From owner-chemistry@ccl.net Fri May 9 06:53:00 2014 From: "Joop van Lenthe j.h.vanlenthe[A]uu.nl" To: CCL Subject: CCL:G: Resonance forms Message-Id: <-50057-140509065003-17059-GYEzD94zrQ6QUxQqPA3vZg() server.ccl.net> X-Original-From: Joop van Lenthe Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 9 May 2014 12:49:53 +0200 Mime-Version: 1.0 (Mac OS X Mail 7.2 \(1874\)) Sent to CCL by: Joop van Lenthe [j.h.vanlenthe(-)uu.nl] you need VB we have a vb program, but there are many more Joop On 9 May 2014, at 1:06 am, Nico G nicogreen6**gmail.com wrote: > > Sent to CCL by: Nico G [nicogreen6^gmail.com] > Dear all, > > I have some systems that contain phenols rings. I need to get the optimized geometries of all the possible resonance forms. > > The problem is that i am unable to find how to tell gaussian that certain atoms, for example, must have a charge. > > ie: > > The resonance form of the phenol where the alcohol becomes a keto, so the oxigen atom still protonated carries a positive charge and there is a negative charge on one of the carbon atoms. > The normal optimization on gaussian will end in the phenol. > > Thank you all > > Best Regards, > > Nicohttp://www.ccl.net/chemistry/sub_unsub.shtml> > From owner-chemistry@ccl.net Fri May 9 07:27:00 2014 From: "Salter-Duke, Brian James - brian.james.duke#gmail.com" To: CCL Subject: CCL:G: Resonance forms Message-Id: <-50058-140509054355-21577-uKxuO21mT4w7naKs8bEBYw---server.ccl.net> X-Original-From: "Salter-Duke, Brian James -" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Fri, 9 May 2014 19:43:44 +1000 MIME-Version: 1.0 Sent to CCL by: "Salter-Duke, Brian James -" [brian.james.duke-.-gmail.com] On Thu, May 08, 2014 at 08:06:37PM -0300, Nico G nicogreen6**gmail.com wrote: > > Sent to CCL by: Nico G [nicogreen6^gmail.com] > Dear all, > > I have some systems that contain phenols rings. I need to get the > optimized geometries of all the possible resonance forms. > > The problem is that i am unable to find how to tell gaussian that > certain atoms, for example, must have a charge. > > ie: > > The resonance form of the phenol where the alcohol becomes a keto, > so the oxigen atom still protonated carries a positive charge and > there is a negative charge on one of the carbon atoms. > The normal optimization on gaussian will end in the phenol. I think you are making a category mistake here. Resonance structures are artificial so you certainly can not optimise their geometries with Gaussian. They are artifacts of a valence bond description of the molecule. It might be possible to define a valence bond calculation with just one resonance structure and then optimise the geometry of that valence bond function. You would need a valence bond program and few allow geometry optimisations. The only one that does is, I think, the TURTLE code which is in GAMESS(UK) (N.B. NOT GAMESS(US)). You might be able to get some kind of answer with that code. However I am not clear why you might want to do so. Brian. > Thank you all > > Best Regards, > > NicoConferences: > http://server.ccl.net/chemistry/announcements/conferences/> -- Brian Salter-Duke (Brian Duke) Brian.Salter-Duke],[monash.edu Adjunct Associate Professor Monash Institute of Pharmaceutical Sciences Monash University Parkville Campus, VIC 3052, Australia From owner-chemistry@ccl.net Fri May 9 09:56:00 2014 From: "Lescic Sergiu s_lescic|,|mail.ru" To: CCL Subject: CCL: Gamess Error Question : PCM calculation Message-Id: <-50059-140506085931-32646-Z9TJZpS2khAePrFFiXvhmg,,server.ccl.net> X-Original-From: "Lescic Sergiu" Date: Tue, 6 May 2014 08:59:30 -0400 Sent to CCL by: "Lescic Sergiu" [s_lescic::mail.ru] Hi All, It's a question for GAMESS users. I am trying to run a MCSCF+MP2 energy calculation with a solvent (water). In the official website (http://www.msg.ameslab.gov/GAMESS/capabilities.html) its marked that we can do a PCM energy calculation for MP2 level using MCSCF wavefunction, but when I tried to run this kind of calculation for a nitroxide anion I am getting an error msg: ERROR: INAPPROPRIATE SOLVENT CALCULATION. SOLVENT MODELS (ALL TYPES) ARE INCOMPATIBLE WITH MANY TYPE OF CORRELATED OR SEMI-EMPIRICAL COMPUTATIONS: SCFTYP=MCSCF MPLEVL= 2 USING GRADIENTS, CITYP=NONE CCTYP=NONE VBTYP=NONE OR MPCTYP=NONE Here is the input which I use for the test: $CONTRL SCFTYP=MCSCF RUNTYP=ENERGY MPLEVL=2 ICHARG=-1 MULT=1 $END $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 $END $MCSCF MAXIT=120 CISTEP=ALDET FULLNR=.T. $END $DET NCORE=71 NACT=6 NELS=10 $END $GUESS GUESS=MOREAD NORB=316 $END $SYSTEM MWORDS=2000 MEMDDI=2500 $END $PCM SOLVNT=H2O $END $DATA ddd C1 C 6.0 -0.0428803989 -0.0424443861 0.1672418969 N 7.0 -0.0249982047 -0.0722027575 1.6202198689 C 6.0 1.3382114206 0.0393378088 2.0814085589 C 6.0 2.2241673056 0.3086354086 0.8636723025 C 6.0 1.4097059351 -0.3098318915 -0.2742919459 O 8.0 -0.8243020048 0.9973357986 2.0319894034 O 8.0 1.8443182472 -1.1840878474 2.6041297701 O 8.0 1.1181041056 -1.4747706922 3.8718333702 P 15.0 -0.5646397607 1.6782589957 -0.2891968951 O 8.0 -2.1393515393 1.9306796258 -0.2195275948 C 6.0 -2.7461302003 2.8030802824 0.7262872714 C 6.0 -4.1492400474 3.1146395623 0.2452858195 C 6.0 -1.0384543970 -1.0616837070 -0.3935189317 O 8.0 0.2627462226 2.8443032110 0.0824866755 O 8.0 -0.4704997692 1.4533008486 -1.8948080168 C 6.0 -0.6378668095 2.5243530855 -2.8050626506 C 6.0 -0.2774608150 2.0344873705 -4.1938584478 H 1.0 1.3881553531 0.7868788847 2.8556005870 H 1.0 2.3160067901 1.3768176523 0.7233520419 H 1.0 3.2172366054 -0.1114988528 0.9696728430 H 1.0 1.6417676099 0.0963453234 -1.2492587194 H 1.0 1.5731703789 -1.3827751918 -0.3162564927 H 1.0 -2.0377852391 -0.8580194102 -0.0283661319 H 1.0 -0.7479881434 -2.0498384976 -0.0529032264 H 1.0 -1.0569120635 -1.0569289764 -1.4765818189 H 1.0 -0.0008719974 3.3486629651 -2.5124976984 H 1.0 -1.6667297193 2.8643354368 -2.7734315079 H 1.0 -0.9178100070 1.2102357702 -4.4889383397 H 1.0 0.7524667515 1.6949936400 -4.2221890938 H 1.0 -0.3949982357 2.8360019195 -4.9164813839 H 1.0 -2.1574630256 3.7066154005 0.8011166587 H 1.0 -2.7525267855 2.3183790758 1.6873139365 H 1.0 -4.7352990979 2.2066177039 0.1509900642 H 1.0 -4.1273412686 3.6105454642 -0.7193589853 H 1.0 -4.6460082334 3.7692340878 0.9550246466 C 6.0 0.5292015558 -2.7348757451 3.6831494528 H 1.0 -0.0022376111 -2.9435571460 4.6036326690 H 1.0 -0.1579399735 -2.7125065552 2.8509341484 H 1.0 1.2840070669 -3.4956736649 3.5234758959 $END E(MCSCF)= -1235.2758257870, E(NUC)= 1756.0463288674 $VEC 1 1-3.65205327E-05-8.40025961E-05-4.07970446E-05 1.66197059E-05 3.56227789E-06 1 2 1.08690929E-03 7.28384183E-05 4.99632967E-04 1.38715170E-04-5.95289047E-0 I would be much grateful if somebody will tell me why a get this error msg and how can I do a PCM energy calculation in GAMESS. Sergiu Lescic From owner-chemistry@ccl.net Fri May 9 10:31:00 2014 From: "Robert Molt r.molt.chemical.physics-#-gmail.com" To: CCL Subject: CCL:G: Resonance forms Message-Id: <-50060-140508203246-32049-/Z0XddEeZFGElZ//lS+oAw]~[server.ccl.net> X-Original-From: Robert Molt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 08 May 2014 20:32:39 -0400 MIME-Version: 1.0 Sent to CCL by: Robert Molt [r.molt.chemical.physics .. gmail.com] There is no such things as the charge of an atom, rigorously. Charge is a property of a total system (the entire molecule, or molecules). It's not a local property. Resonance structures are a crude simplification > from organic chemistry. You cannot "tell" the software the charge of atoms (it does not exist). Dr. Robert Molt Jr., Ph.D. r.molt.chemical.physics!^!gmail.com Nigel Richards Research Group Department of Chemistry & Chemical Biology Indiana University-Purdue University Indianapolis LD 326 402 N. Blackford St. Indianapolis, IN 46202 On 5/8/14 7:06 PM, Nico G nicogreen6**gmail.com wrote: > > Sent to CCL by: Nico G [nicogreen6^gmail.com] > Dear all, > > I have some systems that contain phenols rings. I need to get the > optimized geometries of all the possible resonance forms. > > The problem is that i am unable to find how to tell gaussian that > certain atoms, for example, must have a charge. > > ie: > > The resonance form of the phenol where the alcohol becomes a keto, so > the oxigen atom still protonated carries a positive charge and there > is a negative charge on one of the carbon atoms. > The normal optimization on gaussian will end in the phenol. > > Thank you all > > Best Regards, > > Nicohttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > From owner-chemistry@ccl.net Fri May 9 11:06:00 2014 From: "Alan Shusterman alan::reed.edu" To: CCL Subject: CCL:G: Resonance forms Message-Id: <-50061-140508211505-19414-OFUNW9gYltZiQct4YWPq3A**server.ccl.net> X-Original-From: Alan Shusterman Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Thu, 08 May 2014 18:15:02 -0700 MIME-Version: 1.0 Sent to CCL by: Alan Shusterman [alan*o*reed.edu] Nico, Quantum packages like Gaussian will calculate the best distribution of electrons for your molecule assuming that each electron interacts in a physically plausible way with *all* of the nuclei and *all* of the other electrons. This calculation will lead to partial bonds and charges around any phenol rings in your molecule. Once you get the results of the calculation, you can analyze the results using resonance theory. The reverse method: to start by defining resonance structures (assigning bond patterns and charges) and then asking the software to calculate weights for these structures is rarely attempted in modeling calculations. Alan On Thursday, May 08, 2014 4:06:37 PM, Nico G nicogreen6**gmail.com wrote: > > Sent to CCL by: Nico G [nicogreen6^gmail.com] > Dear all, > > I have some systems that contain phenols rings. I need to get the > optimized geometries of all the possible resonance forms. > > The problem is that i am unable to find how to tell gaussian that > certain atoms, for example, must have a charge. > > ie: > > The resonance form of the phenol where the alcohol becomes a keto, so > the oxigen atom still protonated carries a positive charge and there > is a negative charge on one of the carbon atoms. > The normal optimization on gaussian will end in the phenol. > > Thank you all > > Best Regards, > > Nicohttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > -- Alan Shusterman Chemistry Department Reed College 3203 SE Woodstock Blvd Portland, OR 97202-8199 503-517-7699 http://blogs.reed.edu/alan/ "Nature doesn't make long speeches." Lao Tzu 23 From owner-chemistry@ccl.net Fri May 9 11:41:00 2014 From: "Tina Ritschel tina.ritschel::radboudumc.nl" To: CCL Subject: CCL: International Chemical Discovery & Design Course, 16-27 June 2014 Message-Id: <-50062-140509041435-4837-Pta1e2IITl73tnqPI1HRBg.@.server.ccl.net> X-Original-From: "Tina Ritschel" Date: Fri, 9 May 2014 04:14:34 -0400 Sent to CCL by: "Tina Ritschel" [tina.ritschel=-=radboudumc.nl] International Chemical Discovery & Design Course, 16-27 June 2014, Nijmegen, The Netherlands. I would like to draw your attention to the 10th annual International Chemical Discovery & Design Course (http://www2.cmbi.ru.nl/groups/computational-discovery- and-design/icdd2014/) which will be held from 16-27 June 2014 at the Radboud University Nijmegen, The Netherlands. This course covers the recent advances in discovery informatics, with a focus on the application to real life problems. The course, combining practicals and lectures, will introduce and discuss different scientific concepts as well as providing an opportunity to gain practical experience using industry standard software. You can expect lectures and practicals on the following topics: Introduction to Computational Discovery & Design Comparative Protein Modelling Sequence Retrieval, Analysis and Alignment Techniques Computational Medicinal Chemistry; Molecular Descriptors & Library Design The Application of Computational Drug Design to Real Life Problems Molecular Docking and Virtual Screening Advanced 3D Database Searches and Scaffold Hopping QSAR and COMFA methods Structure Based Drug Design Techniques Confirmed speakers: For the third time we were able to invite keynote speakers from the Netherlands and abroad. As experts in their field of research they will summarize the core message of the course in their presentations Gerard JP van Westen, EBI, Hinxton, UK. ChEMBL: A large-scale open access bioactivity database for drug discovery and medicinal chemistry The course is targeted to MSc students, PhD students and post-docs. A basic background in bioinformatics or computational chemistry is a prerequisite for attendance. Registration via email to (see course website). Please, provide information about your background and your motivation to participate in the course. The course is free. You should however pay for travelling and lodging expenses yourself. Best regards Tina Ritschel (CDD/CMBI/UMC Nijmegen) From owner-chemistry@ccl.net Fri May 9 13:03:01 2014 From: "Victor Rosas Garcia rosas.victor|,|gmail.com" To: CCL Subject: CCL: Gamess Error Question : PCM calculation Message-Id: <-50063-140509121902-15334-AvDr9vTG4KwALzPWWa6tVg::server.ccl.net> X-Original-From: Victor Rosas Garcia Content-Type: multipart/alternative; boundary=047d7bdc17504c428d04f8f9f41c Date: Fri, 9 May 2014 11:18:55 -0500 MIME-Version: 1.0 Sent to CCL by: Victor Rosas Garcia [rosas.victor]*[gmail.com] --047d7bdc17504c428d04f8f9f41c Content-Type: text/plain; charset=UTF-8 The error message is telling you why: the solvent model is incompatible with many correlated treatments, MCSCF among them. You may have to look for another quantum chemistry package that is able to do what you want. Hope this helps Victor 2014-05-06 7:59 GMT-05:00 Lescic Sergiu s_lescic|,|mail.ru < owner-chemistry^ccl.net>: > > Sent to CCL by: "Lescic Sergiu" [s_lescic::mail.ru] > Hi All, > It's a question for GAMESS users. > I am trying to run a MCSCF+MP2 energy calculation with a solvent (water). > In the official website ( > http://www.msg.ameslab.gov/GAMESS/capabilities.html) its marked that we > can do a PCM energy calculation for MP2 level using MCSCF wavefunction, but > when I tried > to run this kind of calculation for a nitroxide anion I am getting an > error msg: > > > ERROR: INAPPROPRIATE SOLVENT CALCULATION. > SOLVENT MODELS (ALL TYPES) ARE INCOMPATIBLE WITH MANY > TYPE OF CORRELATED OR SEMI-EMPIRICAL COMPUTATIONS: > SCFTYP=MCSCF > MPLEVL= 2 USING GRADIENTS, CITYP=NONE CCTYP=NONE > VBTYP=NONE OR MPCTYP=NONE > > Here is the input which I use for the test: > $CONTRL SCFTYP=MCSCF RUNTYP=ENERGY MPLEVL=2 > ICHARG=-1 MULT=1 $END > > $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 > $END > > $MCSCF MAXIT=120 CISTEP=ALDET FULLNR=.T. > $END > $DET NCORE=71 NACT=6 NELS=10 $END > $GUESS GUESS=MOREAD NORB=316 $END > $SYSTEM MWORDS=2000 MEMDDI=2500 $END > $PCM SOLVNT=H2O $END > $DATA > ddd > C1 > C 6.0 -0.0428803989 -0.0424443861 0.1672418969 > N 7.0 -0.0249982047 -0.0722027575 1.6202198689 > C 6.0 1.3382114206 0.0393378088 2.0814085589 > C 6.0 2.2241673056 0.3086354086 0.8636723025 > C 6.0 1.4097059351 -0.3098318915 -0.2742919459 > O 8.0 -0.8243020048 0.9973357986 2.0319894034 > O 8.0 1.8443182472 -1.1840878474 2.6041297701 > O 8.0 1.1181041056 -1.4747706922 3.8718333702 > P 15.0 -0.5646397607 1.6782589957 -0.2891968951 > O 8.0 -2.1393515393 1.9306796258 -0.2195275948 > C 6.0 -2.7461302003 2.8030802824 0.7262872714 > C 6.0 -4.1492400474 3.1146395623 0.2452858195 > C 6.0 -1.0384543970 -1.0616837070 -0.3935189317 > O 8.0 0.2627462226 2.8443032110 0.0824866755 > O 8.0 -0.4704997692 1.4533008486 -1.8948080168 > C 6.0 -0.6378668095 2.5243530855 -2.8050626506 > C 6.0 -0.2774608150 2.0344873705 -4.1938584478 > H 1.0 1.3881553531 0.7868788847 2.8556005870 > H 1.0 2.3160067901 1.3768176523 0.7233520419 > H 1.0 3.2172366054 -0.1114988528 0.9696728430 > H 1.0 1.6417676099 0.0963453234 -1.2492587194 > H 1.0 1.5731703789 -1.3827751918 -0.3162564927 > H 1.0 -2.0377852391 -0.8580194102 -0.0283661319 > H 1.0 -0.7479881434 -2.0498384976 -0.0529032264 > H 1.0 -1.0569120635 -1.0569289764 -1.4765818189 > H 1.0 -0.0008719974 3.3486629651 -2.5124976984 > H 1.0 -1.6667297193 2.8643354368 -2.7734315079 > H 1.0 -0.9178100070 1.2102357702 -4.4889383397 > H 1.0 0.7524667515 1.6949936400 -4.2221890938 > H 1.0 -0.3949982357 2.8360019195 -4.9164813839 > H 1.0 -2.1574630256 3.7066154005 0.8011166587 > H 1.0 -2.7525267855 2.3183790758 1.6873139365 > H 1.0 -4.7352990979 2.2066177039 0.1509900642 > H 1.0 -4.1273412686 3.6105454642 -0.7193589853 > H 1.0 -4.6460082334 3.7692340878 0.9550246466 > C 6.0 0.5292015558 -2.7348757451 3.6831494528 > H 1.0 -0.0022376111 -2.9435571460 4.6036326690 > H 1.0 -0.1579399735 -2.7125065552 2.8509341484 > H 1.0 1.2840070669 -3.4956736649 3.5234758959 > $END > E(MCSCF)= -1235.2758257870, E(NUC)= 1756.0463288674 > $VEC > 1 1-3.65205327E-05-8.40025961E-05-4.07970446E-05 1.66197059E-05 > 3.56227789E-06 > 1 2 1.08690929E-03 7.28384183E-05 4.99632967E-04 > 1.38715170E-04-5.95289047E-0 > > > I would be much grateful if somebody will tell me why a get this error > msg and how can I do a PCM energy calculation in GAMESS. > > Sergiu Lescic> > > --047d7bdc17504c428d04f8f9f41c Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
The error message is telling you why: the solven= t model is incompatible with many correlated treatments, MCSCF among them. = You may have to look for another quantum chemistry package that is able to = do what you want.

Hope this helps

Victor


2014-05-06 7:59 GMT-05:00 Lescic = Sergiu s_lescic|,|mail.ru = <owner-chem= istry^ccl.net>:

Sent to CCL by: "Lescic =C2=A0Sergiu" [s_lescic::mail.ru]
Hi All,
It's a question for GAMESS users.
I am trying to run a MCSCF+MP2 energy calculation with a solvent (water). I= n the official website (http://www.msg.ameslab.gov/GAMESS/capabiliti= es.html) its marked that we can do a PCM energy calculation for MP2 lev= el using MCSCF wavefunction, but when I tried
to run this kind of calculation =C2=A0for a nitroxide anion =C2=A0I am gett= ing an error msg:


ERROR: INAPPROPRIATE SOLVENT CALCULATION.
=C2=A0SOLVENT MODELS (ALL TYPES) ARE INCOMPATIBLE WITH MANY
=C2=A0TYPE OF CORRELATED OR SEMI-EMPIRICAL COMPUTATIONS:
=C2=A0SCFTYP=3DMCSCF
=C2=A0MPLEVL=3D 2 USING GRADIENTS, CITYP=3DNONE =C2=A0 =C2=A0 CCTYP=3DNONE<= br> =C2=A0VBTYP=3DNONE =C2=A0 =C2=A0 OR MPCTYP=3DNONE

Here is the input which I use for the test:
$CONTRL =C2=A0SCFTYP=3DMCSCF RUNTYP=3DENERGY MPLEVL=3D2
ICHARG=3D-1 MULT=3D1 $END

=C2=A0$BASIS GBASIS=3DN31 NGAUSS=3D6 NDFUNC=3D1
=C2=A0$END

=C2=A0$MCSCF =C2=A0MAXIT=3D120 CISTEP=3DALDET FULLNR=3D.T.
=C2=A0$END
=C2=A0$DET NCORE=3D71 NACT=3D6 NELS=3D10 $END
=C2=A0$GUESS GUESS=3DMOREAD NORB=3D316 =C2=A0$END
=C2=A0$SYSTEM MWORDS=3D2000 MEMDDI=3D2500 =C2=A0$END
=C2=A0$PCM SOLVNT=3DH2O $END
=C2=A0$DATA
ddd
C1
=C2=A0C =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 6.0 =C2=A0-0.0428803989 =C2=A0-0= .0424443861 =C2=A0 0.1672418969
=C2=A0N =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 7.0 =C2=A0-0.0249982047 =C2=A0-0= .0722027575 =C2=A0 1.6202198689
=C2=A0C =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 6.0 =C2=A0 1.3382114206 =C2=A0 0= .0393378088 =C2=A0 2.0814085589
=C2=A0C =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 6.0 =C2=A0 2.2241673056 =C2=A0 0= .3086354086 =C2=A0 0.8636723025
=C2=A0C =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 6.0 =C2=A0 1.4097059351 =C2=A0-0= .3098318915 =C2=A0-0.2742919459
=C2=A0O =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 8.0 =C2=A0-0.8243020048 =C2=A0 0= .9973357986 =C2=A0 2.0319894034
=C2=A0O =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 8.0 =C2=A0 1.8443182472 =C2=A0-1= .1840878474 =C2=A0 2.6041297701
=C2=A0O =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 8.0 =C2=A0 1.1181041056 =C2=A0-1= .4747706922 =C2=A0 3.8718333702
=C2=A0P =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A015.0 =C2=A0-0.5646397607 =C2=A0 1= .6782589957 =C2=A0-0.2891968951
=C2=A0O =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 8.0 =C2=A0-2.1393515393 =C2=A0 1= .9306796258 =C2=A0-0.2195275948
=C2=A0C =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 6.0 =C2=A0-2.7461302003 =C2=A0 2= .8030802824 =C2=A0 0.7262872714
=C2=A0C =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 6.0 =C2=A0-4.1492400474 =C2=A0 3= .1146395623 =C2=A0 0.2452858195
=C2=A0C =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 6.0 =C2=A0-1.0384543970 =C2=A0-1= .0616837070 =C2=A0-0.3935189317
=C2=A0O =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 8.0 =C2=A0 0.2627462226 =C2=A0 2= .8443032110 =C2=A0 0.0824866755
=C2=A0O =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 8.0 =C2=A0-0.4704997692 =C2=A0 1= .4533008486 =C2=A0-1.8948080168
=C2=A0C =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 6.0 =C2=A0-0.6378668095 =C2=A0 2= .5243530855 =C2=A0-2.8050626506
=C2=A0C =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 6.0 =C2=A0-0.2774608150 =C2=A0 2= .0344873705 =C2=A0-4.1938584478
=C2=A0H =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.0 =C2=A0 1.3881553531 =C2=A0 0= .7868788847 =C2=A0 2.8556005870
=C2=A0H =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.0 =C2=A0 2.3160067901 =C2=A0 1= .3768176523 =C2=A0 0.7233520419
=C2=A0H =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.0 =C2=A0 3.2172366054 =C2=A0-0= .1114988528 =C2=A0 0.9696728430
=C2=A0H =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.0 =C2=A0 1.6417676099 =C2=A0 0= .0963453234 =C2=A0-1.2492587194
=C2=A0H =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.0 =C2=A0 1.5731703789 =C2=A0-1= .3827751918 =C2=A0-0.3162564927
=C2=A0H =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.0 =C2=A0-2.0377852391 =C2=A0-0= .8580194102 =C2=A0-0.0283661319
=C2=A0H =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.0 =C2=A0-0.7479881434 =C2=A0-2= .0498384976 =C2=A0-0.0529032264
=C2=A0H =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.0 =C2=A0-1.0569120635 =C2=A0-1= .0569289764 =C2=A0-1.4765818189
=C2=A0H =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.0 =C2=A0-0.0008719974 =C2=A0 3= .3486629651 =C2=A0-2.5124976984
=C2=A0H =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.0 =C2=A0-1.6667297193 =C2=A0 2= .8643354368 =C2=A0-2.7734315079
=C2=A0H =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.0 =C2=A0-0.9178100070 =C2=A0 1= .2102357702 =C2=A0-4.4889383397
=C2=A0H =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.0 =C2=A0 0.7524667515 =C2=A0 1= .6949936400 =C2=A0-4.2221890938
=C2=A0H =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.0 =C2=A0-0.3949982357 =C2=A0 2= .8360019195 =C2=A0-4.9164813839
=C2=A0H =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.0 =C2=A0-2.1574630256 =C2=A0 3= .7066154005 =C2=A0 0.8011166587
=C2=A0H =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.0 =C2=A0-2.7525267855 =C2=A0 2= .3183790758 =C2=A0 1.6873139365
=C2=A0H =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.0 =C2=A0-4.7352990979 =C2=A0 2= .2066177039 =C2=A0 0.1509900642
=C2=A0H =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.0 =C2=A0-4.1273412686 =C2=A0 3= .6105454642 =C2=A0-0.7193589853
=C2=A0H =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.0 =C2=A0-4.6460082334 =C2=A0 3= .7692340878 =C2=A0 0.9550246466
=C2=A0C =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 6.0 =C2=A0 0.5292015558 =C2=A0-2= .7348757451 =C2=A0 3.6831494528
=C2=A0H =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.0 =C2=A0-0.0022376111 =C2=A0-2= .9435571460 =C2=A0 4.6036326690
=C2=A0H =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.0 =C2=A0-0.1579399735 =C2=A0-2= .7125065552 =C2=A0 2.8509341484
=C2=A0H =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.0 =C2=A0 1.2840070669 =C2=A0-3= .4956736649 =C2=A0 3.5234758959
=C2=A0$END
=C2=A0E(MCSCF)=3D =C2=A0 =C2=A0-1235.2758257870, E(NUC)=3D =C2=A0 =C2=A0 17= 56.0463288674
=C2=A0$VEC
=C2=A01 =C2=A01-3.65205327E-05-8.40025961E-05-4.07970446E-05 1.66197059E-05= 3.56227789E-06
=C2=A01 =C2=A02 1.08690929E-03 7.28384183E-05 4.99632967E-04 1.38715170E-04= -5.95289047E-0


I would be much grateful if somebody will tell me why a get =C2=A0this erro= r msg and =C2=A0how can I do a PCM energy calculation =C2=A0in GAMESS.

Sergiu Lescic



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--047d7bdc17504c428d04f8f9f41c-- From owner-chemistry@ccl.net Fri May 9 15:51:00 2014 From: "Jim Kress jimkress35[*]gmail.com" To: CCL Subject: CCL: Gamess Error Question : PCM calculation Message-Id: <-50064-140509154936-26312-flvDCICoSzbki9b1gOXkzg{:}server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_037B_01CF6B9E.3ACEA620" Date: Fri, 9 May 2014 15:49:14 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [jimkress35-,-gmail.com] This is a multipart message in MIME format. ------=_NextPart_000_037B_01CF6B9E.3ACEA620 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable No. If you look at the link the questioner provided, the GAMESS (US) = chart clearly declares the input provided by the user should work. =20 SCFTYP=3D RHF ROHF UHF GVB = MCSCF --- ---- --- --- = ----- SCF energy CDFpEP CDFpEP CD-pEP CD-pEP = CDFpEP SCF analytic gradient CDFpEP CD-pEP CD-pEP CD-pEP = CDFpEP SCF analytic Hessian CD-p-- CD-p-- ------ CD-p-- = -D-p-- MP2 energy CDFpEP CDFpEP CD-pEP ------ = CD-pEP MP2 gradient CDFpEP -D-pEP CD-pEP ------ = ------ CI energy CDFp-- CD-p-- ------ CD-p-- = CD-p-- CI gradient CD---- ------ ------ ------ = ------ CC energy CDFp-- CDF--- ------ ------ = ------ EOMCC excitations CD---- ------ ------ ------ = ------ DFT energy CDFpEP CD-pEP CD-pEP n/a n/a DFT gradient CDFpEP CD-pEP CD-pEP n/a n/a TD-DFT energy CDFpEP ------ CD-p-- n/a n/a TD-DFT gradient CDFpEP ------ ------ n/a n/a MOPAC energy yes yes yes yes n/a MOPAC gradient yes yes yes no n/a =20 Here:=20 C=3D conventional storage of AO integrals on disk D=3D direct evaluation of AO integrals whenever needed F=3D Fragment Molecular Orbital methodology is enabled, "F" pertains to = the gas phase; for FMO with PCM or EFP see manual. p=3D parallel execution E=3D Effective Fragment Potential discrete solvation P=3D Polarizable Continuum Model continuum solvation =20 However, the GAMESS version being used by the questioner has in its = error message a curious item: =20 ERROR: INAPPROPRIATE SOLVENT CALCULATION. SOLVENT MODELS (ALL TYPES) ARE INCOMPATIBLE WITH MANY TYPE OF CORRELATED OR SEMI-EMPIRICAL COMPUTATIONS: SCFTYP=3DMCSCF MPLEVL=3D 2 USING GRADIENTS, CITYP=3DNONE CCTYP=3DNONE VBTYP=3DNONE OR MPCTYP=3DNONE Now, the input file did not request gradients, just a single point = energy calculation. So, we are led to believe =20 1) The table provided in the GAMESS documentation is wrong =20 2) There is a bug in the code that causes GAMESS to erroneously infer = the user is requesting gradients for the input file given. =20 Any GAMESS mavens who know the code and can check to see which is the = problem? =20 Jim =20 =20 =20 > From: owner-chemistry+jimkress35=3D=3Dgmail.com,ccl.net = [mailto:owner-chemistry+jimkress35=3D=3Dgmail.com,ccl.net] On Behalf Of = Victor Rosas Garcia rosas.victor|,|gmail.com Sent: Friday, May 09, 2014 12:19 PM To: Kress, Jim Subject: CCL: Gamess Error Question : PCM calculation =20 The error message is telling you why: the solvent model is incompatible = with many correlated treatments, MCSCF among them. You may have to look = for another quantum chemistry package that is able to do what you want. Hope this helps Victor =20 2014-05-06 7:59 GMT-05:00 Lescic Sergiu s_lescic|,|mail.ru = >: Sent to CCL by: "Lescic Sergiu" [s_lescic::mail.ru ] Hi All, It's a question for GAMESS users. I am trying to run a MCSCF+MP2 energy calculation with a solvent = (water). In the official website = (http://www.msg.ameslab.gov/GAMESS/capabilities.html) its marked that we = can do a PCM energy calculation for MP2 level using MCSCF wavefunction, = but when I tried to run this kind of calculation for a nitroxide anion I am getting an = error msg: ERROR: INAPPROPRIATE SOLVENT CALCULATION. SOLVENT MODELS (ALL TYPES) ARE INCOMPATIBLE WITH MANY TYPE OF CORRELATED OR SEMI-EMPIRICAL COMPUTATIONS: SCFTYP=3DMCSCF MPLEVL=3D 2 USING GRADIENTS, CITYP=3DNONE CCTYP=3DNONE VBTYP=3DNONE OR MPCTYP=3DNONE Here is the input which I use for the test: $CONTRL SCFTYP=3DMCSCF RUNTYP=3DENERGY MPLEVL=3D2 ICHARG=3D-1 MULT=3D1 $END $BASIS GBASIS=3DN31 NGAUSS=3D6 NDFUNC=3D1 $END $MCSCF MAXIT=3D120 CISTEP=3DALDET FULLNR=3D.T. $END $DET NCORE=3D71 NACT=3D6 NELS=3D10 $END $GUESS GUESS=3DMOREAD NORB=3D316 $END $SYSTEM MWORDS=3D2000 MEMDDI=3D2500 $END $PCM SOLVNT=3DH2O $END $DATA ddd C1 C 6.0 -0.0428803989 -0.0424443861 0.1672418969 N 7.0 -0.0249982047 -0.0722027575 1.6202198689 C 6.0 1.3382114206 0.0393378088 2.0814085589 C 6.0 2.2241673056 0.3086354086 0.8636723025 C 6.0 1.4097059351 -0.3098318915 -0.2742919459 O 8.0 -0.8243020048 0.9973357986 2.0319894034 O 8.0 1.8443182472 -1.1840878474 2.6041297701 O 8.0 1.1181041056 -1.4747706922 3.8718333702 P 15.0 -0.5646397607 1.6782589957 -0.2891968951 O 8.0 -2.1393515393 1.9306796258 -0.2195275948 C 6.0 -2.7461302003 2.8030802824 0.7262872714 C 6.0 -4.1492400474 3.1146395623 0.2452858195 C 6.0 -1.0384543970 -1.0616837070 -0.3935189317 O 8.0 0.2627462226 2.8443032110 0.0824866755 O 8.0 -0.4704997692 1.4533008486 -1.8948080168 C 6.0 -0.6378668095 2.5243530855 -2.8050626506 C 6.0 -0.2774608150 2.0344873705 -4.1938584478 H 1.0 1.3881553531 0.7868788847 2.8556005870 H 1.0 2.3160067901 1.3768176523 0.7233520419 H 1.0 3.2172366054 -0.1114988528 0.9696728430 H 1.0 1.6417676099 0.0963453234 -1.2492587194 H 1.0 1.5731703789 -1.3827751918 -0.3162564927 H 1.0 -2.0377852391 -0.8580194102 -0.0283661319 H 1.0 -0.7479881434 -2.0498384976 -0.0529032264 H 1.0 -1.0569120635 -1.0569289764 -1.4765818189 H 1.0 -0.0008719974 3.3486629651 -2.5124976984 H 1.0 -1.6667297193 2.8643354368 -2.7734315079 H 1.0 -0.9178100070 1.2102357702 -4.4889383397 H 1.0 0.7524667515 1.6949936400 -4.2221890938 H 1.0 -0.3949982357 2.8360019195 -4.9164813839 H 1.0 -2.1574630256 3.7066154005 0.8011166587 H 1.0 -2.7525267855 2.3183790758 1.6873139365 H 1.0 -4.7352990979 2.2066177039 0.1509900642 H 1.0 -4.1273412686 3.6105454642 -0.7193589853 H 1.0 -4.6460082334 3.7692340878 0.9550246466 C 6.0 0.5292015558 -2.7348757451 3.6831494528 H 1.0 -0.0022376111 -2.9435571460 4.6036326690 H 1.0 -0.1579399735 -2.7125065552 2.8509341484 H 1.0 1.2840070669 -3.4956736649 3.5234758959 $END E(MCSCF)=3D -1235.2758257870, E(NUC)=3D 1756.0463288674 $VEC 1 1-3.65205327E-05-8.40025961E-05-4.07970446E-05 1.66197059E-05 = 3.56227789E-06 1 2 1.08690929E-03 7.28384183E-05 4.99632967E-04 = 1.38715170E-04-5.95289047E-0 I would be much grateful if somebody will tell me why a get this error = msg and how can I do a PCM energy calculation in GAMESS. Sergiu Lescic -=3D This is automatically added to each message by the mailing script = =3D-
or use:E-mail to administrators: CHEMISTRY-REQUEST!^!ccl.net = or usehttp://www.ccl.net/chemistry/sub_unsub.shtml

No.=C2=A0 If you look at the link the questioner provided, the GAMESS = (US) chart clearly declares the input provided by the user should = work.

 


=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 SCFTYP=3D = RHF=C2=A0=C2=A0=C2=A0 ROHF=C2=A0=C2=A0 UHF=C2=A0=C2=A0=C2=A0 = GVB=C2=A0=C2=A0=C2=A0 MCSCF

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 = =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0---=C2=A0=C2=A0=C2= =A0 ----=C2=A0=C2=A0 ---=C2=A0=C2=A0=C2=A0 ---=C2=A0=C2=A0=C2=A0 = -----

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 SCF = energy=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0 CDFpEP CDFpEP CD-pEP CD-pEP CDFpEP

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 SCF analytic gradient=C2=A0 CDFpEP = CD-pEP CD-pEP CD-pEP CDFpEP

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 SCF analytic Hessian=C2=A0=C2=A0 = CD-p-- CD-p-- ------ CD-p-- -D-p--

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 MP2 = energy=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0 CDFpEP CDFpEP CD-pEP ------ CD-pEP

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 MP2 = gradient=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 = CDFpEP -D-pEP CD-pEP ------ ------

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 CI = energy=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 CDFp-- CD-p-- ------ CD-p-- CD-p--

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 =C2=A0=C2=A0=C2=A0=C2=A0CI = gradient=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= CD---- ------ ------ ------ ------

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 CC = energy=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 CDFp-- CDF--- ------ ------ ------

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 EOMCC = excitations=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 CD---- ------ ------ ------ = ------

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 DFT = energy=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0 CDFpEP CD-pEP CD-pEP=C2=A0 n/a=C2=A0=C2=A0=C2=A0 = n/a

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 DFT = gradient=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 = CDFpEP CD-pEP CD-pEP=C2=A0 n/a=C2=A0=C2=A0=C2=A0 = n/a

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 TD-DFT = energy=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 CDFpEP = ------ CD-p--=C2=A0 n/a=C2=A0=C2=A0=C2=A0 n/a

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 TD-DFT = gradient=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 CDFpEP ------ = ------=C2=A0 n/a=C2=A0=C2=A0=C2=A0 n/a

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0 =C2=A0=C2=A0MOPAC = energy=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 = yes=C2=A0=C2=A0=C2=A0 yes=C2=A0=C2=A0=C2=A0=C2=A0 yes=C2=A0=C2=A0=C2=A0 = yes=C2=A0=C2=A0=C2=A0 n/a

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 MOPAC = gradient=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 = yes=C2=A0=C2=A0=C2=A0 yes=C2=A0=C2=A0=C2=A0=C2=A0 yes=C2=A0=C2=A0=C2=A0 = no=C2=A0=C2=A0=C2=A0=C2=A0 n/a

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0

He= re: 
C=3D conventional storage of AO integrals on disk
D=3D = direct evaluation of AO integrals whenever needed
F=3D Fragment = Molecular Orbital methodology is enabled, "F" pertains to the = gas phase; for FMO with PCM or EFP see manual.
p=3D parallel = execution
E=3D Effective Fragment Potential discrete = solvation
P=3D Polarizable Continuum Model continuum = solvation

 

However, the GAMESS version being used by the questioner has in its = error message a curious item:

 

ERROR: INAPPROPRIATE = SOLVENT CALCULATION.
 SOLVENT MODELS (ALL TYPES) ARE = INCOMPATIBLE WITH MANY
 TYPE OF CORRELATED OR SEMI-EMPIRICAL = COMPUTATIONS:
 SCFTYP=3DMCSCF
 MPLEVL=3D 2 USING GRADIENTS, CITYP=3DNONE =     CCTYP=3DNONE
 VBTYP=3DNONE     OR = MPCTYP=3DNONE

Now, the input file did not request gradients, just a single point = energy calculation.=C2=A0 So, we are led to = believe

 

1) The table provided in the GAMESS documentation is = wrong

 

2) There is a bug in the code that causes GAMESS to erroneously infer = the user is requesting gradients for the input file = given.

 

Any GAMESS mavens who know the code and can check to see which is the = problem?

 

Jim

 

 

 

From: = owner-chemistry+jimkress35=3D=3Dgmail.com,ccl.net = [mailto:owner-chemistry+jimkress35=3D=3Dgmail.com,ccl.net] On Behalf = Of Victor Rosas Garcia rosas.victor|,|gmail.com
Sent: = Friday, May 09, 2014 12:19 PM
To: Kress, Jim =
Subject: CCL: Gamess Error Question : PCM = calculation

 

The error message is = telling you why: the solvent model is incompatible with many correlated = treatments, MCSCF among them. You may have to look for another quantum = chemistry package that is able to do what you = want.

Hope this helps

Victor

 

2014-05-06 7:59 GMT-05:00 Lescic Sergiu s_lescic|,|mail.ru <owner-chemistry!^!ccl.net>:


Sent to CCL by: "Lescic =  Sergiu" [s_lescic::mail.ru]
Hi All,
It's a question for GAMESS = users.
I am trying to run a MCSCF+MP2 energy calculation with a = solvent (water). In the official website (http://www.msg.ameslab.gov/GAMESS/capabilities.html= ) its marked that we can do a PCM energy calculation for MP2 level using = MCSCF wavefunction, but when I tried
to run this kind of calculation =  for a nitroxide anion  I am getting an error = msg:


ERROR: INAPPROPRIATE SOLVENT = CALCULATION.
 SOLVENT MODELS (ALL TYPES) ARE INCOMPATIBLE WITH = MANY
 TYPE OF CORRELATED OR SEMI-EMPIRICAL = COMPUTATIONS:
 SCFTYP=3DMCSCF
 MPLEVL=3D 2 USING = GRADIENTS, CITYP=3DNONE     CCTYP=3DNONE
 VBTYP=3DNONE =     OR MPCTYP=3DNONE

Here is the input which I use for = the test:
$CONTRL  SCFTYP=3DMCSCF RUNTYP=3DENERGY = MPLEVL=3D2
ICHARG=3D-1 MULT=3D1 $END

 $BASIS GBASIS=3DN31 = NGAUSS=3D6 NDFUNC=3D1
 $END

 $MCSCF =  MAXIT=3D120 CISTEP=3DALDET = FULLNR=3D.T.
 $END
 $DET NCORE=3D71 NACT=3D6 NELS=3D10 = $END
 $GUESS GUESS=3DMOREAD NORB=3D316 =  $END
 $SYSTEM MWORDS=3D2000 MEMDDI=3D2500 =  $END
 $PCM SOLVNT=3DH2O = $END
 $DATA
ddd
C1
 C         =   6.0  -0.0428803989  -0.0424443861   = 0.1672418969
 N           7.0 =  -0.0249982047  -0.0722027575   1.6202198689
 C =           6.0   1.3382114206   = 0.0393378088   2.0814085589
 C         =   6.0   2.2241673056   0.3086354086   = 0.8636723025
 C           6.0   = 1.4097059351  -0.3098318915  -0.2742919459
 O   =         8.0  -0.8243020048   0.9973357986 =   2.0319894034
 O           8.0 =   1.8443182472  -1.1840878474   2.6041297701
 O =           8.0   1.1181041056 =  -1.4747706922   3.8718333702
 P       =    15.0  -0.5646397607   1.6782589957 =  -0.2891968951
 O           8.0 =  -2.1393515393   1.9306796258  -0.2195275948
 C =           6.0  -2.7461302003   = 2.8030802824   0.7262872714
 C         =   6.0  -4.1492400474   3.1146395623   = 0.2452858195
 C           6.0 =  -1.0384543970  -1.0616837070  -0.3935189317
 O =           8.0   0.2627462226   = 2.8443032110   0.0824866755
 O         =   8.0  -0.4704997692   1.4533008486 =  -1.8948080168
 C           6.0 =  -0.6378668095   2.5243530855  -2.8050626506
 C =           6.0  -0.2774608150   = 2.0344873705  -4.1938584478
 H         =   1.0   1.3881553531   0.7868788847   = 2.8556005870
 H           1.0   = 2.3160067901   1.3768176523   0.7233520419
 H   =         1.0   3.2172366054  -0.1114988528 =   0.9696728430
 H           1.0 =   1.6417676099   0.0963453234  -1.2492587194
 H =           1.0   1.5731703789 =  -1.3827751918  -0.3162564927
 H       =     1.0  -2.0377852391  -0.8580194102 =  -0.0283661319
 H           1.0 =  -0.7479881434  -2.0498384976  -0.0529032264
 H =           1.0  -1.0569120635 =  -1.0569289764  -1.4765818189
 H       =     1.0  -0.0008719974   3.3486629651 =  -2.5124976984
 H           1.0 =  -1.6667297193   2.8643354368  -2.7734315079
 H =           1.0  -0.9178100070   = 1.2102357702  -4.4889383397
 H         =   1.0   0.7524667515   1.6949936400 =  -4.2221890938
 H           1.0 =  -0.3949982357   2.8360019195  -4.9164813839
 H =           1.0  -2.1574630256   = 3.7066154005   0.8011166587
 H         =   1.0  -2.7525267855   2.3183790758   = 1.6873139365
 H           1.0 =  -4.7352990979   2.2066177039   0.1509900642
 H =           1.0  -4.1273412686   = 3.6105454642  -0.7193589853
 H         =   1.0  -4.6460082334   3.7692340878   = 0.9550246466
 C           6.0   = 0.5292015558  -2.7348757451   3.6831494528
 H   =         1.0  -0.0022376111  -2.9435571460 =   4.6036326690
 H           1.0 =  -0.1579399735  -2.7125065552   2.8509341484
 H =           1.0   1.2840070669 =  -3.4956736649   = 3.5234758959
 $END
 E(MCSCF)=3D   =  -1235.2758257870, E(NUC)=3D     = 1756.0463288674
 $VEC
 1 =  1-3.65205327E-05-8.40025961E-05-4.07970446E-05 1.66197059E-05 = 3.56227789E-06
 1  2 1.08690929E-03 7.28384183E-05 = 4.99632967E-04 1.38715170E-04-5.95289047E-0


I would be much = grateful if somebody will tell me why a get  this error msg and =  how can I do a PCM energy calculation  in = GAMESS.

Sergiu Lescic



-=3D This is automatically = added to each message by the mailing script =3D-<br


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------=_NextPart_000_037B_01CF6B9E.3ACEA620-- From owner-chemistry@ccl.net Fri May 9 17:01:00 2014 From: "Jim Kress jimkress35%a%gmail.com" To: CCL Subject: CCL: Why Most Published Research Findings Are False Message-Id: <-50065-140509154043-25865-T5s21wlOxNORx0hKFImlCA . server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 9 May 2014 15:40:21 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [jimkress35:_:gmail.com] Here's an interesting article that reflects on many of the point that have been made in our discussions. Why Most Published Research Findings Are False John P. A. Ioannidis Published: August 30, 2005 DOI: 10.1371/journal.pmed.0020124 http://www.plosmedicine.org/article/info%3Adoi%2F10.1371%2Fjournal.pmed.0020 124 Abstract Summary There is increasing concern that most current published research findings are false. The probability that a research claim is true may depend on study power and bias, the number of other studies on the same question, and, importantly, the ratio of true to no relationships among the relationships probed in each scientific field. In this framework, a research finding is less likely to be true when the studies conducted in a field are smaller; when effect sizes are smaller; when there is a greater number and lesser preselection of tested relationships; where there is greater flexibility in designs, definitions, outcomes, and analytical modes; when there is greater financial and other interest and prejudice; and when more teams are involved in a scientific field in chase of statistical significance. Simulations show that for most study designs and settings, it is more likely for a research claim to be false than true. Moreover, for many current scientific fields, claimed research findings may often be simply accurate measures of the prevailing bias. In this essay, I discuss the implications of these problems for the conduct and interpretation of research. This has spawned a new center at Stanford: http://www.the-scientist.com/?articles.view/articleNo/39838/title/Researchin g-Research/ Researching Research Stanford University starts new center to study how scientific research can be improved. By Jef Akst | April 28, 2014 The recently launched Meta-Research Innovation Center (METRICS) at Stanford University aims to change how research is done. Professors of Medicine John Ioannidis and Steven Goodman will head the new center, which is funded by a $6 million grant from the Laura and John Arnold Foundation and will host scientists from diverse fields to share their findings and discuss the challenges of performing rigorous research. The end goal is to identify common errors and biases that may be contributing to the rise in irreproducible research. Jim -----Original Message----- > From: owner-chemistry+jimkress35==gmail.com:_:ccl.net [mailto:owner-chemistry+jimkress35==gmail.com:_:ccl.net] On Behalf Of Jim Kress jimkress35[a]gmail.com Sent: Sunday, May 04, 2014 3:18 PM To: Kress, Jim Subject: CCL: Name of authors during review ...!!! Sent to CCL by: "Jim Kress" [jimkress35|,|gmail.com] Here is an interesting link that helps illustrates a few examples of the existence of the concern with "peer review" vs "pal review" and reviewer/ author anonymity: http://www.forbes.com/sites/patrickmichaels/2011/06/16/peer-review-and-pal-r eview-in-climate-science/ Jim -----Original Message----- > From: owner-chemistry+jimkress35==gmail.com__ccl.net [mailto:owner-chemistry+jimkress35==gmail.com__ccl.net] On Behalf Of Eric Bennett ericb-,-pobox.com Sent: Sunday, May 04, 2014 12:34 AM To: Kress, Jim Subject: CCL: Name of authors during review ...!!! Sent to CCL by: Eric Bennett [ericb[#]pobox.com] Suppose you received an article to review that contained shoddy science pushing a politically popular view. Wouldn't you be concerned authors who think politics are more important than good science might retaliate against you for holding them to proper scientific standards? It would become even easier to blacklist people who don't conform to a consensus view. A relevant question for this discussion is... on the whole, is there a bigger problem with good work not being published because of vendettas, or bad work being published because of insufficient stringency and lack of criticism during the review process? I'd be more likely to say the latter... in the former case even if journal A occasionally rejects a paper due to a biased anonymous reviewer, if the work is good, journal B is probably going to take it. -Eric On May 2, 2014, at 11:27 AM, Jim Kress jimkress35]![gmail.com wrote: > > Sent to CCL by: "Jim Kress" [jimkress35=-=gmail.com] Why should the > names of the reviewers be confidential? It is only reasonable, given > the level of personal and professional antipathy present in todays > "Science" that the authors of an article be allowed to see who > reviewed their work. As we have seen exposed in the media, e.g. on > the topic of "Global Warming", reviewers who object to your political > views will ignore the scientific aspects of your work and deny > publication, just on the basis of their personal animosity toward you and/or your politics. > > Authors should be allowed to ensure this type of nonscientific bias is > not allowed to interfere with the publication of their scientific work. > > Jim Kress > > -----Original Message----- >> From: owner-chemistry+jimkress35==gmail.com(-)ccl.net > [mailto:owner-chemistry+jimkress35==gmail.com(-)ccl.net] On Behalf Of > tarzan p tarzan11_11..yahoo.com > Sent: Thursday, May 01, 2014 11:19 PM > To: Kress, Jim > Subject: CCL: Name of authors during review ...!!! > > > Sent to CCL by: "tarzan p" [tarzan11_11=-=yahoo.com] Dear All........ > It is often(or probably always ...) that a submitted article to > journal goes for a peer review. Of course the reviewers are confidential. Justified. > But why is that the reviewers get to know the names of the authors and > his affiliation during the review process ..? Unfair ...!!! > Will it not put a sort of bias into the reviewers head ...?? > Will it be not possible for the journal editors to adopt a policy of > non-disclosure of the authors till the work is accepted...? > > I hope to get some views..... > with best wishes and happy computing > ....http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/ > chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > -- Eric Bennett, ericb _ pobox.com Always try to associate yourself with and learn as much as you can from those who know more than you do, who do better than you, who see more clearly than you. - Dwight Eisenhowerhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/ chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://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 Fri May 9 17:35:00 2014 From: "Fabio cardenas fabiocarden,gmail.com" To: CCL Subject: CCL:G: Gaussian processor Message-Id: <-50066-140509164953-10125-fbiJ8S24KCoLl+21ZxNysg+*+server.ccl.net> X-Original-From: Fabio cardenas Content-Type: multipart/alternative; boundary=001a11c377d6dba73204f8fdbcd2 Date: Fri, 9 May 2014 15:49:45 -0500 MIME-Version: 1.0 Sent to CCL by: Fabio cardenas [fabiocarden^gmail.com] --001a11c377d6dba73204f8fdbcd2 Content-Type: text/plain; charset=UTF-8 Quick two questions, I am reusing to figure out what I can buy for the money I have. I would like to build a computer to run Gaussian 09 64 bit. Few calculations (Fround states, transition states, TDDFT) on organic small molecules. Does Gaussian uses the hyper threading of intel processors? For a computer that would be running these calculations for few days, may be a week non-stop, would a AMD still be OK to buy? Any recommendation on the hardware I could buy without going for the top of today's technology? Thanks --001a11c377d6dba73204f8fdbcd2 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Quick two questions,
I am reusing to figure out what I can buy for the = money I have. I would like to build a computer to run Gaussian 09 64 bit. F= ew calculations (Fround states, transition states, TDDFT) on organic small = molecules.=C2=A0
Does Gaussian uses the hyper threading = of intel processors?
= For a computer that would be running these=C2=A0calculations for few days,= =C2=A0 may be=C2=A0a week non-stop, would a AMD still be OK to buy? Any rec= ommendation on the hardware I could buy without going for the top of today&= #39;s technology?

Thanks
--001a11c377d6dba73204f8fdbcd2-- From owner-chemistry@ccl.net Fri May 9 20:05:00 2014 From: "Moumita Bhattacharya m.bhattacharya-*-aggiemail.usu.edu" To: CCL Subject: CCL:G: Calculation of HOMO-LUMO for a square planar complex of Nickel Message-Id: <-50067-140509195529-30918-JS9b6Y1Q5T3Q76NulgrzjQ++server.ccl.net> X-Original-From: "Moumita Bhattacharya" Date: Fri, 9 May 2014 19:55:28 -0400 Sent to CCL by: "Moumita Bhattacharya" [m.bhattacharya#%#aggiemail.usu.edu] Hello, I am trying to get the HOMO-LUMO of a square planar Ni complex using Gaussian. > From my calculation I am getting d(xz) on the Ni contributing as HOMO, which is not expected from a square planar complex. I am using the optimized geometry for my calculation. Can anyone suggest what should I try differently? Isn't it really weird to get d(xz) as the HOMO for sq. pl. geometry? From owner-chemistry@ccl.net Fri May 9 21:08:00 2014 From: "Nico G nicogreen6+*+gmail.com" To: CCL Subject: CCL:G: Gaussian processor Message-Id: <-50068-140509184507-25143-TiJbdoUoZ+PmcExQvaT33g/a\server.ccl.net> X-Original-From: Nico G Content-Type: multipart/alternative; boundary="------------060804070702040008090800" Date: Fri, 09 May 2014 19:44:56 -0300 MIME-Version: 1.0 Sent to CCL by: Nico G [nicogreen6/a\gmail.com] This is a multi-part message in MIME format. --------------060804070702040008090800 Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit Fabio I assume your are talking of a desktop pc. In my experience intel is far better than AMD, even at lower clocks speeds. Gaussian takes advantage of the HyperThreading technology. In the lab we have a couple of I7 all from different generations and there is no huge difference between them. The Motherboard although is really important. I cannot say anything for the RAM speed, because they are all 1600MHz. Those computers are most of the year on. Just be sure to select a good case with good airflow and a robust power supply for the most known vendors (thermaltake, Cooler Master, Antec, etc). SSD if you can afford them are also great addition. Hope that helps Nico On 09/05/2014 17:49, Fabio cardenas fabiocarden,gmail.com wrote: > Quick two questions, > I am reusing to figure out what I can buy for the money I have. I > would like to build a computer to run Gaussian 09 64 bit. Few > calculations (Fround states, transition states, TDDFT) on organic > small molecules. > Does Gaussian uses the hyper threading of intel processors? > For a computer that would be running these calculations for few days, > may be a week non-stop, would a AMD still be OK to buy? Any > recommendation on the hardware I could buy without going for the top > of today's technology? > > Thanks --------------060804070702040008090800 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 8bit Fabio

I assume your are talking of a desktop pc.
In my experience intel is far better than AMD, even at lower clocks speeds. Gaussian takes advantage of the HyperThreading technology.
In the lab we have a couple of I7 all from different generations and there is no huge difference between them. The Motherboard although is really important. I cannot say anything for the RAM speed, because they are all 1600MHz.
Those computers are most of the year on. Just be sure to select a good case with good airflow and a robust power supply for the most known vendors (thermaltake, Cooler Master, Antec, etc).
SSD if you can afford them are also great addition.

Hope that helps

Nico

On 09/05/2014 17:49, Fabio cardenas fabiocarden,gmail.com wrote:
Quick two questions,
I am reusing to figure out what I can buy for the money I have. I would like to build a computer to run Gaussian 09 64 bit. Few calculations (Fround states, transition states, TDDFT) on organic small molecules. 
Does Gaussian uses the hyper threading of intel processors?
For a computer that would be running these calculations for few days,  may be a week non-stop, would a AMD still be OK to buy? Any recommendation on the hardware I could buy without going for the top of today's technology?

Thanks

--------------060804070702040008090800-- From owner-chemistry@ccl.net Fri May 9 22:25:00 2014 From: "Salter-Duke, Brian James - brian.james.duke_-_gmail.com" To: CCL Subject: CCL:G: Calculation of HOMO-LUMO for a square planar complex of Nickel Message-Id: <-50069-140509221542-14958-S1exKwugBEd0Ae9hg1klpw(a)server.ccl.net> X-Original-From: "Salter-Duke, Brian James -" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Sat, 10 May 2014 12:15:26 +1000 MIME-Version: 1.0 Sent to CCL by: "Salter-Duke, Brian James -" [brian.james.duke||gmail.com] On Fri, May 09, 2014 at 07:55:28PM -0400, Moumita Bhattacharya m.bhattacharya-*-aggiemail.usu.edu wrote: > > Sent to CCL by: "Moumita Bhattacharya" [m.bhattacharya#%#aggiemail.usu.edu] > Hello, > > I am trying to get the HOMO-LUMO of a square planar Ni complex using Gaussian. > > From my calculation I am getting d(xz) on the Ni contributing as HOMO, which is > not expected from a square planar complex. I am using the optimized geometry > for my calculation. Can anyone suggest what should I try differently? Isn't it > really weird to get d(xz) as the HOMO for sq. pl. geometry? How did you select you intial guess MOs? It is quite common for the algorithms used for the initial guess orbitals to not be the correct MOs for the RHF (UHF or ROHF) ground state. However, once selected, they can get frozen in so you do not get the correct ground state. You may have to swap the inital guess occupied and unoccupied orbitals until you get the ones that lead to the lowest energy. Brian.> -- Brian Salter-Duke (Brian Duke) Brian.Salter-Duke]_[monash.edu Adjunct Associate Professor Monash Institute of Pharmaceutical Sciences Monash University Parkville Campus, VIC 3052, Australia