From owner-chemistry@ccl.net Wed Jul 15 00:34:00 2009 From: "Vincent Xianlong Wang xloongw#%#yahoo.com" To: CCL Subject: CCL: pKa calculation of strong acid Message-Id: <-39781-090714221402-11925-QEJdciRoC8MpcnAohxxw3A{:}server.ccl.net> X-Original-From: Vincent Xianlong Wang Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 14 Jul 2009 18:13:46 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Vincent Xianlong Wang [xloongw|yahoo.com] On this week's Science, there is a research paper on this subject. The expe= riments were conducted at extreme conditions (below 1 K) though. =0A=0A=0A= Science 324, 1545 (2009);=0AAnna Gutberlet, et al.=0ABelow 1 K: The Smalles= t Droplet of Acid=0A=0A=0ABest regards,=0A=0AVincent=0A=0A--- On Wed, 7/15/= 09, VITORGE Pierre 094605 Pierre.VITORGE[-]cea.fr = wrote:=0A=0A> From: VITORGE Pierre 094605 Pierre.VITORGE[-]cea.fr =0A> Subject: CCL: pKa calculation of strong acid=0A> To: = "Wang, Xianlong " =0A> Date: Wednesday, July 15,= 2009, 2:28 AM=0A> =0A> Sent to CCL by: "VITORGE Pierre 094605"=0A> [Pierre= .VITORGE[a]cea.fr]=0A> Yes using umbrella sampling is certainly a method, b= ut I do=0A> not know whether it will work. HCl/H2O(l) is such a common=0A> = system that estimation of its pKa might exist in the=0A> literature: in old= times people have tried to make general=0A> pKa scales in different solven= ts -not only water- the pKa=0A> value you are looking might have been estim= ated this way.=0A> When you wrote below "the pKa in aqueous solution is aro= und=0A> -6", where does this -6 value come from? Isn't it enough for=0A> yo= ur estimation? Note that 1 log10 uncertainty on pKa (which=0A> is a big unc= ertainty for solution chemistry) corresponds to=0A> only less that 6 kJ.mol= -1, which might be less than the=0A> accuracy of deltaG calculations by mol= ecular modelling in=0A> liquid water.=0A> =0A> Pierre Vitorge=0A> =0A> =0A>= -----Message d'origine-----=0A> De=A0: owner-chemistry+pierre.vitorge=3D= =3Dcea.fr-#-ccl.net=0A> [mailto:owner-chemistry+pierre.vitorge=3D=3Dcea.fr-= #-ccl.net] De=0A> la part de Kefa Lu kefa.lu!A!gmail.com=0A> Envoy=E9=A0: j= eudi 9 juillet 2009 23:53=0A> =C0=A0: VITORGE Pierre 094605=0A> Objet=A0: C= CL: pKa calculation of strong acid=0A> =0A> =0A> Sent to CCL by: Kefa Lu [k= efa.lu!^!gmail.com]=0A> Hi, all,=0A> Really appreciate for all the replys.= =0A> What I actually need to know is the difference of=0A> dissociation ene= rgy H+ =0A> or binding energy of=A0 H+ to Cl- in water and in a=0A> protein= I'm studying =0A> right now. A problem is, HCl usually completely dissocia= tes=0A> into H+ and =0A> Cl-. So how can I find a way to estimate the free = energy of=0A> binding a H+ =0A> to Cl-? Just calculate the potential of mea= n force using=0A> umbrella =0A> sampling method? Or is there any better ide= a to do this?=0A> =0A> Thanks.=0A> =0A> Kefa=0A> =0A> VITORGE Pierre 094605= Pierre.VITORGE%a%cea.fr wrote:=0A> > Sent to CCL by: "VITORGE Pierre 09460= 5"=0A> [Pierre.VITORGE*cea.fr]=0A> > Dave,=0A> >=0A> > pKa =3D -6 in aqueou= s solution, means it cannot be=0A> measured. We are both right: the value c= annot be measured,=0A> but it might very well be the good value, which I am= =0A> explaining below.=0A> >=0A> > pKa =3D -lgKa is a definition of pKa, wh= ere =0A> > Ka =3D [H+] [Cl-] / [HCl]=0A> > [X] is the concentration of spec= ies X, here X is an=0A> aqueous specie (H+, Cl- or HCl). For simplicity I a= m using=0A> concentrations meaning the (small) activity corrections are=0A>= included in Ka.=0A> >=0A> > A first (chemical) meaning of pKa is (pH) half= point=0A> reaction, namely for 50% dissociation [Cl-]_1/2 =3D [HCl]_1/2,= =0A> where subscript _1/2 is to stress=A0 concentrations are=0A> for specia= l (chemical) conditions. Consequently=0A> > Ka =3D [H+]_1/2 equivalently=0A= > > pKa =3D -lg[H+]_1/2 and=0A> > pKa=B0 =3D pH_1/2 a well known formula in= solution=0A> chemistry, where superscript=B0 is for standard conditions=0A= > (infinite dilution where -lg[H+] -> pH)=0A> >=0A> > In this respect pKa o= f strong acid has no finite=0A> value, since strong acid means completely d= issociated in any=0A> chemical conditions, namely [HCl]=3D0; which is indee= d not=0A> possible for finite values of Ka.=0A> > However, Ka can directly = be measured only when the=0A> dissociated form can be detected, typically i= f the detection=0A> limit is 1% only pKa > -2 can be directly measured, and= =0A> "no finite value" actually means "> -2".=0A> >=0A> > (Partial) conclus= ion: do not write pKa of strong acid;=0A> it is chocking for those who curr= ently measure or use pKas=0A> knowing the meanings of the concept.=0A> >=0A= > > Another meaning of pKa is form thermodynamics:=0A> delta_rG =3D -RTlnK = here applied to K =3D Ka. You can very well=0A> calculate=0A> > delta_rGa = =3D G(H+) + G(Cl-) - G(HCl)=0A> > (again note they are aqueous species, esp= ecially not=0A> HCl(g)), where G(X) can be taken from thermochemical data= =0A> bases (as G(X) =3D delta_fG(X)) or calculated by molecular=0A> modelli= ng. =0A> > Now imagine delta_rGa have been estimated in this way=0A> giving= pKa=3D-6. This means that in the most favourable=0A> conditions to form HC= l, typically 10 mol.L-1 total HCl=0A> concentration, the concentrations of = the actual species in=0A> solution would be=0A> > [H+] # 10 mol.L-1=0A> > [= Cl-] # 10 mol.L-1=0A> > [HCl] =3D 10^-6 mol.L-1, which can probably not be= =0A> detected, but might very well exist. The reasoning still=0A> stand eve= n for concentrations less than Avogadro Number per=0A> litre, and the resul= t is meaningful: the (Ka) reaction can=0A> be used in thermodynamic cycles,= typically with another=0A> acid-base reaction to decide in which way the p= roton will be=0A> transferred.=0A> >=0A> > Conclusion: what is your actual = problem? Do you really=0A> need the pKa of HCl in liquid water? Or is it on= ly part of=0A> your calculations? In this later case can it be cancelled=0A= > out by using other calculation strategies? =0A> > This was actually the o= rigin of my remark.=0A> >=0A> > Pierre Vitorge=0A> >=0A> > -----Message d'o= rigine-----=0A> > De : owner-chemistry+pierre.vitorge=3D=3Dcea.fr*|*ccl.net= =0A> [mailto:owner-chemistry+pierre.vitorge=3D=3Dcea.fr*|*ccl.net] De=0A> l= a part de case case~!~biomaps.rutgers.edu=0A> > Envoy=E9 : mercredi 8 juill= et 2009 16:44=0A> > =C0 : VITORGE Pierre 094605=0A> > Objet : CCL: pKa calc= ulation of strong acid=0A> >=0A> >=0A> > Sent to CCL by: case [case##biomap= s.rutgers.edu]=0A> >=0A> > On Tue, Jul 07, 2009, VITORGE Pierre 094605=0A> = Pierre.VITORGE^^cea.fr wrote:=0A> >=A0=A0=A0=0A> >> The pKa of a strong aci= d have no finite value,=0A> namely it does not exist.=0A> >>=A0 =A0=A0=A0= =0A> >=0A> > These values certainly exist.=A0 For the HCl=0A> example that = was in the=0A> > original post, the pKa in aqueous solution is around=0A> -= 6, although this=0A> > seems to have a big uncertainty.=A0 You would have= =0A> to spend some time to=0A> > find the original determination -- a secon= dary=0A> reference to start from=0A> > would be Albert and Serjeant, "The D= etermination of=0A> Ionization Constants",=0A> > Chapman & Hall, 1984.=0A> = >=0A> > ....dave casehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://= www.ccl.net/spammers.txt=0A> >=0A> >=0A> > -=3Dhis is automatically added t= o each message by the=0A> mailing script =3D->=0A> >=0A> >=0A> =0A> =0A> = =0A> -=3D This is automatically added to each message by the=0A> mailing sc= ript =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscri= be:=0Ahttp://www.ccl.net/spammers.txt=0A> = =0A> =0A> -=3D This is automatically added to each message by the=0A> maili= ng script =3D-=0A> To recover the email address of the author of the messag= e,=0A> please change=0A> the strange characters on the top line to the +/- si= gn. You=0A> can also=0A> look up the X-Original-From: line in the mail head= er.=0A> =0A> E-mail to subscribers: CHEMISTRY+/-ccl.net=0A> or use:=0A> =A0 = =A0 =A0=0A> =0A> E-mail to = administrators: CHEMISTRY-REQUEST+/-ccl.net=0A> or use=0A> =A0 =A0 =A0 http:/= /www.ccl.net/cgi-bin/ccl/send_ccl_message=0A> =0A> Subscribe/Unsubscribe:= =0A> =A0 =A0 =A0=0A> =0A> Befo= re posting, check wait time at: http://www.ccl.net=0A> =0A> Job: http://www= .ccl.net/jobs=0A> Conferences: http://server.ccl.net/chemistry/announcement= s/conferences/=0A> =0A> Search Messages: http://www.ccl.net/chemistry/searc= hccl/index.shtml=0A> =0A> If your mail bounces from CCL with 5.7.1 error, c= heck:=0A> =A0 =A0 =A0=0A> =0A> RTFI: http:/= /www.ccl.net/chemistry/aboutccl/instructions/=0A> =0A> =0A> =0A=0A=0A From owner-chemistry@ccl.net Wed Jul 15 03:16:00 2009 From: "Harald Lanig harald.lanig#%#chemie.uni-erlangen.de" To: CCL Subject: CCL: Molecular Modeling Workshop and Model(l)ing'09 in Erlangen, Germany Message-Id: <-39782-090714105355-3401-Q1QY/E7gpHW5oeWuhqNlKw|*|server.ccl.net> X-Original-From: Harald Lanig Content-Disposition: inline Content-Type: text/plain; charset="US-ASCII"; format="flowed" Date: Tue, 14 Jul 2009 16:01:35 +0200 MIME-Version: 1.0 Sent to CCL by: Harald Lanig [harald.lanig*|*chemie.uni-erlangen.de] Dear list subscribers, this year, the Molecular Modeling Workshop in Erlangen (formerly known as "Darmstadt workshop") takes place Sunday 6th - Monday 7th September 2009 as a satellite meeting to Model(l)ing'09, an international conference on occasion to Tim Clark's 60th birthday. As every year, an interesting and successful workshop depends on your contributions. Therefore let me invite you to submit talks and/or poster titles for the workshop via the registration form http://www.chemie.uni-erlangen.de/modeling09/modeling09_register.php I also want to encourage you to attend Model(l)ing'09 - A Molecular Graphics and Modeling Society (MGMS) International Meeting focussing on all aspects of Computational Chemistry and Drug Design. Abstracts for contributed posters are most welcome! Plenary Speakers at Model(l)ing'09 are: Richard Catlow (London) Andreas Hirsch (Erlangen) Pavel Jungwirth (Prague) Frank Neese (Bonn) Leo Radom (Sydney) Arieh Warshel (Los Angeles) ** The registration for both events is open! ** Please take into account that the deadline for all abstract submissions is Friday 31 July 2009. I am happy to announce that a limited number of bursaries for students is available upon request. Please apply for travel support to modeling09!A!chemie.uni-erlangen.de For details about both meetings, especially the **completed list of invited speakers** please visit http://www.modeling09.com I am looking forward to seeing you in Erlangen! -Harald Lanig -- ------------------------------------------------------------------------ Dr. Harald Lanig Universitaet Erlangen/Nuernberg Computer-Chemie-Centrum Naegelsbachstr. 25, D-91052 Erlangen Phone +49(0)9131-85 26525 harald DOT lanig AT chemie.uni-erlangen.de Fax +49(0)9131-85 26565 http://www.chemie.uni-erlangen.de/lanig Visit Erlangen - join us at Model(l)ing 2009 http://www.modeling09.com ------------------------------------------------------------------------ From owner-chemistry@ccl.net Wed Jul 15 05:47:01 2009 From: "MUDIT DIXIT dixitmuditk(a)gmail.com" To: CCL Subject: CCL: MOF-5 Message-Id: <-39783-090715054541-25204-ct5whbAfNZow6KsqmTyCeg/a\server.ccl.net> X-Original-From: "MUDIT DIXIT" Date: Wed, 15 Jul 2009 05:45:37 -0400 Sent to CCL by: "MUDIT DIXIT" [dixitmuditk::gmail.com] I am faceing problems in getting MOF-5 unit cell coordinates(106) . Please tell me how to get these . Thanks, Regards, MD From owner-chemistry@ccl.net Wed Jul 15 09:33:00 2009 From: "Matthew Clark mclark|a|pharmatrope.com" To: CCL Subject: CCL: force fields for torsion rotations Message-Id: <-39784-090715090745-32108-pzT5OgVGz/sw5S9TD+XpSQ^-^server.ccl.net> X-Original-From: Matthew Clark Content-Type: multipart/alternative; boundary="=-idrjLEQiXAqlS8B1g+h9" Date: Wed, 15 Jul 2009 08:34:58 -0400 Mime-Version: 1.0 Sent to CCL by: Matthew Clark [mclark(0)pharmatrope.com] --=-idrjLEQiXAqlS8B1g+h9 Content-Type: text/plain Content-Transfer-Encoding: 7bit Is there a standard method to modify force field potentials to get the correct energy profile for torsion rotation when using rigid rotations? That is, rotating a torsion while leaving the bond lengths and angles constant. Matthew Clark Pharmatrope --=-idrjLEQiXAqlS8B1g+h9 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: 7bit
Is there a standard method to modify force field potentials to get the correct energy profile for torsion rotation when using rigid rotations? 
That is, rotating a torsion while leaving the bond lengths and angles constant.


Matthew Clark
Pharmatrope --=-idrjLEQiXAqlS8B1g+h9-- From owner-chemistry@ccl.net Wed Jul 15 10:08:01 2009 From: "Jean Christophe Poully jean-christophe.poully ~~ univ-paris13.fr" To: CCL Subject: CCL:G: ONIOM Optimization Message-Id: <-39785-090713133617-30093-nAxgjRwRFgqwAVWT8rYd0Q||server.ccl.net> X-Original-From: Jean Christophe Poully Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1"; format=flowed Date: Mon, 13 Jul 2009 19:36:08 +0200 Mime-Version: 1.0 Sent to CCL by: Jean Christophe Poully [jean-christophe.poully[]univ-paris13.fr] Dear Ajanta, Did you try the GDIIS algorithm for optimization?=20 It may be more efficient that the default=20 algorithm in your specific case... You just have=20 to type "opt=3Dgdiis" in the input file. Another=20 solution would be to include more atoms in the=20 high layer, if you have enough RAM to do so, it has already worked for me. Hope it helps! JC At 14:10 13/07/2009, you wrote: >Sent to CCL by: "Ajanta Deka" [ajanta*tezu.ernet.in] >Dear All, > >I am trying to do an optimzation using ONIOM method (Gaussian 03)for >faujasite zeolite. For the QM part I am using uB3LYP/6-31g(d,p) and >uB3LYP/LanL2dz and UFF for the MM part. I observe something strange in the >output. When I look at the energy values in the subsequent steps of >optimization, this is what I find > >SCF Done: E(UB+HF-LYP) =3D -2190.15693744 A.U. after 24 cycles >SCF Done: E(UB+HF-LYP) =3D -2190.15700719 A.U. after 24 cycles >SCF Done: E(UB+HF-LYP) =3D -2190.15693744 A.U. after 24 cycles >SCF Done: E(UB+HF-LYP) =3D -2190.15700718 A.U. after 24 cycles >SCF Done: E(UB+HF-LYP) =3D -2190.15693745 A.U. after 24 cycles >SCF Done: E(UB+HF-LYP) =3D -2190.15700721 A.U. after 24 cycles >SCF Done: E(UB+HF-LYP) =3D -2190.15693745 A.U. after 24 cycles >SCF Done: E(UB+HF-LYP) =3D -2190.15700720 A.U. after 24 cycles >SCF Done: E(UB+HF-LYP) =3D -2190.15693744 A.U. after 24 cycles >SCF Done: E(UB+HF-LYP) =3D -2190.15700718 A.U. after 24 cycles > >Thus, the energy is approaching two different values. >Ultimately, the job fails with the following messaqe > >Error termination request processed by link 9999. >Error termination via Lnk1e in /home/ramesh/g03/l9999.exe at Sat Jul 11 >18:01:11 2009 >Job cpu time: 6 days 21 hours 53 minutes 6.0 seconds. >File lengths (MBytes): RWF=3D 100 Int=3D 0 D2E=3D 0 Chk=3D = 20 >Scr=3D 1 > >I have tried by changing the initial geometry slightly, but I get the same >result. I have successfully got the optimized geometry for a similiar >system (with slightly different charge). I do not know how to overcome >this error. Please help me. > >with warm regards, >Ajanta Deka > > > >-=3D This is automatically added to each message by the mailing script =3D-Jean-Christophe POULLY Doctorant dans l'=E9quipe AMIBES Laboratoire de Physique des Lasers Institut Galil=E9e Universit=E9 Paris 13 99 avenue JB Cl=E9ment 93430 VILLETANEUSE 0149403853 B=E2timent B bureau B002 =20 From owner-chemistry@ccl.net Wed Jul 15 10:43:00 2009 From: "Noel M O Boyle baoilleach++gmail.com" To: CCL Subject: CCL: Call For Papers: Visual Analysis of Chemical Data (ACS Spring 2010) Message-Id: <-39786-090715102746-3003-EtCAPjz+f9WC7hfUeBdJ7w++server.ccl.net> X-Original-From: "Noel M O Boyle" Date: Wed, 15 Jul 2009 10:27:42 -0400 Sent to CCL by: "Noel M O Boyle" [baoilleach]_[gmail.com] First Call for Papers: Visual Analysis of Chemical Data 239th ACS National Meeting San Francisco, March 21-25, 2010 CINF Division ---------------------------------- Dear Colleagues, We wish to announce an upcoming symposium focusing on innovative methods for visual representation and analysis of chemical data. Just as Edward Tufte has championed maximizing clarity and information content in statistical graphics, there is a need for methods to display chemical information that will maximize understanding, and allow rapid analysis and decision making. We invite you to submit contributions that address various aspects of visualization of chemical data (such as structures, SAR data, literature, patents) including, but not limited to, the following topics: * With an ever increasing pool of descriptors, along with new and more sophisticated machine learning methods, QSAR models are becoming more difficult to interpret. How can information on model reliability, the presence of activity cliffs, and the range of applicability of a model and other relevant model properties be easily depicted? * Recently, virtual worlds 3D such as Second Life have presented new opportunities and challenges for the representation of chemical data. What is the potential of such a medium in education and communicating with the chemistry community? * Social software allows for rapid and convenient sharing of chemical data. Examples include Google Spreadsheets, ManyEyes, DabbleDB, and wikis, including Wikipedia. What are the implications for chemical research and education? * The visualization of the contents of large chemical datasets presents particular problems. How can an overview of the dataset be visualized so that it presents both the nature of the contents as well as the degree of diversity and similarity within the dataset? How can different datasets be visually compared? * Depicting 3D chemical information in 2D involves a loss of information. However, innovative 2D visualization methods can restore the most relevant information. * Chemical information comprises a diverse array of data types including chemical structures and diagrams (2D and 3D), associated assay results, conformations, QSAR models and their predictions. The visualization and integration of all these data into a single interface that aids interpretation and analysis is a continuing challenge. We would also like to point out that sponsorship opportunities are available. The on-line abstract submission system (OASYS) will be open for submissions from 24th August (http://oasys.acs.org/acs/239nm/oasys.htm). A second announcement will be made at that time. Please contact Andrew, Jean-Claude or myself if you have any questions. Yours sincerely, Noel O'Boyle On behalf of the symposium organizers: Dr. Jean-Claude Bradley, Drexel University, PA bradlejc : drexel.edu Dr. Andrew Lang, Oral Roberts University, OK alang : oru.edu Dr. Noel OBoyle, Cambridge Crystallographic Data Centre, U.K. oboyle : ccdc.cam.ac.uk From owner-chemistry@ccl.net Wed Jul 15 12:10:01 2009 From: "John McKelvey jmmckel ~ gmail.com" To: CCL Subject: CCL: TD-DFT and what it means again... Message-Id: <-39787-090715120759-26369-Izd4amwwRwsDcAZNjg84uQ|server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=0016368e1e7b9e86e1046ec0c168 Date: Wed, 15 Jul 2009 12:07:47 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel#%#gmail.com] --0016368e1e7b9e86e1046ec0c168 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Folks, I have a proposal... I would propose the following: If in the terminology of RPA or TDDFT, one does not have the B matrix, then one should use the terminology CIS-HF or CIS-DFT, as neither would seem to have any time-dependence, and should not be called TD-HF or TD-DFT. CIS is simply CIS, and nothing more, whether in HF or DFT. I guess, though, that using Tamm-Dankoff-Approximation [TDA] with HF or DFT looks spiffier... OK.. tell me what you think.. I can take it... :-) John --0016368e1e7b9e86e1046ec0c168 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Folks,

I have a proposal...

I would propose the following:=A0= If in the terminology of RPA or TDDFT,=A0 one does not have the B matrix, = then one should use the terminology CIS-HF or CIS-DFT, as neither would see= m to have any time-dependence, and should not be called TD-HF or TD-DFT.=A0= CIS is simply CIS, and nothing more, whether in HF or DFT.=A0 I guess, tho= ugh, that using Tamm-Dankoff-Approximation [TDA]=A0 with HF or DFT looks sp= iffier...

OK.. tell me what you think.. I can take it...=A0 :-)

John
--0016368e1e7b9e86e1046ec0c168-- From owner-chemistry@ccl.net Wed Jul 15 14:34:00 2009 From: "maxim totrov max:_:molsoft.com" To: CCL Subject: CCL: force fields for torsion rotations Message-Id: <-39788-090715141058-31226-Yz55mH/NEoc1dA2geEAyXg(~)server.ccl.net> X-Original-From: maxim totrov Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Wed, 15 Jul 2009 10:23:42 -0700 Mime-Version: 1.0 (Apple Message framework v935.3) Sent to CCL by: maxim totrov [max#,#molsoft.com] This is a non-trivial but often overlooked problem. You may want to take a look at our paper ICFF: a new method to incorporate implicit flexibility into an internal coordinate force field. Katritch V, Totrov M, Abagyan R. J Comput Chem. 2003 Jan 30;24(2):254-65. Max Totrov, Molsoft > > Is there a standard method to modify force field potentials to get > the correct energy profile for torsion rotation when using rigid > rotations? > That is, rotating a torsion while leaving the bond lengths and > angles constant. > > > Matthew Clark > Pharmatrope From owner-chemistry@ccl.net Wed Jul 15 21:51:01 2009 From: "Sarah MOHAMED mohamedsarah78]_[yahoo.fr" To: CCL Subject: CCL:G: Error 502 in G03 Message-Id: <-39789-090715144418-4968-klLzgQ8t/R86nwJL4UpC3w###server.ccl.net> X-Original-From: "Sarah MOHAMED" Date: Wed, 15 Jul 2009 14:44:14 -0400 Sent to CCL by: "Sarah MOHAMED" [mohamedsarah78 a yahoo.fr] Dear CCL subscribers, I have to calculate "the energy" with gaussian 03 of a dimer in water as solvent with PCM model: please which commandes are used in the end of the input file to create a cavity (Rmin=0.5 and OFac=0.8?), or (RADII=PAULING, ALPHA=1.2, TABS =298.158, TSNUM=70 and TSARE=0.4) or (RADII=PAULING). With the last commande and the route section below: # b3lyp/6-31g(d) scf=(xqc,tight,maxcycle=512,vshift=100) nosymm guess=alter scrf=(iefpcm,solvent=water,read) geom=connectivity calculations end with the below error: Using the following non-standard input for PCM: RADII=PAULING --- end of non-standard input. ------------------------------------------------------------------------------ Polarizable Continuum Model (PCM) ================================= Model : PCM. Atomic radii : Pauling. Polarization charges : Total charges. Charge compensation : None. Solution method : Matrix inversion. Cavity : GePol (RMin=0.200 OFac=0.890). Default sphere list used, NSphG= 48. Tesserae with average area of 0.200 Ang**2. Solvent : Water, Eps= 78.390000. ------------------------------------------------------------------------------ One-electron integrals computed using PRISM. NBasis= 494 RedAO= T NBF= 494 NBsUse= 494 1.00D-06 NBFU= 494 Harris functional with IExCor= 402 diagonalized for initial guess. ExpMin= 1.17D-01 ExpMax= 2.19D+04 ExpMxC= 3.30D+03 IAcc=1 IRadAn= 1 AccDes= 1.00D-06 HarFok: IExCor= 402 AccDes= 1.00D-06 IRadAn= 1 IDoV=1 ScaDFX= 1.000000 1.000000 1.000000 1.000000 No Alpha orbitals switched. Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. Requested convergence on MAX density matrix=1.00D-06. Requested convergence on energy=1.00D-06. Virtual orbitals will be shifted by 0.100 hartree. No special actions if energy rises. PCMQM-DMIVC allocation failure: iend,mxcore= 31443780 7429158 Error termination via Lnk1e in C:\G03W\l502.exe at Wed Jul 15 18:58:45 2009. Job cpu time: 0 days 0 hours 7 minutes 57.0 seconds. File lengths (MBytes): RWF= 871 Int= 0 D2E= 0 Chk= 1 Scr= 1 Please can anyone tell me why this error is occuring and how i might resolve this problem. Thank you very much for your help and for any input file.