From owner-chemistry@ccl.net Mon Aug 25 01:00:00 2008 From: "lizhe3[*]mail.ustc.edu.cn lizhe3[*]mail.ustc.edu.cn" To: CCL Subject: CCL:G: How to do Double 3d Shell Calculation Message-Id: <-37608-080823220328-11874-w/WLxU45qkX+lpMiT1RWYg(_)server.ccl.net> X-Original-From: "lizhe3(a)mail.ustc.edu.cn" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Sun, 24 Aug 2008 09:33:25 +0800 Mime-Version: 1.0 Sent to CCL by: "lizhe3-*-mail.ustc.edu.cn" [lizhe3-*-mail.ustc.edu.cn] Dear All, I read in literature that the 3d shell of transition metals has a correlation effect called "3d double shell effect"(eg. K Andersson, BO Roos. Chem Phys Letters 191:507–514, 1992.and TH Dunning Jr, BH Botch, JF Harrison. J Chem Phys 72:3419–3420, 1980.). They described the way to address this problem by adding a second more diffuse d shell to the electron configuration in CASSCF calculation, eg. the original configuration of Cu atom is 3d(10)4s(1) can be transformed to 3d(9)3d'(1)4s(1), with 3d' a more diffuse shell. But I do not know how to do this practically. It seems in the CASSCF method of Gaussian software I can only include the 3d orbital. Should I also include the 4d orbital or just use more diffuse basis set? Does anyone know how to add the 3d' orbital? From owner-chemistry@ccl.net Mon Aug 25 02:58:01 2008 From: "Johannes Hachmann jh388*_*cornell.edu" To: CCL Subject: CCL:G: How to do Double 3d Shell Calculation Message-Id: <-37609-080825022344-11713-XoD/hx10ws1Pgm8iiiAYnw_._server.ccl.net> X-Original-From: "Johannes Hachmann" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 25 Aug 2008 01:52:59 -0400 MIME-Version: 1.0 Sent to CCL by: "Johannes Hachmann" [jh388|a|cornell.edu] Hi, 1) I haven't used g03 for CAS calcs, but as far as I have heard, this is not one of g03s particular strengths. There are other codes like MOLCAS or MOLPRO which are more specialized in the field of multireference methods. 2) Basis set choice is an issue in TM calcs because you usually have a lot of dynamic correlation. So it is perhaps not a good idea to take apart the contraction of a single d basis function to get a second one (i.e. 3d(10)-> 3d(9)3d'(1)). Instead, you should use a proper basis set (e.g. from the EMSL data base) with a d double shell (usually you might actually want to consider something significantly bigger than that for more quantitative results, e.g. when doing CASPT2). 3) To get your active space, do an HF calc (or e.g. BLYP or OLYP, which tend to give orbs with a more physical shape), look at the MOs, identify the 10 MOs which look most like the TM (double shell) d AOs, and put them into the active space. Usually you also want to add orbitals from your ligand. You have to design the active space depending on the physics you expect in a particular complex (i.e. to accomodate sigma bonding, or pi donation, or pi back bonding), and have to validate it against alternatives (e.g. by comparing the natural orbital occupations). Putting orbitals into the active space often requires swapping MOs to get the desired active space around the Fermi level, as well as a lot of fiddling... Other practical tricks are starting from a small basis or doing rotations in your orbital spaces (i.e. localizations) to get a better starting guess for your CAS. Things get more complicated if you want to design a balenced active space along a dissociation curve... Good luck Johannes --------------------------------------------------------------- Dipl.-Chem. Johannes Hachmann Chan Research Group 140D Baker Laboratory Department of Chemistry and Chemical Biology Cornell University Ithaca, NY 14853-1301 USA --------------------------------------------------------------- > -----Original Message----- > From: owner-chemistry * ccl.net [mailto:owner-chemistry * ccl.net] > Sent: Saturday, August 23, 2008 9:33 PM > To: Hachmann, Johannes > Subject: CCL:G: How to do Double 3d Shell Calculation > > > Sent to CCL by: "lizhe3-*-mail.ustc.edu.cn" > [lizhe3-*-mail.ustc.edu.cn] > > Dear All, > > I read in literature that the 3d shell of transition metals > has a correlation effect called "3d double shell effect"(eg. > K Andersson, BO Roos. Chem Phys Letters 191:507-514, 1992.and > TH Dunning Jr, BH Botch, JF Harrison. J Chem Phys > 72:3419-3420, 1980.). They described the way to address this > problem by adding a second more diffuse d shell to the > electron configuration in CASSCF calculation, eg. the > original configuration of Cu atom is 3d(10)4s(1) can be > transformed to 3d(9)3d'(1)4s(1), with 3d' a more diffuse > shell. But I do not know how to do this practically. It seems > in the CASSCF method of Gaussian software I can only include > the 3d orbital. Should I also include the 4d orbital or just > use more diffuse basis set? Does anyone know how to add the > 3d' orbital? > > > > -= 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 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 Mon Aug 25 05:29:01 2008 From: "Nuno A. G. Bandeira nuno.bandeira^-^ist.utl.pt" To: CCL Subject: CCL:G: how G03 builds promolecule density for Hirshfeld population analysis? Message-Id: <-37610-080825050006-22077-kJVO9zUeUe9dZ4LjJlrJTQ ~ server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 25 Aug 2008 09:22:05 +0100 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira[]ist.utl.pt] Dear Alvaro, Hirshfeld charges are an experimental feature in Gaussian03. If you run tests with any model you will obtain nonsensical results for Hirshfeld charges. Regarding LiF question the Hirshfeld definition states that the promolecule is always built up from the neutral atomic constituents in their ground state i.e. rho(r) = Sum (rho_at) where rho_at is the atomic ground state density of each atom. Cheers, Nuno -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student (0) IST,Lisbon -- From owner-chemistry@ccl.net Mon Aug 25 07:52:01 2008 From: "Orlin Blajiev Orlin.Blajiev]|[vub.ac.be" To: CCL Subject: CCL:G: End of a frequency job Message-Id: <-37611-080825060009-7282-rjiNxuItwFaQHg4vf19zBA*server.ccl.net> X-Original-From: Orlin Blajiev Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 25 Aug 2008 11:25:44 +0200 MIME-Version: 1.0 Sent to CCL by: Orlin Blajiev [Orlin.Blajiev++vub.ac.be] Hi everybody, I ave a question about the Gaussian output. After the freq job was written to the output the following appears just before the end: ================ Item Value Threshold Converged? Maximum Force 0.011836 0.000450 NO RMS Force 0.003572 0.000300 NO Maximum Displacement 0.195621 0.001800 NO RMS Displacement 0.037814 0.001200 NO Predicted change in Energy=-2.775552D-03 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Test job not archived. 1\1\GINC-HYDRA18\Freq\UB3LYP\Gen\C2H2Ag12N3S2(2)\BLAJIEV\25-Aug-2008\0 \\# freq ub3lyp/Gen pop=full geom=checkpoint gfprint # scf=(cdiis MaxC onventionalCycles=1000 maxcycle=1000) nosymm iop(7/33=1) # charge=chec kpoint Pseudo=cards\\0amtd\\0,2\Ag,-2.845453,2.096181,-0.064019\Ag,-0. 76016,2.494365,2.185292\Ag,-3.413304,-0.025746, ================================== Why it is trying the optimization step again if the optimization was succefuly completed already? Best regards, Orlin -- Orlin Blajiev Department Materials and Chemistry(MACH)/Research Group META Vrije Universiteit Brussel Pleinlaan 2 - B 1050 Brussels - Belgium tel: 32 2 6293538 (secr. 3255) fax: 32 2 6293200 mail: blajiev+/-vub.ac.be http://www.vub.ac.be/META From owner-chemistry@ccl.net Mon Aug 25 08:54:02 2008 From: "Close, David M. CLOSED^-^mail.etsu.edu" To: CCL Subject: CCL:G: End of a frequency job Message-Id: <-37612-080825085221-8771-U+SVJjY7jCqa4B1UKx5tBw]*[server.ccl.net> X-Original-From: "Close, David M." Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Mon, 25 Aug 2008 08:52:06 -0400 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED,,mail.etsu.edu] Orlin: This is not right. The calculation found the input geometries in the geom=3Dcheckfile. But did it find the right checkfile? Check the geometry and make sure the energy at the end of the first scf cycle in the frequency agrees with the energy in the original optimization calculation. Also to speed up the scf calculation in the frequency job, you should use guess=3Dread. Also, we don't have your input file for = the optimization calculation. Is everything the same in both calculations? Regards, Dave Close. -----Original Message----- > From: owner-chemistry a ccl.net [mailto:owner-chemistry a ccl.net]=20 Sent: Monday, August 25, 2008 5:26 AM To: Close, David M. Subject: CCL:G: End of a frequency job Sent to CCL by: Orlin Blajiev [Orlin.Blajiev++vub.ac.be] Hi everybody, I ave a question about the Gaussian output. After the freq job was=20 written to the output the following appears just before the end: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Item Value Threshold Converged? Maximum Force 0.011836 0.000450 NO RMS Force 0.003572 0.000300 NO Maximum Displacement 0.195621 0.001800 NO RMS Displacement 0.037814 0.001200 NO Predicted change in Energy=3D-2.775552D-03 =20 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Test job not archived. 1\1\GINC-HYDRA18\Freq\UB3LYP\Gen\C2H2Ag12N3S2(2)\BLAJIEV\25-Aug-2008\0 \\# freq ub3lyp/Gen pop=3Dfull geom=3Dcheckpoint gfprint # scf=3D(cdiis = MaxC onventionalCycles=3D1000 maxcycle=3D1000) nosymm iop(7/33=3D1) # = charge=3Dchec kpoint = Pseudo=3Dcards\\0amtd\\0,2\Ag,-2.845453,2.096181,-0.064019\Ag,-0. 76016,2.494365,2.185292\Ag,-3.413304,-0.025746, =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D Why it is trying the optimization step again if the optimization was=20 succefuly completed already? Best regards, Orlin --=20 Orlin Blajiev Department Materials and Chemistry(MACH)/Research Group META Vrije Universiteit Brussel Pleinlaan 2 - B 1050 Brussels - Belgium tel: 32 2 6293538 (secr. 3255) fax: 32 2 6293200 mail: blajiev#,#vub.ac.be http://www.vub.ac.be/META -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Aug 25 09:42:01 2008 From: "amine amine m-22 _ hotmail.fr" To: CCL Subject: CCL: bad fd number Message-Id: <-37613-080825063731-3942-hnR6G9kgjLoPyytDwVW8Og . server.ccl.net> X-Original-From: "amine amine" Date: Mon, 25 Aug 2008 06:37:27 -0400 Sent to CCL by: "amine amine" [m-22!=!hotmail.fr] Hi I have amber10 and when i put antechamber -i ~/T/moll.pdb -fi pdb -o ~/T/moll.prepi -fo prepi -c bcc -j 5 I recive this message ------------------------------------ Total number of electrons: 532; net charge: 0 Running: home/az/amber10/bin/mopac.sh home/az/amber10/bin/mopac.sh: 12: Syntax error: Bad fd number Error: cannot run "/home/mohamed/amber10/bin/mopac.sh" of bcc() in charge.c properly, exit ---------------------------------------- If i dont put ( -c bcc) , there is no probleme.???????? From owner-chemistry@ccl.net Mon Aug 25 10:16:01 2008 From: "Alcides Simao alsimao[#]gmail.com" To: CCL Subject: CCL:G: End of a frequency job Message-Id: <-37614-080825094437-3947-taquGaRCuZgQZdOp2wtNPA(0)server.ccl.net> X-Original-From: "Alcides Simao" Content-Type: multipart/alternative; boundary="----=_Part_78725_5275074.1219671863481" Date: Mon, 25 Aug 2008 14:44:23 +0100 MIME-Version: 1.0 Sent to CCL by: "Alcides Simao" [alsimao ~ gmail.com] ------=_Part_78725_5275074.1219671863481 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Orlin: This is a routine check from GAUSSIAN, made after *all* frequency jobs. You can safely discart it. Gaussian will always do that, even if you don't flag the 'OPT' option. Best, Alcides ------=_Part_78725_5275074.1219671863481 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Orlin:

This is a routine check from GAUSSIAN, made after *all* frequency jobs. You can safely discart it. Gaussian will always do that, even if you don't flag the 'OPT' option.

Best,

Alcides
------=_Part_78725_5275074.1219671863481-- From owner-chemistry@ccl.net Mon Aug 25 10:52:01 2008 From: "Bienstock, Rachelle (NIH/NIEHS) C biensto1 a niehs.nih.gov" To: CCL Subject: CCL: Announcing Special CINF Symposium on Fragment-Based Ligand Design at the Spring National ACS Meeting March 2009 Salt Lake City, Utah Message-Id: <-37615-080825102624-15042-qZ4XzJUqunxVEVxADJqfxA _ server.ccl.net> X-Original-From: "Bienstock, Rachelle (NIH/NIEHS) [C]" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C906BA.1FB56F03" Date: Mon, 25 Aug 2008 09:54:42 -0400 MIME-Version: 1.0 Sent to CCL by: "Bienstock, Rachelle (NIH/NIEHS) [C]" [biensto1]|[niehs.nih.gov] This is a multi-part message in MIME format. ------_=_NextPart_001_01C906BA.1FB56F03 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable Hi CCL net members: =20 I am organizing a special symposium for the CINF division at the National ACS Spring 2009 Meeting (March 22-26, 2009) to be held in Salt Lake City, Utah on Fragment Based Drug Design. =20 This is a description of the symposium: Library Design, Search Methods and Applications of Fragment-Based Drug Design=20 Computational methodologies used for fragment library and scaffold design, optimization, and computational fragment docking, growing and linking techniques. Successful applications of these computational techniques which demonstrate enhanced conformational space sampling and novel lead generation with increased chemical diversity. =20 I would like to invite you all to participate through attendance and/or by giving a presentation at the symposium. =20 =20 All abstracts must be submitted through the ACS online OASYS system, which for this symposium=20 will be available beginning August 25th The abstract submission URL will be http://oasys.acs.org/acs/237nm/cinf/papers/index.cgi=20 25th August - OASYS author submission opens=20 20th October - OASYS author submission closes=20 3rd November - OASYS closes to symposium organizers) =20 We are also looking for sponsors for the Symposium, so if any of you are members of organizations or companies that might be interested in taking a role in sponsorship, please contact me. =20 I am really hoping to organize an outstanding symposium and I hope that you will all help in achieving that goal. If you have any suggestions for speakers or recommendations,=20 I would appreciate any input to make this an interesting and stimulating symposium. =20 Thanks, and Best Regards,=20 Rachelle =20 =20 Dr. Rachelle J. Bienstock Senior Research Scientist=20 National Institute of Environmental Health Sciences=20 Research Triangle Park, NC 27709 919-541-3397 voice=20 biensto1*niehs.nih.gov =20 =20 Dr. Rachelle J. Bienstock Senior Research Scientist=20 Constella Group, LLC=20 Contractor to NIEHS/DIR=20 National Institute of Environmental Health Sciences=20 Research Triangle Park, NC 27709 919-541-3397 voice=20 biensto1*niehs.nih.gov =20 ------_=_NextPart_001_01C906BA.1FB56F03 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable

Hi CCL net members:

 

I am organizing a special symposium for the CINF = division at the National ACS Spring 2009 Meeting (March 22-26, 2009) to be held in = Salt Lake City, Utah on Fragment Based Drug Design.

 

This is a description of the = symposium:

Library Design, Search Methods and Applications of Fragment-Based Drug Design

Computational methodologies used for fragment library = and scaffold design, optimization, and computational fragment docking, = growing and linking techniques.  Successful applications of these computational techniques which demonstrate enhanced conformational space sampling and = novel lead generation with increased chemical = diversity.

 

I would like to invite you all to participate through attendance and/or

by giving a presentation at the symposium. =  

 

All abstracts must be submitted through the ACS = online OASYS system, which for this symposium

will be available beginning August 25th = The abstract submission URL will be

http://oas= ys.acs.org/acs/237nm/cinf/papers/index.cgi

25th August - OASYS author submission opens =

20th October - OASYS author submission closes =

3rd November - OASYS closes to symposium = organizers)

 

We are also looking for sponsors for the Symposium, = so if any of you are members

of organizations or companies that might be = interested in taking a role in sponsorship,

please contact me.

 

I am really hoping to organize an outstanding = symposium and I hope

that you will all help in achieving that goal. If you = have any suggestions for speakers or recommendations, =

I would appreciate any input to make this an = interesting and stimulating

symposium.

 

Thanks, and Best Regards, =

Rachelle

 

 

Dr. Rachelle J. Bienstock
Senior Research Scientist
National Institute of Environmental Health Sciences
Research Triangle Park, NC 27709=
919-541-3397 voice
biensto1*niehs.nih.gov

 

 

Dr. Rachelle J. Bienstock
Senior Research Scientist
Constella Group, LLC
Contractor to NIEHS/DIR
National Institute of Environmental Health Sciences
Research Triangle Park, NC 27709=
919-541-3397 voice
biensto1*niehs.nih.gov

 

------_=_NextPart_001_01C906BA.1FB56F03-- From owner-chemistry@ccl.net Mon Aug 25 11:26:00 2008 From: "Pablo Englebienne pablo.englebienne. .. .mcgill.ca" To: CCL Subject: CCL: Bioinformatics software for protein digestion prediction Message-Id: <-37616-080825105631-18562-Dvg8/0luo/yPBn4QmhK1qQ .. server.ccl.net> X-Original-From: Pablo Englebienne Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 25 Aug 2008 10:25:49 -0400 MIME-Version: 1.0 Sent to CCL by: Pablo Englebienne [pablo.englebienne*mcgill.ca] Did you look at PeptideCutter in the Expasy website? http://ca.expasy.org/tools/peptidecutter/ I don't have any personal experience with it, but it looks pretty complete and exactly what you're looking for... Cheers! -- Pablo Englebienne, PhD Student, Moitessier research group Department of Chemistry, McGill University 801 Sherbrooke Street West Otto Maass bldg, room 206 H3A 2K6 Montréal, Québec, Canada Tel (514) 398-5501 Fax (514) 398-2382 "Progress is made by lazy men looking for easier ways to do things." - Robert A. Heinlein Sandeep Kumar Rambhajo%x%gmail.com wrote: > Sent to CCL by: "Sandeep Kumar" [Rambhajo|-|gmail.com] > > Dear All, > > I was wondering if somebody knows about a free bioinformatics software that can identify potential proteolytic sites for all known proteases in a given protein sequence. A software that uses protein structures to do this job would be simply awesome! > > Many thanks in advance. > > Best regards, > Sandeep Kumar, Ph.D. > Pfizer Global Biologics, > St. Louis, MO.> > > From owner-chemistry@ccl.net Mon Aug 25 12:58:01 2008 From: "Orlin Blajiev Orlin.Blajiev---vub.ac.be" To: CCL Subject: CCL:G: End of a frequency job Message-Id: <-37617-080825112857-23559-ItWG7Zx/wQL/p5x9Oqw60A(~)server.ccl.net> X-Original-From: Orlin Blajiev Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 25 Aug 2008 17:28:44 +0200 MIME-Version: 1.0 Sent to CCL by: Orlin Blajiev [Orlin.Blajiev,vub.ac.be] David, Alcides, Thanks for the info. I guess G03 reports the geometry as non-converged because I use different BS in Opt and Freq. Best regards, Orlin Alcides Simao alsimao[#]gmail.com wrote: > Orlin: > > This is a routine check from GAUSSIAN, made after *all* frequency > jobs. You can safely discart it. Gaussian will always do that, even if > you don't flag the 'OPT' option. > > Best, > > Alcides -- Orlin Blajiev Department Materials and Chemistry(MACH)/Research Group META Vrije Universiteit Brussel Pleinlaan 2 - B 1050 Brussels - Belgium tel: 32 2 6293538 (secr. 3255) fax: 32 2 6293200 mail: blajiev:_:vub.ac.be http://www.vub.ac.be/META From owner-chemistry@ccl.net Mon Aug 25 13:48:01 2008 From: "Close, David M. CLOSED^mail.etsu.edu" To: CCL Subject: CCL:G: End of a frequency job Message-Id: <-37618-080825134652-22495-q9T5DuWlKz+n4+JMrthcYg a server.ccl.net> X-Original-From: "Close, David M." Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Mon, 25 Aug 2008 13:46:30 -0400 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED__mail.etsu.edu] Yes, that is exactly right. As a check you could try a frequency calc. using the same basis set. Usually 3 out of 4 of the "yes" are ok. For some reason the third "yes" is sometimes a "no". I don't know why. Now a more basic question. If you are taking a course on doing calculations, you are always told you must use the same basis sets in frequency calculations as on the original optimizations. But people seem to be getting away from this are very large calculations. If it takes a week to do an optimization, it might take 3-4 weeks to do a frequency calculation. So people are now using smaller basis sets to do faster frequency calcs. I do not happen to know if this leads to problems. I do know that Berny Schlegel warned about this some time ago, but I do not know the current thinking on this. -----Original Message----- > From: owner-chemistry:_:ccl.net [mailto:owner-chemistry:_:ccl.net]=20 Sent: Monday, August 25, 2008 11:29 AM To: Close, David M. Subject: CCL:G: End of a frequency job Sent to CCL by: Orlin Blajiev [Orlin.Blajiev,vub.ac.be] David, Alcides, Thanks for the info. I guess G03 reports the geometry as non-converged because I use different BS in Opt and Freq. Best regards, Orlin Alcides Simao alsimao[#]gmail.com wrote: > Orlin: > > This is a routine check from GAUSSIAN, made after *all* frequency=20 > jobs. You can safely discart it. Gaussian will always do that, even if > you don't flag the 'OPT' option. > > Best, > > Alcides --=20 Orlin Blajiev Department Materials and Chemistry(MACH)/Research Group META Vrije Universiteit Brussel Pleinlaan 2 - B 1050 Brussels - Belgium tel: 32 2 6293538 (secr. 3255) fax: 32 2 6293200 mail: blajiev[#]vub.ac.be http://www.vub.ac.be/META -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Aug 25 14:23:01 2008 From: "Alcides Simao alsimao*o*gmail.com" To: CCL Subject: CCL:G: End of a frequency job Message-Id: <-37619-080825135023-25161-r3N8xY+WhBaSqYr2G4wOxw:+:server.ccl.net> X-Original-From: "Alcides Simao" Content-Type: multipart/alternative; boundary="----=_Part_81339_3023415.1219686612058" Date: Mon, 25 Aug 2008 18:50:12 +0100 MIME-Version: 1.0 Sent to CCL by: "Alcides Simao" [alsimao:+:gmail.com] ------=_Part_81339_3023415.1219686612058 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Orlin, IMVHO, GAUSSIAN just perform that check in order to see if the geometry has become distorted AFTER the freq calculations. It's kind of error checking. And be careful! Using diferent BS for OPT and FREQ is not a very good options. Remember that the PES using a particular BS can be diferent than that of other BS. Hence, you may have a minima in one BS and a TS in another! For the sake of being correct, one must use the same BS for both opt and freq. Only then will you ensure that your calculations reflect something physically relevant, otherwise is just a pure waste of time! Best, Alcides PS: There are quite a few articles that can show this reality. If you wish, I may post those articles here. ------=_Part_81339_3023415.1219686612058 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Dear Orlin,

IMVHO, GAUSSIAN just perform that check in order to see if the geometry has become distorted AFTER the freq calculations. It's kind of error checking.

And be careful! Using diferent BS for OPT and FREQ is not a very good options. Remember that the PES using a particular BS can be diferent than that of other BS. Hence, you may have a minima in one BS and a TS in another! For the sake of being correct, one must use the same BS for both opt and freq. Only then will you ensure that your calculations reflect something physically relevant, otherwise is just a pure waste of time!

Best,

Alcides

PS: There are quite a few articles that can show this reality. If you wish, I may post those articles here.
------=_Part_81339_3023415.1219686612058-- From owner-chemistry@ccl.net Mon Aug 25 16:37:00 2008 From: "errol lewars elewars+*+trentu.ca" To: CCL Subject: CCL:G: End of a frequency job Message-Id: <-37620-080825162831-21329-SD6n+YI/WZ0C5ccRzXd83A###server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Mon, 25 Aug 2008 16:28:18 -0400 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars-#-trentu.ca] 2008 August 25 The general view is that it is simply wrong to use one method/basis for the optimization and another for the frequencies: consult some standard books on computational chemistry. E. Lewars === Close, David M. CLOSED^mail.etsu.edu wrote: >Sent to CCL by: "Close, David M." [CLOSED__mail.etsu.edu] >Yes, that is exactly right. As a check you could try a frequency calc. >using the same basis set. Usually 3 out of 4 of the "yes" are ok. For >some reason the third "yes" is sometimes a "no". I don't know why. >Now a more basic question. If you are taking a course on doing >calculations, you are always told you must use the same basis sets in >frequency calculations as on the original optimizations. But people >seem to be getting away from this are very large calculations. If it >takes a week to do an optimization, it might take 3-4 weeks to do a >frequency calculation. So people are now using smaller basis sets to do >faster frequency calcs. I do not happen to know if this leads to >problems. I do know that Berny Schlegel warned about this some time >ago, but I do not know the current thinking on this. > > >-----Original Message----- > > >>From: owner-chemistry ~~ ccl.net [mailto:owner-chemistry ~~ ccl.net] >> >> >Sent: Monday, August 25, 2008 11:29 AM >To: Close, David M. >Subject: CCL:G: End of a frequency job > > >Sent to CCL by: Orlin Blajiev [Orlin.Blajiev,vub.ac.be] >David, Alcides, > > > >Thanks for the info. I guess G03 reports the geometry as non-converged > >because I use different BS in Opt and Freq. > >Best regards, >Orlin > > >Alcides Simao alsimao[#]gmail.com wrote: > > >>Orlin: >> >>This is a routine check from GAUSSIAN, made after *all* frequency >>jobs. You can safely discart it. Gaussian will always do that, even if >> >> > > > >>you don't flag the 'OPT' option. >> >>Best, >> >>Alcides >> >> > > > > From owner-chemistry@ccl.net Mon Aug 25 17:11:01 2008 From: "Steve Williams willsd.:.appstate.edu" To: CCL Subject: CCL:G: End of a frequency job Message-Id: <-37621-080825152923-14384-+/Nxz4BN9qsQ7Nzo7DWrVA*server.ccl.net> X-Original-From: Steve Williams Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 25 Aug 2008 14:30:36 -0400 MIME-Version: 1.0 Sent to CCL by: Steve Williams [willsd[a]appstate.edu] I think this is a problem... The transformation from energies to Hessian eigenvalues to vibrational frequencies is valid ONLY if the energy first derivatives are zero (or very close to zero). This condition will not be met if the geometry is optimized with a different method (or basis set) from the one used to compute the Hessian. If you want to attribute any physical meaning to the frequencies, you must compute the Hessian with the same method and basis set used for the geometry optimization. In G03 this is more or less automatic if you include both opt and freq in the route line on the input file. Steve Williams Orlin Blajiev Orlin.Blajiev---vub.ac.be wrote: > > Sent to CCL by: Orlin Blajiev [Orlin.Blajiev,vub.ac.be] > David, Alcides, > > > > Thanks for the info. I guess G03 reports the geometry as > non-converged because I use different BS in Opt and Freq. > > Best regards, > Orlin > > > Alcides Simao alsimao[#]gmail.com wrote: >> Orlin: >> >> This is a routine check from GAUSSIAN, made after *all* frequency >> jobs. You can safely discart it. Gaussian will always do that, even >> if you don't flag the 'OPT' option. >> >> Best, >> >> Alcides > > From owner-chemistry@ccl.net Mon Aug 25 18:35:00 2008 From: "A VM fray.gory[*]gmail.com" To: CCL Subject: CCL:G: how G03 builds promolecule density for Hirshfeld population analysis? Message-Id: <-37622-080825182905-18201-N5CC0qojmc7A7NHxe+xkNA()server.ccl.net> X-Original-From: "A VM" Content-Type: multipart/alternative; boundary="----=_Part_88269_14998833.1219703332533" Date: Mon, 25 Aug 2008 17:28:52 -0500 MIME-Version: 1.0 Sent to CCL by: "A VM" [fray.gory---gmail.com] ------=_Part_88269_14998833.1219703332533 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dears Nuno, Ol Ga, Thanks very much by the answer, Nuno wrote: >If you run tests with any model you will obtain nonsensical results for >Hirshfeld charges. I think that is the reason that I can not reproduce the same values published in the paper mentionend by OI Ga with Gaussian03 >F. DE PROFT, ALSENOY, PEETERS, LANGENAEKER, GEERLINGS >Atomic Charges, Dipole Moments, and Fukui Functions >Using the Hirshfeld Partitioning of the Electron Density, J Comput Chem 23: 11981209, 2002 I used the same parameters used on this paper and I got the same results but using my own code. I suspect that the atomic densities used for promolecule are not in the same level as the molecular calculation is. Of course, the tendency is correct but the hard numbers are quite different. Thanks you again! Alvaro On Mon, Aug 25, 2008 at 3:22 AM, Nuno A. G. Bandeira nuno.bandeira^-^ ist.utl.pt wrote: > > Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira[]ist.utl.pt] > Dear Alvaro, > > Hirshfeld charges are an experimental feature in Gaussian03. > > If you run tests with any model you will obtain nonsensical results for > Hirshfeld charges. > > Regarding LiF question the Hirshfeld definition states that the promolecule > is always built up from the neutral atomic constituents in their ground > state i.e. rho(r) = Sum (rho_at) where rho_at is the atomic ground state > density of each atom. > > Cheers, > Nuno > > > > -- > Nuno A. G. Bandeira, AMRSC > Graduate researcher and molecular sculptor > Inorganic and Theoretical Chemistry Group, > Faculty of Science > University of Lisbon - C8 building, Campo Grande, > 1749-016 Lisbon,Portugal > http://cqb.fc.ul.pt/intheochem/nuno.html > Doctoral student [a] IST,Lisbon > --http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > ------=_Part_88269_14998833.1219703332533 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Dears Nuno, Ol Ga,

Thanks very much by the answer,

Nuno wrote:
>If you run tests with any model you will obtain nonsensical results for >Hirshfeld charges.

I think that is the reason that I can not reproduce the same values published in the paper mentionend by OI Ga with Gaussian03
>F. DE PROFT, ALSENOY, PEETERS, LANGENAEKER, GEERLINGS
>Atomic Charges, Dipole Moments, and Fukui Functions
>Using the Hirshfeld Partitioning of the Electron Density, J Comput Chem
23: 11981209, 2002

I used the same parameters used on this paper and I got the same results but using my own code.
I suspect that the atomic densities used for promolecule are not in the same level as the molecular calculation is. Of course, the tendency is correct but the hard numbers are quite different.

Thanks you again!
Alvaro

On Mon, Aug 25, 2008 at 3:22 AM, Nuno A. G. Bandeira nuno.bandeira^-^ist.utl.pt <owner-chemistry++ccl.net> wrote:

Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira[]ist.utl.pt]
Dear Alvaro,

Hirshfeld charges are an experimental feature in Gaussian03.

If you run tests with any model you will obtain nonsensical results for Hirshfeld charges.

Regarding LiF question the Hirshfeld definition states that the promolecule is always built up from the neutral atomic constituents in their ground state i.e. rho(r) = Sum (rho_at) where rho_at is the atomic ground state density of each atom.

Cheers,
Nuno



--
Nuno A. G. Bandeira, AMRSC
Graduate researcher and molecular sculptor
Inorganic and Theoretical Chemistry Group,
Faculty of Science
University of Lisbon - C8 building, Campo Grande,
1749-016 Lisbon,Portugal
http://cqb.fc.ul.pt/intheochem/nuno.html
Doctoral student [a] IST,Lisbon
--



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------=_Part_88269_14998833.1219703332533-- From owner-chemistry@ccl.net Mon Aug 25 21:11:01 2008 From: "Brian Salter-Duke brian.james.duke!^!gmail.com" To: CCL Subject: CCL:G: End of a frequency job Message-Id: <-37623-080825190822-2853-APXAUPT2ISiNCRvfz8GO2A^server.ccl.net> X-Original-From: Brian Salter-Duke Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 26 Aug 2008 07:53:02 +1000 MIME-Version: 1.0 Sent to CCL by: Brian Salter-Duke [brian.james.duke[-]gmail.com] errol lewars elewars+*+trentu.ca wrote: > > Sent to CCL by: errol lewars [elewars-#-trentu.ca] > 2008 August 25 > > The general view is that it is simply wrong to use one method/basis for > the optimization and another for the frequencies: consult some standard > books on computational chemistry. > > E. Lewars > === Yes, it is indeed wrong. If you do a frequency calculation at a geometry which is not a stationary point for the method and basis set employed for the frequency calculation, then the calculated frequencies do not mean anything. You do not have the 6 nominally zero frequencies corresponding to rotations and vibrations. It is quite likely that you will not be able to identify those 6 and you may have imaginary frequencies even if the original optimization was to a local minimum. Brian. > > Close, David M. CLOSED^mail.etsu.edu wrote: > >> Sent to CCL by: "Close, David M." [CLOSED__mail.etsu.edu] >> Yes, that is exactly right. As a check you could try a frequency calc. >> using the same basis set. Usually 3 out of 4 of the "yes" are ok. For >> some reason the third "yes" is sometimes a "no". I don't know why. >> Now a more basic question. If you are taking a course on doing >> calculations, you are always told you must use the same basis sets in >> frequency calculations as on the original optimizations. But people >> seem to be getting away from this are very large calculations. If it >> takes a week to do an optimization, it might take 3-4 weeks to do a >> frequency calculation. So people are now using smaller basis sets to do >> faster frequency calcs. I do not happen to know if this leads to >> problems. I do know that Berny Schlegel warned about this some time >> ago, but I do not know the current thinking on this. >> >> >> -----Original Message----- >> >> >>> From: owner-chemistry ~~ ccl.net [mailto:owner-chemistry ~~ ccl.net] >> Sent: Monday, August 25, 2008 11:29 AM >> To: Close, David M. >> Subject: CCL:G: End of a frequency job >> >> >> Sent to CCL by: Orlin Blajiev [Orlin.Blajiev,vub.ac.be] >> David, Alcides, >> >> >> >> Thanks for the info. I guess G03 reports the geometry as non-converged >> >> because I use different BS in Opt and Freq. >> >> Best regards, >> Orlin >> >> >> Alcides Simao alsimao[#]gmail.com wrote: >> >> >>> Orlin: >>> >>> This is a routine check from GAUSSIAN, made after *all* frequency >>> jobs. You can safely discart it. Gaussian will always do that, even if >>> >> >> >> >>> you don't flag the 'OPT' option. >>> >>> Best, >>> >>> Alcideshttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> -- Brian Salter-Duke (Brian Duke) Brian.James.Duke(0)gmail.com Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia http://www.salter-duke.bigpondhosting.com/brian/index.htm Honorary Researcher Fellow, Monash Institute of Pharmaceutical Sciences