From owner-chemistry@ccl.net Thu Aug 25 07:09:01 2011 From: "quartarolo,unical.it" To: CCL Subject: CCL: MP2 single points with such a small basis set? Message-Id: <-45325-110824164700-21089-qcxJvpiPKK+T3Fu2BFThsw++server.ccl.net> X-Original-From: quartarolo-$-unical.it Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Wed, 24 Aug 2011 22:46:48 +0200 MIME-Version: 1.0 Sent to CCL by: quartarolo]~[unical.it Dear Hamdy, a good alternative for your calculations, could the MP2 with the resolution of identity approximation method (RIMP2), implemented in Turbomole and Orca packages. It is faster and allow you to use large all-electron basis set also for iodine (as the triple-zeta basis set) or otherwise a pseudopotential for iodine. Your results could be more "realistic" than with the 3-21G** basis set. Best regards Quartarolo Domenico Università della Calabria (Italy) ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. **** Riservatezza / Confidentiality **** In ottemperanza al D.Lgs. n. 196 del 30/6/2003 in materia di protezione dei dati personali, le informazioni contenute in questo messaggio sono strettamente riservate ed esclusivamente indirizzate al destinatario indicato (oppure alla persona responsabile di rimetterlo al destinatario). Vogliate tener presente che qualsiasi uso, riproduzione o divulgazione di questo messaggio e' vietato. Nel caso in cui aveste ricevuto questo messaggio per errore, vogliate cortesemente avvertire il mittente e distruggere il presente messaggio. From owner-chemistry@ccl.net Thu Aug 25 10:07:01 2011 From: "Jens Spanget-Larsen spanget{=}ruc.dk" To: CCL Subject: CCL: MP2 single points with such a small basis set? Message-Id: <-45326-110825035827-1723-x/MfsrppDozGCbGMEPqcTQ:server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Type: multipart/alternative; boundary="------------020202040502040907050106" Date: Thu, 25 Aug 2011 09:58:02 +0200 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget-.-ruc.dk] This is a multi-part message in MIME format. --------------020202040502040907050106 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Dear Hamdy, we used with succes the all-electrons basis DGDZVP in DFT calculations on iodine containing compounds, obtaining excellent predictions of molecular structures and vibrational frequencies: E. Karlsen, J. Spanget-Larsen, Chem. Phys. Lett. 473 (2009) 227-232 + supplementary data. Yours, Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget(_)ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ On 8/24/2011 18:00, Abrash, Sam sabrash**richmond.edu wrote: > Sent to CCL by: "Abrash, Sam" [sabrash,,richmond.edu] > You should use an effective core potential (ECP) basis set for iodine. Otherwise you'll get significant errors because of relativistic effects. > > > > Samuel A. Abrash > Department of Chemistry > University of Richmond > Richmond, VA 23173 > Phone: 804-289-8248 > Fax: 804-287-1897 > E-mail: sabrash]|[richmond.edu > Web-page: http://www.richmond.edu/~sabrash > "In 1893 Charles Hinton left Japan to become a mathematics instructor at Princeton University, where he invented a baseball-pitching machine that used gunpowder to propel the balls, like a cannon. After several accidents, the device was abandoned and Hinton lost his job ..." Terry Pratchett, Ian Steward and Jack Cohen, The Science of Diskworld III > > -----Original Message----- >> From: owner-chemistry+sabrash==richmond.edu]|[ccl.net [mailto:owner-chemistry+sabrash==richmond.edu]|[ccl.net] On Behalf Of Hamdy El Sheshtawy h.elsheshtawy,jacobs-university.de > Sent: Wednesday, August 24, 2011 9:34 AM > To: Abrash, Sam > Subject: CCL: MP2 single points with such a small basis set? > > > Sent to CCL by: Hamdy El Sheshtawy [h.elsheshtawy=jacobs-university.de] > Dear Dr. Robinson, > Thank you for your kind comment, actually, I am doing my calculation > with molecular iodine, which, 6-31G and 6-31G* do not support. > unfortunately, if I used higher than this basis set, I also have > problems with the convergence. > Best > Hamdy > On Aug 24, 2011, at 2:19 PM, James Robinson jameschums|*|yahoo.com > wrote: > >> Sent to CCL by: "James Robinson" [jameschums]*[yahoo.com] >> Dear Hamdy, >> >> Please acually think about what you are asking, is it really a good >> idea to use MP2 with such a small basis set? Perhaps you might >> consider 6-31G or 6-31G(d). Appropriate basis set selection for >> calculations is a key consideration when one considers potential >> errors in relation to the useful information to be gained from the >> calculation. >> >> Regards >> >> Dr J J Robinson >> Bioinformatician, Graz, Austria. >> >> >> >> -= 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/http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > --------------020202040502040907050106 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit
Dear Hamdy,
we used with succes the all-electrons basis DGDZVP in DFT calculations on iodine containing compounds, obtaining excellent predictions of molecular structures and vibrational frequencies: E. Karlsen, J. Spanget-Larsen, Chem. Phys. Lett. 473 (2009) 227-232 + supplementary data.
Yours, Jens >--<
 
  ------------------------------------------------------
  JENS SPANGET-LARSEN         Office:      +45 4674 2710
  Dept. of Science (18.1)     Fax:         +45 4674 3011
  Roskilde University         Mobile:      +45 2320 6246
  P.O.Box 260                 E-Mail:     spanget(_)ruc.dk
  DK-4000 Roskilde, Denmark   http://www.ruc.dk/~spanget
  ------------------------------------------------------

On 8/24/2011 18:00, Abrash, Sam sabrash**richmond.edu wrote: 
Sent to CCL by: "Abrash, Sam" [sabrash,,richmond.edu]
You should use an effective core potential (ECP) basis set for iodine.  Otherwise you'll get significant errors because of relativistic effects.



Samuel A. Abrash
Department of Chemistry
University of Richmond
Richmond, VA 23173
Phone:  804-289-8248
Fax:  804-287-1897
E-mail:  sabrash]|[richmond.edu
Web-page:  http://www.richmond.edu/~sabrash
"In 1893 Charles Hinton left Japan to become a mathematics instructor at Princeton University, where he invented a baseball-pitching machine that used gunpowder to propel the balls, like a cannon.  After several accidents, the device was abandoned and Hinton lost his job ..." Terry Pratchett, Ian Steward and Jack Cohen, The Science of Diskworld III

-----Original Message-----

From: owner-chemistry+sabrash==richmond.edu]|[ccl.net [mailto:owner-chemistry+sabrash==richmond.edu]|[ccl.net] On Behalf Of Hamdy El Sheshtawy h.elsheshtawy,jacobs-university.de

Sent: Wednesday, August 24, 2011 9:34 AM
To: Abrash, Sam
Subject: CCL: MP2 single points with such a small basis set?


Sent to CCL by: Hamdy El Sheshtawy [h.elsheshtawy=jacobs-university.de]
Dear Dr. Robinson,
Thank you for your kind comment, actually, I am doing my calculation  
with molecular iodine, which, 6-31G and 6-31G* do not support.
unfortunately, if I used higher than this basis set, I also have  
problems with the convergence.
Best
Hamdy
On Aug 24, 2011, at 2:19 PM, James Robinson jameschums|*|yahoo.com  
wrote:


Sent to CCL by: "James  Robinson" [jameschums]*[yahoo.com]
Dear Hamdy,

Please acually think about what you are asking, is it really a good  
idea to use MP2 with such a small basis set? Perhaps you might  
consider 6-31G or 6-31G(d). Appropriate basis set selection for  
calculations is a key consideration when one considers potential  
errors in relation to the useful information to be gained from the  
calculation.

Regards

Dr J J Robinson
Bioinformatician, Graz, Austria.> Conferences: http://server.ccl.net/chemistry/announcements/ 
conferences/http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

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--------------020202040502040907050106-- From owner-chemistry@ccl.net Thu Aug 25 10:42:01 2011 From: "Frank Neese frank.neese- -mpi-mail.mpg.de" To: CCL Subject: CCL: Hints for Performing SORCI Calculations Message-Id: <-45327-110825052103-26373-eTV4VU/pEWHPZfJVxI97+A:server.ccl.net> X-Original-From: Frank Neese Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 25 Aug 2011 11:20:55 +0200 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Frank Neese [frank.neese[#]mpi-mail.mpg.de] Dear Gustavo, > Someone once told me that, in a MRCI-type calculation, if you want to obtain the excitation energies of N states, you need to request N+2 or N+3 excited states in the calculation. Is this rule still valid in a SORCI calculation? I don't think so. It may even be counterproductive as the aproximate average natural orbitals involved in SORCI become worse. > I think that the calculation should run faster if I request fewer states. yes > Is there an efficient rule to obtain the number of orbitals included in the CAS reference for the excited states? The idea of performing several calculations, increasing the number of orbitals in each calculation, for each molecule does not sound very appealing. true, but this is how every multireference method works. You can certainly get a pretty good idea about the necessary orbitals from a preceeding CIS or limited RAS-CI calculation. > My final question is about using Improved Virtual Orbitals (IVOs) to start the SORCI calculation. I am interested exclusively in the valence excited states of my molecules and I am planning to use a basis set with diffuse functions in my calculations. I was told that, in order to differentiate the valence excited states from the Rydberg states, all I need to do is to make sure that the dominant configuration involves an excitation to a valence unoccupied orbital. I am curious to know if, by using IVOs in my calculations, I will not be mixing some non-valence unoccupied orbitals within the valence unoccupied orbitals. No, it will make the much too diffuse HF virtual orbitals more appropriate. it also depends on whether you have diffuse basis functions in your set. But you don't have to use IVOs. They were coming from a time when ORCA did not have a CASSCF module. Nowadays most people (and many referees :-)) will prefer to start from a CASSCF calculations. Finally an announcement: the ORCA MRCI module has finally been parallelized and will be available in parallel form in the fall release. The download site will soon move to the MPI for bioinorganic chemistry in Muelheim/Ruhr where the ORCA development team has moved to. All the best, Frank Neese ------------------------------------------------------------------------- ++++ NOTE CHANGE OF ADDRESS ON 1.7.2011 ++++ Prof. Dr. Frank Neese Max-Planck Institut für Bioanorganische Chemie Stiftstr. 34-36 D-45470 Mülheim an der Ruhr Germany E-Mail: Frank.Neese^-^mpi-mail.mpg.de ------------------------------------------------------------------------- From owner-chemistry@ccl.net Thu Aug 25 11:17:00 2011 From: "DIEGOI GOMEZ darkego21]_[yahoo.com" To: CCL Subject: CCL: MP2 single points with such a small basis set? Message-Id: <-45328-110824125324-6417-DlsZACLiLa/KfYh7zA3rNw_._server.ccl.net> X-Original-From: DIEGOI GOMEZ Content-Type: multipart/alternative; boundary="0-1786573699-1314204795=:18214" Date: Wed, 24 Aug 2011 17:53:15 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: DIEGOI GOMEZ [darkego21*yahoo.com] --0-1786573699-1314204795=:18214 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hello...=0A=0AIt is just a comment...=0A=0AI have perfomed some MP2 calcula= tions for the evaluation of weak interactions, =0Adriven mainly by dispersi= on. Some of them with transition metal atoms and in =0Asome cases I had con= vergence problems.=0A=0AFrom my short experience, I found that the Ahlrichs= basis set (def2-XXX) seems =0Ato work pretty quite. Particularly if you w= ant to improve systematically your =0Aresults with bigger basis set (which = can be done also by applying the =0Aresolution of identity approach for wh= ich auxiliary basis set are available). =0A=0ATo my knowledge there is not= an all-electron def2-XXXX basis set for the Iodine, =0Abut I believe that = with the right ECP you can get very good results.=0A=0ABest regards...=0A= =0ADiego A G=F3mez.=0A=0A=0A________________________________=0ADe: "Hamdy E= l Sheshtawy h.elsheshtawy,jacobs-university.de" =0A=0APara: "Gomez, Diego Armando " =0AEnviado: = mi=E9,24 agosto, 2011 15:34=0AAsunto: CCL: MP2 single points with such a sm= all basis set?=0A=0A=0ASent to CCL by: Hamdy El Sheshtawy [h.elsheshtawy=3D= jacobs-university.de]=0ADear Dr. Robinson,=0AThank you for your kind commen= t, actually, I am doing my calculation with =0Amolecular iodine, which, 6-3= 1G and 6-31G* do not support.=0Aunfortunately, if I used higher than this b= asis set, I also have problems with =0Athe convergence.=0ABest=0AHamdy=0AOn= Aug 24, 2011, at 2:19 PM, James Robinson jameschums|*|yahoo.com wrote:=0A= =0A> =0A> Sent to CCL by: "James Robinson" [jameschums]*[yahoo.com]=0A> De= ar Hamdy,=0A> =0A> Please acually think about what you are asking, is it re= ally a good idea to use =0A>MP2 with such a small basis set? Perhaps you mi= ght consider 6-31G or 6-31G(d). =0A>Appropriate basis set selection for cal= culations is a key consideration when one =0A>considers potential errors in= relation to the useful information to be gained =0A>from the calculation.= =0A> =0A> Regards=0A> =0A> Dr J J Robinson=0A> Bioinformatician, Graz, Aust= ria.=0A> =0A> =0A> =0A> -=3D This is automatically added to each message by= the mailing script =3D-=0A> To recover the email address of the author of = the message, please change> =0A>Conferences: http://server.ccl.net/chemistr= y/announcements/conferences/>=0A> =0A=0A=0A=0A-=3D This is automatically ad= ded to each message by the mailing script =3D-=0ATo recover the email addre= ss 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: lin= e in the mail header.=0A=0A= =0A=0A=0AE-mail to admin= istrators: CHEMISTRY-REQUEST]_[ccl.net or use=0A http://www.ccl.net/cgi-bi= n/ccl/send_ccl_message=0A=0Ahttp://www.ccl.net/ch= emistry/sub_unsub.shtml=0A=0ABefore posting, check wait time at: http://www= .ccl.net=0A=0AJob: http://www.ccl.net/jobsConferences: =0Ahttp://server.ccl= .net/chemistry/announcements/conferences/=0A=0ASearch Messages: http://www.= ccl.net/chemistry/searchccl/index.shtml=0A=0AIf your mail bounces from CCL = with 5.7.1 error, check:=0A=0A=0ARTFI: h= ttp://www.ccl.net/chemistry/aboutccl/instructions/ --0-1786573699-1314204795=:18214 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hello...

It i= s just a comment...

I have perfomed some MP2 calculations for the evaluation= of weak interactions, driven mainly by dispersion. Some of them with trans= ition metal atoms and in some cases I had convergence problems.

From my short experience, I found th= at the Ahlrichs basis set (def2-XXX)  seems to work pret= ty quite. Particularly if you want to improve systematically your results w= ith bigger basis set (which can be done also by applying  the res= olution of identity approach for which auxiliary basis set are available). =  

To my knowledge there is not an all-elec= tron def2-XXXX basis set for the Iodine, but I believe that with the right = ECP you can get very good results.

Best rega= rds...

Diego A G=F3mez.

De: "Hamdy El Shesh= tawy h.elsheshtawy,jacobs-university.de" <owner-chemistry]_[ccl.net>
= Para: "Gomez, Diego Armando -= id#3sf-" <darkego21]_[yahoo.com>
Enviado: mi=E9,24 agosto, 2011 15:34
Asunto: CCL: MP2 single points with such a smal= l basis set?


Sent to CCL by: Hamdy El Sheshtawy [h.elshes= htawy=3Djacobs-university.de]
Dear Dr. Robinson,
Thank you for your k= ind comment, actually, I am doing my calculation with molecular iodine, whi= ch, 6-31G and 6-31G* do not support.
unfortunately, if I used higher tha= n this basis set, I also have problems with the convergence.
Best
Ham= dy
On Aug 24, 2011, at 2:19 PM, James Robinson jameschums|*|yahoo.com wr= ote:

>
> Sent to CCL by: "James  Robinson" [jameschum= s]*[yahoo.com]
> Dear Hamdy,
>
> Please acually think about what you are asking, is it really a good idea to use MP2 with such a= small basis set? Perhaps you might consider 6-31G or 6-31G(d). Appropriate= basis set selection for calculations is a key consideration when one consi= ders potential errors in relation to the useful information to be gained fr= om the calculation.
>
> Regards
>
> Dr J J Robins= on
> Bioinformatician, Graz, Austria.
>
>
>
&= gt; -=3D This is automatically added to each message by the mailing script = =3D-
> To recover the email address of the author of the message, ple= ase change> Conferences: http://server.ccl.net/chemistry/a= nnouncements/conferences/>
>



-=3D This is auto= matically added to each message by the mailing script =3D-
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=0A=0A=0A --0-1786573699-1314204795=:18214-- From owner-chemistry@ccl.net Thu Aug 25 16:14:01 2011 From: "Jenae Garrett jenae.garrett .. accelrys.com" To: CCL Subject: CCL: Building the Drug Discovery Portal with Dr. Blair Johnston Message-Id: <-45329-110825114814-15149-eJ9s/Mp8/sWLLLm7VN7KNw]|[server.ccl.net> X-Original-From: "Jenae Garrett" Date: Thu, 25 Aug 2011 11:48:10 -0400 Sent to CCL by: "Jenae Garrett" [jenae.garrett{:}accelrys.com] Interesting webinar: Dr. Blair Johnston from the University of Strathclyde will share his work on the Drug Discovery Portal (DDP) - an online service which is helping bring chemists, biologists and modelers together to collaborate on drug discovery and optimization projects. The DDP is based on a unique assembly of diverse compounds which are used for virtual screening and linked to the originating chemists so that samples are available for physical screening and analogues can be rapidly designed and synthesized to better understand structure-activity relationships. Dr. Johnston will present an analysis of the DDP compound library and provide an overview of how the DDP works and its use of virtual screening protocols. Registration: https://www3.gotomeeting.com/register/501486958 From owner-chemistry@ccl.net Thu Aug 25 16:49:01 2011 From: "Aniko Simon aniko{:}simbiosys.ca" To: CCL Subject: CCL: Webinar: molecular docking & hit screening with SimBioSys' eHiTS+ Message-Id: <-45330-110825140813-30581-CR2BFzwRdXc4iJNMGdDELQ^-^server.ccl.net> X-Original-From: "Aniko Simon" Date: Thu, 25 Aug 2011 14:08:09 -0400 Sent to CCL by: "Aniko Simon" [aniko{=}simbiosys.ca] Dear Colleague, > From the many molecular docking tools, only one applies an exhaustive conformational search, an automated protonation state handling, and a tunable scoring function. Whether you are a current user, or are considering adding a fast and accurate docking algorithm top your toolbox, join us for an interactive webinar, on 1 Sep at noon EDT, with live demonstration of the latest release of eHiTS and other tools from SimBioSys. Get acquainted with one of the top performers in the field, that many researchers consider: "the fastest" [1], "the most accurate" [2], and "the easiest to use with automated protonation / tatutomerization assigments" [3]. The list of tools included into the SimBioSys' docking and screening portfolio are: * eHiTS - flexible ligand docker * CheVi - 3D graphical user interface * LASSO - virtual screening tool based on ligand-similarity of surface properties * Score - scoring utility allowing rescoring bound conformations obtained with other tools * Tune - score tuning utility, allowing customizing the scoring to your system of interests using your own data This software package is available for Linux computers (lap-tops, desk-tops or clusters). For more info see: http://www.simbiosys.com/ehits The webinar sessions are live, and they provide you with an opportunity to ask questions and receive immediate feedback. Don't miss out this opportunity, register now at: http://www.simbiosys.com/products/webinar_request.html What: * INTERACTIVE WEBINAR with call-in teleconferencing * SimBioSys' eHiTS live demonstrations included in the presentation When: * Sep 1, 2011 WEBINAR * NOON: 12:00 pm - 1:00 pm EDT Instructor: * Dr Orr Ravitz, Applications Scientist, SimBioSys, Inc. We are looking forward seeing you at the webinar! Best regards, Aniko Simon References: [1]: Quote from Dr. Katie Simmons, University of Leeds, UK [2]: http://onlinelibrary.wiley.com/doi/10.1002/jcc.21643/abstract [3]: Quote from Dr. Mihaly Mezei, Mount Sinai School of Medicine, NY, USA -- Aniko Simon, Ph.D. | SimBioSys Inc. | Tel: 1-416-741-4263 | http://www.simbiosys.com/ From owner-chemistry@ccl.net Thu Aug 25 17:24:01 2011 From: "Lothar Esser lesser__helix.nih.gov" To: CCL Subject: CCL: Run TINKER non-interactively Message-Id: <-45331-110825130841-9353-M+yFSxZT+S8BcEcrsGC8IQ---server.ccl.net> X-Original-From: "Lothar Esser" Date: Thu, 25 Aug 2011 13:08:38 -0400 Sent to CCL by: "Lothar Esser" [lesser(0)helix.nih.gov] Hi, I am a first time user of TINKER 5.1 Feb. 2010 (by JW Ponder) and found that it can do what I wanted it to do (generate a helix) in the interactive mode using the program protein. However for my life I cannot figure out how to run it non-interactively. I prepared a file that contains exactly the answers to the question protein might ask in the right order and did the usual protein < input_file_to_protein It ran but created no useful output. Apparently all it received was empty statements. Several alternatives failed as well. I think I am missing something perhaps a commandline switch ??? Compiled Tinker 5.1 source using gfortran 4.1.2 on Linux x64 Centos 5.6 Any hint is appreciated. Lothar From owner-chemistry@ccl.net Thu Aug 25 17:58:00 2011 From: "Gustavo Laureano Coelho de Moura gustavo.moura,+,ufpe.br" To: CCL Subject: CCL: Hints for Performing SORCI Calculations Message-Id: <-45332-110825165205-25686-2RDTRT2msSiDENvGEGjzDA!A!server.ccl.net> X-Original-From: Gustavo Laureano Coelho de Moura Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Thu, 25 Aug 2011 17:50:44 -0300 (BRT) MIME-Version: 1.0 Sent to CCL by: Gustavo Laureano Coelho de Moura [gustavo.moura{=}ufpe.br] Dear Prof. Neese, Thank you very much for your thorough answer to my question. You have made some very interesting suggestions that I had not thought about before. Sincerely yours, Gustavo Moura ----- Mensagem original ----- De: "Frank Neese frank.neese- -mpi-mail.mpg.de" Para: "Gustavo L.C. Moura" Enviadas: Quinta-feira, 25 de Agosto de 2011 6:20:55 Assunto: CCL: Hints for Performing SORCI Calculations Sent to CCL by: Frank Neese [frank.neese[#]mpi-mail.mpg.de] Dear Gustavo, > Someone once told me that, in a MRCI-type calculation, if you want to obtain the excitation energies of N states, you need to request N+2 or N+3 excited states in the calculation. Is this rule still valid in a SORCI calculation? I don't think so. It may even be counterproductive as the aproximate average natural orbitals involved in SORCI become worse. > I think that the calculation should run faster if I request fewer states. yes > Is there an efficient rule to obtain the number of orbitals included in the CAS reference for the excited states? The idea of performing several calculations, increasing the number of orbitals in each calculation, for each molecule does not sound very appealing. true, but this is how every multireference method works. You can certainly get a pretty good idea about the necessary orbitals from a preceeding CIS or limited RAS-CI calculation. > My final question is about using Improved Virtual Orbitals (IVOs) to start the SORCI calculation. I am interested exclusively in the valence excited states of my molecules and I am planning to use a basis set with diffuse functions in my calculations. I was told that, in order to differentiate the valence excited states from the Rydberg states, all I need to do is to make sure that the dominant configuration involves an excitation to a valence unoccupied orbital. I am curious to know if, by using IVOs in my calculations, I will not be mixing some non-valence unoccupied orbitals within the valence unoccupied orbitals. No, it will make the much too diffuse HF virtual orbitals more appropriate. it also depends on whether you have diffuse basis functions in your set. But you don't have to use IVOs. They were coming from a time when ORCA did not have a CASSCF module. Nowadays most people (and many referees :-)) will prefer to start from a CASSCF calculations. Finally an announcement: the ORCA MRCI module has finally been parallelized and will be available in parallel form in the fall release. The download site will soon move to the MPI for bioinorganic chemistry in Muelheim/Ruhr where the ORCA development team has moved to. All the best, Frank Neese ------------------------------------------------------------------------- ++++ NOTE CHANGE OF ADDRESS ON 1.7.2011 ++++ Prof. Dr. Frank Neese Max-Planck Institut für Bioanorganische Chemie Stiftstr. 34-36 D-45470 Mülheim an der Ruhr Germany E-Mail: Frank.Neese ~~ mpi-mail.mpg.de -------------------------------------------------------------------------http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Aug 25 19:13:00 2011 From: "lesser],[helix.nih.gov" To: CCL Subject: CCL: Solved: Run TINKER non-interactively Message-Id: <-45333-110825191133-23299-pHZjM1MD3nrg5jtt5OusFg,,server.ccl.net> X-Original-From: Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 25 Aug 2011 19:11:24 -0400 MIME-Version: 1.0 Sent to CCL by: [lesser%%helix.nih.gov] Hi, I found out what was wrong. Running scripts works as indicated: > I am a first time user of TINKER 5.1 Feb. 2010 (by JW Ponder) and found > that it can do what I wanted it to do (generate a helix) in the interactive > mode using the program protein. However for my life I cannot figure out how > to run it non-interactively. I prepared a file that contains exactly the > answers to the question protein might ask in the right order and did the > usual $ protein < input_file_to_protein This actually works. What is strange though is that "protein" just prints input questions without the answers giving you the impression that the input was all "null" or CR/LF. Thanks, Lothar > It ran but created no useful output. Apparently all it received was empty > statements. > > Several alternatives failed as well. I think I am missing something perhaps a > commandline switch ??? > > Compiled Tinker 5.1 source using gfortran 4.1.2 on Linux x64 Centos 5.6 > > Any hint is appreciated. > > Lothar> > From owner-chemistry@ccl.net Thu Aug 25 20:21:00 2011 From: "David Semrouni d.semrouni^gmail.com" To: CCL Subject: CCL: Run TINKER non-interactively Message-Id: <-45334-110825183040-18702-lmFL5J4FVq7Ustaglu+7aQ%server.ccl.net> X-Original-From: David Semrouni Content-Type: multipart/alternative; boundary=90e6ba6e8dbaed696104ab5bf85a Date: Fri, 26 Aug 2011 00:30:13 +0200 MIME-Version: 1.0 Sent to CCL by: David Semrouni [d.semrouni(~)gmail.com] --90e6ba6e8dbaed696104ab5bf85a Content-Type: text/plain; charset=UTF-8 Hi, If you received no error message, your problem may come from the use of an inappropriate parameter file (.key). Beside, no statement present in your input file shall be displayed. If you want to know whether arguments were passed, a .seq should be created by protein and could give you a confirmation that the entered sequence was well interpreted by protein. After the name (1st line) and the title (2nd one), you should enter the name of the key file. By default, Tinker seeks for a key file named either "tinker.key" or called by the name you entered at the first line with the key extension. If a corresponding file is found in the current directory then no key file is asked and the sequence shall directly be entered from the third line. If the key file entered or taken by default is not appropriate for.your sequence then the created coordinate files will be empty except for the title. Is there a key file in your current directory? And does it contain all the required atom files? If the interactive way works correctly with the same file, I would not know where the problem comes from but as you may work non-interactively in another directory and you receive no error message, that is what I think about. David Semrouni On Thu, Aug 25, 2011 at 7:08 PM, Lothar Esser lesser__helix.nih.gov < owner-chemistry],[ccl.net> wrote: > > Sent to CCL by: "Lothar Esser" [lesser(0)helix.nih.gov] > Hi, > > I am a first time user of TINKER 5.1 Feb. 2010 (by JW Ponder) and found > that it can do what I wanted it to do (generate a helix) in the interactive > mode using the program protein. However for my life I cannot figure out how > to run it non-interactively. I prepared a file that contains exactly the > answers to the question protein might ask in the right order and did the > usual > > protein < input_file_to_protein > > It ran but created no useful output. Apparently all it received was empty > statements. > > Several alternatives failed as well. I think I am missing something perhaps > a commandline switch ??? > > Compiled Tinker 5.1 source using gfortran 4.1.2 on Linux x64 Centos 5.6 > > Any hint is appreciated. > > Lothar> > > --90e6ba6e8dbaed696104ab5bf85a Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi,

If you received no error message, your problem may come from the= use of an inappropriate parameter file (.key).
Beside, no statement pre= sent in your input file shall be displayed. If you want to know whether arg= uments were passed, a .seq should be created by protein and could give you = a confirmation that the entered sequence was well interpreted by protein.
After the name (1st line) and the title (2nd one), you should enter the= name of the key file.
By default, Tinker seeks for a key file named eit= her "tinker.key" or called by the name you entered at the first l= ine with the key extension. If a corresponding file is found in the current= directory then no key file is asked and the sequence shall directly be ent= ered from the third line.

If the key file entered or taken by default is not appropriate for.your= sequence then the created coordinate files will be empty except for the ti= tle.

Is there a key file in your current directory? And does it cont= ain all the required atom files?
If the interactive way works correctly with the same file, I would not know= where the problem comes from but as you may work non-interactively in anot= her directory and you receive no error message, that is what I think about.=

David Semrouni

On Thu, Aug 25, 2011 a= t 7:08 PM, Lothar Esser lesser__he= lix.nih.gov <owner-chemistry],[ccl.net> wrote:

Sent to CCL by: "Lothar =C2=A0Esser" [lesser(0)helix.nih.gov]
Hi,

=C2=A0 I am a first time user of TINKER 5.1 Feb. 2010 (by JW Ponder) and f= ound that it can do what I wanted it to do (generate a helix) in the intera= ctive mode using the program protein. However for my life I cannot figure o= ut how to run it non-interactively. I prepared a file that contains exactly= the answers to the question protein might ask in the right order and did t= he usual

protein < input_file_to_protein

It ran but created no useful output. Apparently all it received was empty s= tatements.

Several alternatives failed as well. I think I am missing something perhaps= a commandline switch ???

Compiled Tinker 5.1 source using gfortran 4.1.2 on Linux x64 Centos 5.6

Any hint is appreciated.

Lothar



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