Content-Disposition: inline > > does anyone know how to avoid breaking the symmetry in optimizations in > Gaussian?  for example, here is the end of one my files: >

Leave Link  103 at Fri Oct 13 02:55:01 2006, > MaxMem=   73400320 cpu:      > 10.1
 (Enter /home/chem1/g03_dir/g03/l202.exe) >
 Stoichiometry    C34H53P2Rh
 Framework > group  C2[C2(RhH),X(C34H52P2)]
 Deg. of freedom   > 132
 Full point > group                 > C2      NOp   2
 Omega: Change > in point group or standard orientation.

>  Old FWG=C02  [C2(H1Rh1),X(C34H52P2)]
 New FWG=C02  > [C2(Rh1H1),X(C34H52P2)]
 Error termination via Lnk1e in > /home/chem1/g03_dir/g03/l202.exe at Fri Oct 13 02:55:03 2006.

I've > tried to change the grid, but I've had no success with that idea.  > What about step size? >

Thanks.

> > ------=_Part_54217_32474097.1161011524714--> > > > -- Krzysztof 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 ICQ 158385743 gg 3817259 skype kzys70 From owner-chemistry@ccl.net Tue Oct 17 10:21:01 2006 From: "Ding Xunlei dingxunlei*_*gmail.com" To: CCL Subject: CCL:G: optimizations in gaussian break symmetry Message-Id: <-32819-061017060311-2595-OQ//GkgjmdrHR0RpEOghsg..server.ccl.net> X-Original-From: Ding Xunlei Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="gb2312" Date: Tue, 17 Oct 2006 11:02:14 +0800 Mime-Version: 1.0 Sent to CCL by: Ding Xunlei [dingxunlei{}gmail.com] Dear Ben£º Try to set iop(2/16) IOP(2/16=2) Keep going and leave symmetry on, using the old symmetry. IOP(2/16=3) Keep going and leave symmetry on, using the new symmetry. Yours sincerely, Ding Xunlei 2006-10-17 ______________________________________________ ======= 2006-10-17 08:59:41 You have written: ======= >Sent to CCL by: "Ben Vastine" [vastinator===gmail.com] >------=_Part_54217_32474097.1161011524714 >Content-Type: text/plain; charset=ISO-8859-1; format=flowed >Content-Transfer-Encoding: 7bit >Content-Disposition: inline > >does anyone know how to avoid breaking the symmetry in optimizations in >Gaussian? for example, here is the end of one my files: > >Leave Link 103 at Fri Oct 13 02:55:01 2006, MaxMem= 73400320 cpu: >10.1 > (Enter /home/chem1/g03_dir/g03/l202.exe) > Stoichiometry C34H53P2Rh > Framework group C2[C2(RhH),X(C34H52P2)] > Deg. of freedom 132 > Full point group C2 NOp 2 > Omega: Change in point group or standard orientation. > > Old FWG=C02 [C2(H1Rh1),X(C34H52P2)] > New FWG=C02 [C2(Rh1H1),X(C34H52P2)] > Error termination via Lnk1e in /home/chem1/g03_dir/g03/l202.exe at Fri Oct >13 02:55:03 2006. > >I've tried to change the grid, but I've had no success with that idea. What >about step size? > >Thanks. > >------=_Part_54217_32474097.1161011524714 >Content-Type: text/html; charset=ISO-8859-1 >Content-Transfer-Encoding: 7bit >Content-Disposition: inline > >does anyone know how to avoid breaking the symmetry in optimizations in Gaussian?  for example, here is the end of one my files:

Leave Link  103 at Fri Oct 13 02:55:01 2006, MaxMem=   73400320 cpu:      10.1
 (Enter /home/chem1/g03_dir/g03/l202.exe) >
 Stoichiometry    C34H53P2Rh
 Framework group  C2[C2(RhH),X(C34H52P2)]
 Deg. of freedom   132
 Full point group                 C2      NOp   2
 Omega: Change in point group or standard orientation.

> Old FWG=C02  [C2(H1Rh1),X(C34H52P2)]
 New FWG=C02  [C2(Rh1H1),X(C34H52P2)]
 Error termination via Lnk1e in /home/chem1/g03_dir/g03/l202.exe at Fri Oct 13 02:55:03 2006.

I've tried to change the grid, but I've had no success with that idea.  What about step size? >

Thanks.

> >------=_Part_54217_32474097.1161011524714--> > > = = = = = = = = = = = = = = = = = = = = From owner-chemistry@ccl.net Tue Oct 17 10:56:00 2006 From: "Soren Eustis soren===jhu.edu" To: CCL Subject: CCL:G: sdd basis sets Message-Id: <-32820-061017100307-15975-xMFnDSYB5PWkSHn8UzDnNw .. server.ccl.net> X-Original-From: "Soren Eustis" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 17 Oct 2006 10:02:52 -0400 MIME-Version: 1.0 Sent to CCL by: "Soren Eustis" [soren=jhu.edu] For starters, the SDD basis set is included with Gaussian (at least G03, probably 98 as well). I have used it for Au species and it performs well. Simply enter your information as you normally would (e.g. UB3LYP/SDD) and the ecp are used by default. The easiest way to enter basis sets is to use the GenBasis keyword in Gaussian. See this page from Gaussian, there are helpful examples on the bottom of the page: http://www.gaussian.com/g_ur/k_gen.htm Also, as far as a place to find basis sets of all kinds - by far the best I have found is the EMSL Gaussian Basis Set Order Form: http://www.emsl.pnl.gov/forms/basisform.html You simply put in the elements you have in your species, select the basis set, and voila! - a text file you can copy and save as a basis set file for input. Note: Basis sets only cover specific elements. With something like Au or Xe, I would type "Au Xe" into the "Elements" field and check the box "Show supported elements". This brings up a list of the basis sets that support these elements. Good luck. Soren Eustis +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From owner-chemistry@ccl.net Tue Oct 17 11:31:00 2006 From: "Jim Kress ccl_nospam\a/kressworks.com" To: CCL Subject: CCL:G: Morokuma energy decomposition Message-Id: <-32821-061017081244-19618-VB1IWMwKp9CaTN+XfQazMg%a%server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 17 Oct 2006 08:12:19 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam*o*kressworks.com] Yes, and ADF would be a great tool IF IT WASN'T SO EXPENSIVE! For us individual researchers who support our own work out of our own pockets and are not subsidized by a government, industry, or any academic institution, ADF just COSTS TOO MUCH! My usual grumpy $0.02 Jim > -----Original Message----- > From: Stan van Gisbergen vangisbergen/ascm.com > [mailto:owner-chemistry.%a%.ccl.net] > Sent: Tuesday, October 17, 2006 3:38 AM > To: Kress, Jim > Subject: CCL:G: Morokuma energy decomposition > > Sent to CCL by: Stan van Gisbergen [vangisbergen::scm.com] > Dear Adlane, > > The Amsterdam Density Functional (ADF) software package > supports fragment calculations and energy decomposition > analysis within DFT. > > I quote from our brochure: > "Bond energy analysis > ADF calculates various chemically meaningful terms that add > up to the bond energy, with an adaptation of Morokuma's bond > energy decomposition to the Kohn-Sham MO method. The > individual terms are chemically intuitive quantities such as > electrostatic energy, Pauli repulsion, and orbital > interactions. The latter are symmetry decomposed according to > the Ziegler transition state method." > > Our online tutorial number 8 for the ADF Graphical User > Interface explains how fragment calculations and the > associated energy decomposition are now simplified > drastically in the ADF2006 release: > http://www.scm.com/Doc/Doc2006.01/ADFGUI/ADFGUI_tutorial/page124.html > > Another example explains how to analyze bonding of the PCCP > molecule in terms of the open-shell PC fragments: > http://www.scm.com/Doc/Doc2006.01/ADF/Examples/page29.html > > A free trial is available from our web site if you want to > give this a try. > > Best regards, > Stan van Gisbergen > > On Oct 16, 2006, at 12:14 AM, Sergio Emanuel Galembeck > segalemb]~[usp.br wrote: > > > Sent to CCL by: Sergio Emanuel Galembeck [segalemb%a%usp.br] Adlane, > > > > Gaussian don't do Morokuma analysis. The best alternative is > > Gamess. > > > > Hope this help you, > > > > Sergio > > > > ============================================================== > > Sergio Emanuel Galembeck > > Assistant Professor in Physical Chemistry Laboratorio de Quimica > > Quantica Computacional Departamento de Quimica Faculdade de > Filosofia, > > Ciencias e Letras de Ribeirao Preto Universidade de Sao Paulo Av > > Bandeirantes, 3900 Ribeirao Preto, SP Brasil > > > > phone: +55-16-602-37-65 > > fax: +55-16-633-81-51 > > e-mail: segalemb : usp.br > > ============================================================== > > > > > > Citando "Adlane sayede adlane.sayede_._gmail.com" > > ccl.net>: > > > >> Sent to CCL by: "Adlane sayede" [adlane.sayede]^[gmail.com] > >> ------=_Part_169462_26340894.1160940038555 > >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed > >> Content-Transfer-Encoding: 7bit > >> Content-Disposition: inline > >> > >> Dear CCL users, I am looking for the g03 keyword to > perform Morokuma > >> energy decomposition. > >> > >> Somebody can indicate to me how to do it?? > >> > >> Thank you in advance for your help, > >> > >> Adlane** > >> > >> ------=_Part_169462_26340894.1160940038555 > >> Content-Type: text/html; charset=ISO-8859-1 > >> Content-Transfer-Encoding: 7bit > >> Content-Disposition: inline > >> > >> > >> > >>

Dear CCL users, > >> I am > looking for > >> the g03 keyword to perform Morokuma energy > decomposition.

> >> > >> > >> > >>

>> lang="EN-US">Somebody can > >> indicate to me how to do it??

> >> > >> > >> > >>

>> lang="EN-US">Thank you in > >> advance for your help,

> >> > >> > >> > >>

>> lang="EN-US">Adlane >> lang="EN-US">

> >> > >> > >> ------=_Part_169462_26340894.1160940038555--> To recover the email > >> address of the author of the message, please > > change> > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > > search)> > > > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > > +-+ > > > > > > > > > Dr. S.J.A. van Gisbergen > Scientific Computing & Modelling NV > Theoretical Chemistry, Vrije Universiteit De Boelelaan 1083 > 1081 HV Amsterdam > The Netherlands vangisbergen%scm.com http://www.scm.com > T: +31-20-5987626 > F: +31-20-5987629       > > > > -= 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 .%a%. sign. You can also look up the X-Original-From: line > in the mail header.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > From owner-chemistry@ccl.net Tue Oct 17 12:06:00 2006 From: "Kirk Peterson kipeters%wsu.edu" To: CCL Subject: CCL:G: sdd basis sets Message-Id: <-32822-061017103448-12694-n5dikaJA3MhSysYXvPD2IQ##server.ccl.net> X-Original-From: Kirk Peterson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Tue, 17 Oct 2006 15:39:50 +0200 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Kirk Peterson [kipeters%wsu.edu] Matt, I would check out the basis set download site at Pacific Northwest National Lab (http://www.emsl.pnl.gov/forms/basisform.html) where you can get the ECP's and accompanying basis sets in Gaussian format. At risk of a bit of self promotion, there are a new series of correlation consistent basis sets optimized explicitly for the newest Stuttgart ECPs, denoted by cc-pVDZ-PP, cc-pVTZ-PP, etc. These are available for the p-block elements from Ga-Rn, as well as the coinage metals Cu-Au. These are also available from the EMSL site. good luck! -Kirk Peterson On Oct 17, 2006, at 2:45 PM, matthew tassell mjt22]_[sussex.ac.uk wrote: > Sent to CCL by: "matthew tassell" [mjt22{=}sussex.ac.uk] > dear all, ive just started a project in computational chemistry and > hope to study a gold xenon system. part of the project involves > using ecp's and basis sets that are relativistic. i went to the > Stuttgart site to look at their ecp's but found it quite > technical. and have also searched the ccl database for information > about this,as well as how i add them to gaussian input files. below > is a list of questions that if perhaps anybody could help me with i > would be really gratefull. > > exactly what type of ecp's are there on the Stuttgart site? are > they only ecp's or do they contain the valence basis set as well? > > How would i go about adding a ecp that consists of exponants and > coeficents to a gaussian input gile?( perhaps you may be able to > donate an example of one you have). > > How do i make sence of the format that the ecp's are written in? > > any surgestions about the above questions would be really grate, or > just if you have any comments that might help me out when using > gold or xenon in calculations. thank you in advance, matt > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > From owner-chemistry@ccl.net Tue Oct 17 14:26:00 2006 From: "Kirk Peterson kipeters:_:wsu.edu" To: CCL Subject: CCL:G: sdd basis sets Message-Id: <-32823-061017134326-18124-yyiaQa/TLlivRPq0zoEFUw() server.ccl.net> X-Original-From: Kirk Peterson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Tue, 17 Oct 2006 19:43:39 +0200 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Kirk Peterson [kipeters,,wsu.edu] As a follow-up to my last post, it seems these new basis sets are only available on PNNL's new basis set website, which is accessible from the usual link given below but you have to follow the link to "Basis Set Exchange". -Kirk On Oct 17, 2006, at 6:21 PM, Kirk Peterson kipeters%wsu.edu wrote: > Sent to CCL by: Kirk Peterson [kipeters%wsu.edu] > Matt, > > I would check out the basis set download site at Pacific Northwest > National Lab (http://www.emsl.pnl.gov/forms/basisform.html) where you > can get the ECP's and accompanying basis sets in Gaussian format. At > risk of a bit of self promotion, there are a new series of > correlation consistent basis sets optimized explicitly for the newest > Stuttgart ECPs, denoted by cc-pVDZ-PP, cc-pVTZ-PP, etc. These are > available for the p-block elements from Ga-Rn, as well as the coinage > metals Cu-Au. These are also available from the EMSL site. > > good luck! > > -Kirk Peterson > > On Oct 17, 2006, at 2:45 PM, matthew tassell mjt22]_[sussex.ac.uk > wrote: > >> Sent to CCL by: "matthew tassell" [mjt22{=}sussex.ac.uk] >> dear all, ive just started a project in computational chemistry and >> hope to study a gold xenon system. part of the project involves >> using ecp's and basis sets that are relativistic. i went to the >> Stuttgart site to look at their ecp's but found it quite >> technical. and have also searched the ccl database for information >> about this,as well as how i add them to gaussian input files. below >> is a list of questions that if perhaps anybody could help me with i >> would be really gratefull. >> >> exactly what type of ecp's are there on the Stuttgart site? are >> they only ecp's or do they contain the valence basis set as well? >> >> How would i go about adding a ecp that consists of exponants and >> coeficents to a gaussian input gile?( perhaps you may be able to >> donate an example of one you have). >> >> How do i make sence of the format that the ecp's are written in? >> >> any surgestions about the above questions would be really grate, or >> just if you have any comments that might help me out when using >> gold or xenon in calculations. thank you in advance, matt >> >> >> >> -= This is automatically added to each message by the mailing >> script =- >> To recover the email address of the author of the message, please >> change> Conferences: http://server.ccl.net/chemistry/announcements/ >> conferences/ >> >> Search Messages: http://www.ccl.net/htdig (login: ccl, Password: >> search)> >> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- >> +-+-+ >> >> > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > From owner-chemistry@ccl.net Tue Oct 17 19:26:01 2006 From: "saurabh agrawal imsam100++yahoo.co.in" To: CCL Subject: CCL: Binding energy calculation Message-Id: <-32824-061017150324-18405-DgO5EvwhqLcQx0gI6Pa8xw^^^server.ccl.net> X-Original-From: "saurabh agrawal" Date: Tue, 17 Oct 2006 15:03:24 -0400 Sent to CCL by: "saurabh agrawal" [imsam100 ~ yahoo.co.in] Dear All, I am trying to calculate Binding energy of DNA drug interaction from Delphi and solvation results of insightII software. If anyone has the relation formulae between free energy/solvation energy and binding energy please send that to me. Thanks in advance. saurabh From owner-chemistry@ccl.net Tue Oct 17 21:13:00 2006 From: "gilson{}umbi.umd.edu" To: CCL Subject: CCL: Binding energy calculation Message-Id: <-32825-061017210856-3514-aG3Y9N5jKyF1D8pdWlWCcQ%%server.ccl.net> X-Original-From: Content-Language: en Content-Type: multipart/alternative; boundary="--b9d5a6501a8d4f8d2d55" Date: Tue, 17 Oct 2006 20:14:47 -0400 MIME-Version: 1.0 Sent to CCL by: [gilson%umbi.umd.edu] This is a multi-part message in MIME format. ----b9d5a6501a8d4f8d2d55 Content-Type: text/plain; charset=iso-8859-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Hi Saurabh=2C If I=27ve read your question right=2C then the answer is that there is n= o one-to-one mapping from the energy you are calculating and the standar= d free energy of binding=2E=A0 The latter includes additional influences= =2C such as changes in internal energy and changes in configurational en= tropy=2E=A0 = Regards=2C Mike ----- Original Message ----- > From=3A =22saurabh agrawal imsam100++yahoo=2Eco=2Ein=22 =3Cowner-chemist= ry=40ccl=2Enet=3E Date=3A Tuesday=2C October 17=2C 2006 7=3A45 pm Subject=3A CCL=3A Binding energy calculation To=3A =22Gilson=2C Mike -id=233ut-=22 =3Cgilson=40umbi=2Eumd=2Eedu=3E =3E Sent to CCL by=3A =22saurabh=A0 agrawal=22 =5Bimsam100 =7E yahoo=2Ec= o=2Ein=5D =3E Dear All=2C = =3E I am trying to calculate Binding energy of DNA drug interaction = =3E from Delphi = =3E and solvation results of insightII software=2E If anyone has the = =3E relation = =3E formulae between free energy/solvation energy and binding energy = =3E please = =3E send that to me=2E = =3E =A0 =3E Thanks in advance=2E = =3E saurabh =3E = =3E = =3E = =3E -=3D This is automatically added to each message by the mailing = =3E script =3D- =3E To recover the email address of the author of the message=2C = =3E please change =3E the strange characters on the top line to the =40 sign=2E You can al= so =3E look up the X-Original-From=3A line in the mail header=2E =3E = =3E E-mail to subscribers=3A CHEMISTRY=40ccl=2Enet or use=3A =3E =A0=A0=A0=A0=A0 http=3A//www=2Eccl=2Enet/cgi- =3E bin/ccl/send=5Fccl=5Fmessage =3E E-mail to administrators=3A CHEMISTRY-REQUEST=40ccl=2Enet or use =3E =A0=A0=A0=A0=A0 http=3A//www=2Eccl=2Enet/cgi- =3E bin/ccl/send=5Fccl=5Fmessage =3E Subscribe/Unsubscribe=3A = =3E =A0=A0=A0=A0=A0 = =3E http=3A//www=2Eccl=2Enet/chemistry/sub=5Funsub=2Eshtml =3E Before posting=2C check wait time at=3A http=3A//www=2Eccl=2Enet =3E = =3E Job=3A http=3A//www=2Eccl=2Enet/jobs = =3E Conferences=3A = =3E http=3A//server=2Eccl=2Enet/chemistry/announcements/conferences/ =3E Search Messages=3A http=3A//www=2Eccl=2Enet/htdig=A0 (login=3A ccl=2C= = =3E Password=3A search) =3E = =3E If your mail bounces from CCL with 5=2E7=2E1 error=2C check=3A =3E =A0=A0=A0=A0=A0 http=3A//www=2Eccl=2Enet/spammers=2Etxt =3E = =3E RTFI=3A http=3A//www=2Eccl=2Enet/chemistry/aboutccl/instructions/ =3E = =3E -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- =3E +-+-+-+ =3E = =3E = =3E = =3E ----b9d5a6501a8d4f8d2d55 Content-Type: text/html; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Hi Saurabh=2C=3Cbr=3E=3Cbr=3EIf I=27ve read your question right=2C then = the answer is that there is no one-to-one mapping from the energy you ar= e calculating and the standard free energy of binding=2E=26nbsp=3B The l= atter includes additional influences=2C such as changes in internal ener= gy and changes in configurational entropy=2E=26nbsp=3B =3Cbr=3E=3Cbr=3ER= egards=2C=3Cbr=3EMike=3Cbr=3E=3Cbr=3E----- Original Message -----=3Cbr=3E= > From=3A =22saurabh agrawal imsam100++yahoo=2Eco=2Ein=22 =26lt=3Bowner-ch= emistry=40ccl=2Enet=26gt=3B=3Cbr=3EDate=3A Tuesday=2C October 17=2C 2006= 7=3A45 pm=3Cbr=3ESubject=3A CCL=3A Binding energy calculation=3Cbr=3ETo= =3A =22Gilson=2C Mike -id=233ut-=22 =26lt=3Bgilson=40umbi=2Eumd=2Eedu=26= gt=3B=3Cbr=3E=3Cbr=3E=26gt=3B Sent to CCL by=3A =22saurabh=26nbsp=3B agr= awal=22 =5Bimsam100 =7E yahoo=2Eco=2Ein=5D=3Cbr=3E=26gt=3B Dear All=2C =3C= br=3E=26gt=3B I am trying to calculate Binding energy of DNA drug intera= ction =3Cbr=3E=26gt=3B from Delphi =3Cbr=3E=26gt=3B and solvation result= s of insightII software=2E If anyone has the =3Cbr=3E=26gt=3B relation =3C= br=3E=26gt=3B formulae between free energy/solvation energy and binding = energy =3Cbr=3E=26gt=3B please =3Cbr=3E=26gt=3B send that to me=2E =3Cbr= =3E=26gt=3B =26nbsp=3B=3Cbr=3E=26gt=3B Thanks in advance=2E =3Cbr=3E=26g= t=3B saurabh=3Cbr=3E=26gt=3B =3Cbr=3E=26gt=3B =3Cbr=3E=26gt=3B =3Cbr=3E=26= gt=3B -=3D This is automatically added to each message by the mailing =3C= br=3E=26gt=3B script =3D-=3Cbr=3E=26gt=3B To recover the email address o= f the author of the message=2C =3Cbr=3E=26gt=3B please change=3Cbr=3E=26= gt=3B the strange characters on the top line to the =40 sign=2E You can = also=3Cbr=3E=26gt=3B look up the X-Original-From=3A line in the mail hea= der=2E=3Cbr=3E=26gt=3B =3Cbr=3E=26gt=3B E-mail to subscribers=3A CHEMIST= RY=40ccl=2Enet or use=3A=3Cbr=3E=26gt=3B =26nbsp=3B=26nbsp=3B=26nbsp=3B=26= nbsp=3B=26nbsp=3B http=3A//www=2Eccl=2Enet/cgi-=3Cbr=3E=26gt=3B bin/ccl/= send=5Fccl=5Fmessage=3Cbr=3E=26gt=3B E-mail to administrators=3A CHEMIST= RY-REQUEST=40ccl=2Enet or use=3Cbr=3E=26gt=3B =26nbsp=3B=26nbsp=3B=26nbs= p=3B=26nbsp=3B=26nbsp=3B http=3A//www=2Eccl=2Enet/cgi-=3Cbr=3E=26gt=3B b= in/ccl/send=5Fccl=5Fmessage=3Cbr=3E=26gt=3B Subscribe/Unsubscribe=3A =3C= br=3E=26gt=3B =26nbsp=3B=26nbsp=3B=26nbsp=3B=26nbsp=3B=26nbsp=3B =3Cbr=3E= =26gt=3B http=3A//www=2Eccl=2Enet/chemistry/sub=5Funsub=2Eshtml=3Cbr=3E=26= gt=3B Before posting=2C check wait time at=3A http=3A//www=2Eccl=2Enet=3C= br=3E=26gt=3B =3Cbr=3E=26gt=3B Job=3A http=3A//www=2Eccl=2Enet/jobs =3Cb= r=3E=26gt=3B Conferences=3A =3Cbr=3E=26gt=3B http=3A//server=2Eccl=2Enet= /chemistry/announcements/conferences/=3Cbr=3E=26gt=3B Search Messages=3A= http=3A//www=2Eccl=2Enet/htdig=26nbsp=3B (login=3A ccl=2C =3Cbr=3E=26gt= =3B Password=3A search)=3Cbr=3E=26gt=3B =3Cbr=3E=26gt=3B If your mail bo= unces from CCL with 5=2E7=2E1 error=2C check=3A=3Cbr=3E=26gt=3B =26nbsp=3B= =26nbsp=3B=26nbsp=3B=26nbsp=3B=26nbsp=3B http=3A//www=2Eccl=2Enet/spamme= rs=2Etxt=3Cbr=3E=26gt=3B =3Cbr=3E=26gt=3B RTFI=3A http=3A//www=2Eccl=2En= et/chemistry/aboutccl/instructions/=3Cbr=3E=26gt=3B =3Cbr=3E=26gt=3B -+-= +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-=3Cbr=3E=26= gt=3B +-+-+-+=3Cbr=3E=26gt=3B =3Cbr=3E=26gt=3B =3Cbr=3E=26gt=3B =3Cbr=3E= =26gt=3B ----b9d5a6501a8d4f8d2d55-- From owner-chemistry@ccl.net Tue Oct 17 23:43:00 2006 From: "Rajendran Arivazhagan raji],[anal.chem.tohoku.ac.jp" To: CCL Subject: CCL:G: Effect of basis set on frequency calculations with g03 Message-Id: <-32826-061017234146-25369-FTtaKQ2a6xfrUo7w0B13iA!^!server.ccl.net> X-Original-From: "Rajendran Arivazhagan" Date: Tue, 17 Oct 2006 23:41:46 -0400 Sent to CCL by: "Rajendran Arivazhagan" [raji[a]anal.chem.tohoku.ac.jp] Dear CCL Members, I am doing frequency calculation for protonated organic molecule using g03. My molecule have two protonation sites, say for example site1 and site2. Freq calculation with B3LYP/6-311+G(d) gave an imaginary/negative frequency for site1 and all real frequencies were observed for site2. My input file looks like: B3LYP/6-311+G(d) SCF=Tight test Opt Freq Pop=full gfprint SCRF=(CPCM, Solvent=Water) But the results are completely opposite with B3LYP/3-21G and here negative frequency was observed for site2 and all real frequencies were observed for site1. Input file looks like: B3LYP/3-21G SCF=Tight test Opt Freq Pop=full gfprint SCRF=(CPCM, Solvent=Water) So which result I can believe and where is the problem? Basis set with polarization and diffuse functions are not suitable for frequency calculations? Any suggestion is most welcome. Thank you very much. A.Rajendran.