From owner-chemistry@ccl.net Wed Apr 9 09:01:01 2008 From: "Ridha Khalfa khalfaridha::hotmail.com" To: CCL Subject: CCL:G: Error message inONIOM calculation Message-Id: <-36670-080409081700-29002-/XeYFym9AjsF9J61hPrS8A#server.ccl.net> X-Original-From: "Ridha Khalfa" Date: Wed, 9 Apr 2008 08:16:56 -0400 Sent to CCL by: "Ridha Khalfa" [khalfaridha/a\hotmail.com] hello everyone, I am trying to carry out an ONIOM calculation of two layers to minimize the energy with fixing the amino acids surrounding the QM section. My input section is: $RunGauss %RWF=/tmp/on.rwf %INT=/tmp/on.int %D2E=/tmp/on.d2e %SCR=/tmp/on.scr %NoSave %mem=500mb %chk=oy3_c3.chk #N ONIOM(MPW1PW91/6-31g(d,p):UFF=qeq)=EmbedCharge opt=(z-matrix,Loose) Int(grid=SG1) Guess=read geom=modify however, I get this error message: The electronic state of the initial guess is 1-A. 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. No special actions if energy rises. Spurious integrated density or basis function: NE= 210 NElCor= 0 El error=1.36D+02 rel=6.43D-01 Tolerance=1.00D-03 Shell 137 absolute error=4.05D-04 Tolerance=1.20D-02 Shell 209 signed error=2.30D-04 Tolerance=1.00D-01 Inaccurate quadrature in CalDSu. Error termination via Lnk1e in /bb/che/wilkiej/g03/l502.exe at Wed Apr 9 10:58:21 2008. I guess the problem has to do with the initial guess, so I tried to use different initial guesses (Huckel, core) but unfortunately its not helping same error message. the problem is very annoying as most of my oniom calculations failed like that. I would be very grateful if u could give me some solution to the problem Regards Ridha From owner-chemistry@ccl.net Wed Apr 9 09:59:01 2008 From: "Mariusz Radon mariusz.radon/a\gmail.com" To: CCL Subject: CCL: projected vs. unprojected MPn benchmarks? Message-Id: <-36671-080409094529-2318-hAPApsu2HjhdXL3qOsgJXA%x%server.ccl.net> X-Original-From: Mariusz Radon Content-Type: text/plain; charset=us-ascii Date: Wed, 09 Apr 2008 15:45:07 +0200 MIME-Version: 1.0 Sent to CCL by: Mariusz Radon [mariusz.radon-*-gmail.com] Dear David and Lukasz: Thank you very much for your answers and useful references! However, if anyone could provide me more reference on UMPn vs. PMPn benchmarks I would be very thankful. best regards, Mariusz Radon -- Mariusz Radon Department of Theoretical Chemistry Jagiellonian University mradon /at/ chemia.uj.edu.pl http://www.chemia.uj.edu.pl/~mradon From owner-chemistry@ccl.net Wed Apr 9 12:35:01 2008 From: "Marcelo Puiatti marcelo.puiatti#gmail.com" To: CCL Subject: CCL: How to the obtain a dielectric constant for modelling a protein with PCM models Message-Id: <-36672-080409114434-11016-syM2I3ZlDGcdGmdqzELiPQ^^^server.ccl.net> X-Original-From: "Marcelo Puiatti" Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 9 Apr 2008 11:45:49 -0300 MIME-Version: 1.0 Sent to CCL by: "Marcelo Puiatti" [marcelo.puiatti(-)gmail.com] Hello, everyone. I've read some articles when use DFT calculations with continuum models to take into account the properties of the active site of any protein. My questions are: which is the correct value of the dielectric constant of the continuum? Is there any way to estimate a dielectric constant inside the active site of a protein from a pqr structure, or from molecular dynamics simulations? I'll appreciate if someone could give a piece of advice, or recommend me any article on this subject. Thanks in advance Marcelo Puiatti Departamento de Qu=EDmica Org=E1nica Facultad de Ciencias Qu=EDmicas Universidad Nacional de C=F3rdoba From owner-chemistry@ccl.net Wed Apr 9 13:19:01 2008 From: "Guilherme Menegon Arantes dinamica*|*webcable.com.br" To: CCL Subject: CCL: some group theory / symmetry tables Message-Id: <-36673-080409131709-16891-8G0fq73SLe/ZQ+T06lZIBA###server.ccl.net> X-Original-From: "Guilherme Menegon Arantes" Date: Wed, 9 Apr 2008 13:17:05 -0400 Sent to CCL by: "Guilherme Menegon Arantes" [dinamica[#]webcable.com.br] Hi folks, I am looking for the following group theory tables: 1) Splitting of atomic terms (derived from d^n configurations) in D2h symmetry 2) Correlation table between Td and D2h symmetries 3) Correlation diagrams for d4 and d5 in Td symmetry Pls, let me know in case you are aware of any pointers (www, books, etc) with such info. Kind regards, -- Guilherme Menegon Arantes ------------------------- IQ-USP So Paulo, Brasil From owner-chemistry@ccl.net Wed Apr 9 14:21:00 2008 From: "Kalju Kahn kalju(~)chem.ucsb.edu" To: CCL Subject: CCL: How to the obtain a dielectric constant for modelling a protein with PCM models Message-Id: <-36674-080409141917-18906-Q0/ba8ktyANAsLcovOkC6g _ server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 9 Apr 2008 11:18:59 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju*chem.ucsb.edu] Marcelo, Arieh Warshel has published several papers regarding the use of dielectric constant (property of homogenous matter) when simulating processes in inhomogenous environments such as proteins. You may want to search over the papers in http://futura.usc.edu/wgroup/publications.html Best wishes, Kalju > > Sent to CCL by: "Marcelo Puiatti" [marcelo.puiatti(-)gmail.com] > Hello, everyone. > > I've read some articles when use DFT calculations with continuum > models to take into account the properties of the active site of any > protein. > My questions are: > which is the correct value of the dielectric constant of the continuum? > Is there any way to estimate a dielectric constant inside the active > site of a protein from a pqr structure, or from molecular dynamics > simulations? > > I'll appreciate if someone could give a piece of advice, or recommend > me any article on this subject. > > Thanks in advance > > > Marcelo Puiatti > > > Departamento de Química Orgánica > Facultad de Ciencias Químicas > Universidad Nacional de Córdoba> > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Wed Apr 9 16:50:00 2008 From: "Mariusz Radon mariusz.radon#,#gmail.com" To: CCL Subject: CCL: How to the obtain a dielectric constant for modelling a protein with PCM models Message-Id: <-36675-080409164721-25599-Wd6HoKTgIUg3tbYrWvCE2w],[server.ccl.net> X-Original-From: Mariusz Radon Content-Type: text/plain; charset=us-ascii Date: Wed, 09 Apr 2008 22:47:01 +0200 MIME-Version: 1.0 Sent to CCL by: Mariusz Radon [mariusz.radon=-=gmail.com] "Marcelo Puiatti marcelo.puiatti#gmail.com" writes: > which is the correct value of the dielectric constant of the continuum? > Is there any way to estimate a dielectric constant inside the active > site of a protein from a pqr structure, or from molecular dynamics > simulations? As far as I know... not really. All values widely used are between ~2 and ~6. There is some dependence on the aminoacide groups near the active site. But AFAIK the effective dielectric constant which fits nicely to the PCM model cannot be simply ``computed'' for the given proteine structure. I can recommend some papers from the Siegbahn's group: * Inorg Chem 43, p.3277; * JACS 120, p.8812; * J Inorg. Biochem. 99, p.949 and the following: * JACS 122, p.12892; * Angew. Chem. Int. Ed. 39, p.3851 (see also Chem Rev 105, p.2279) best regards, Mariusz Radon -- Mariusz Radon Department of Theoretical Chemistry Jagiellonian University mradon /at/ chemia.uj.edu.pl http://www.chemia.uj.edu.pl/~mradon From owner-chemistry@ccl.net Wed Apr 9 19:51:01 2008 From: "Wayne Steinmetz WES04747\a/pomona.edu" To: CCL Subject: CCL: some group theory / symmetry tables Message-Id: <-36676-080409135220-6105-xwU1mOd54Oifqkh7XwLX+Q]![server.ccl.net> X-Original-From: "Wayne Steinmetz" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Wed, 9 Apr 2008 10:52:02 -0700 MIME-Version: 1.0 Sent to CCL by: "Wayne Steinmetz" [WES04747|*|pomona.edu] The correlation table that you require for Question 2 can be found in Table XIV on pages 334-340 of Wilson, Decius, Cross, Molecular Vibrations, McGraw-Hill, 1955. The book is a classic and can be found in any proper science library. By the way, D2h is not a subgroup of Td. Td lacks the inversion operation, a symmetry operation in D2h. However, D2d is a subgroup of Td. The answer to your third question can be found on pages 275-278 of Cotton, Chemical Applications of Group Theory, third edition. Cotton's book also provides the theoretical apparatus needed to derive the results required for your first question. Wayne E. Steinmetz Carnegie Professor of Chemistry Woodbadge Course Director Chemistry Department Pomona College 645 North College Avenue Claremont, California 91711-6338 USA phone: 1-909-621-8447 FAX: 1-909-607-7726 Email: wsteinmetz^^pomona.edu WWW: pages.pomona.edu/~wsteinmetz =20 -----Original Message----- > From: owner-chemistry^^ccl.net [mailto:owner-chemistry^^ccl.net]=20 Sent: Wednesday, April 09, 2008 10:17 AM To: Wayne Steinmetz Subject: CCL: some group theory / symmetry tables Sent to CCL by: "Guilherme Menegon Arantes" [dinamica[#]webcable.com.br] Hi folks, I am looking for the following group theory tables: 1) Splitting of atomic terms (derived from d^n configurations) in D2h symmetry 2) Correlation table between Td and D2h symmetries 3) Correlation diagrams for d4 and d5 in Td symmetry Pls, let me know in case you are aware of any pointers (www, books, etc) with such info. Kind regards, -- Guilherme Menegon Arantes ------------------------- IQ-USP So Paulo, Brasil -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt------------------------------------------------------------- This message has been scanned by Postini anti-virus software. =0D From owner-chemistry@ccl.net Wed Apr 9 22:18:01 2008 From: "Ralf Tonner ralf.tonner:+:googlemail.com" To: CCL Subject: CCL: some group theory / symmetry tables Message-Id: <-36677-080409175707-21562-vE5vVC/jTzyqaj0QwLJVZQ*o*server.ccl.net> X-Original-From: Ralf Tonner Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Thu, 10 Apr 2008 09:00:22 +1200 MIME-Version: 1.0 Sent to CCL by: Ralf Tonner [ralf.tonner||googlemail.com] Hi Gulherme, this page has proven to be extremely helpful for me in the past: http://www.phys.ncl.ac.uk/staff/njpg/symmetry/ Crystal classes, correlation tables, examples for each point group etc. Cheers Ralf. -- Dr. Ralf Tonner Centre of Theoretical Chemistry and Physics New Zealand Institute for Advanced Study Massey University Auckland NEW ZEALAND Phone (64) 09 414 0800 extn 9894 Fax (64) 09 443 9779 ---- Guilherme Menegon Arantes dinamica*|*webcable.com.br schrieb: > Sent to CCL by: "Guilherme Menegon Arantes" [dinamica[#]webcable.com.br] > > Hi folks, > > I am looking for the following group theory tables: > > 1) Splitting of atomic terms (derived from d^n configurations) in D2h > symmetry > 2) Correlation table between Td and D2h symmetries > 3) Correlation diagrams for d4 and d5 in Td symmetry > > Pls, let me know in case you are aware of any pointers (www, books, etc) > with such info. > > Kind regards, > > -- > > Guilherme Menegon Arantes > ------------------------- > IQ-USP So Paulo, Brasil> > > From owner-chemistry@ccl.net Wed Apr 9 23:08:00 2008 From: "Mikael Johansson mpjohans*|*chem.au.dk" To: CCL Subject: CCL: How to the obtain a dielectric constant for modelling a protein with PCM models Message-Id: <-36678-080409230502-27003-FTT/jzTaM4V1Jhu/A8Neyw[A]server.ccl.net> X-Original-From: Mikael Johansson Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed" Date: Thu, 10 Apr 2008 05:04:31 +0200 MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mpjohans:+:chem.au.dk] Hello Marcelo! On Wed, 09 Apr 2008 "Marcelo Puiatti marcelo.puiatti#gmail.com" wrote: > which is the correct value of the dielectric constant of the continuum? > Is there any way to estimate a dielectric constant inside the active > site of a protein from a pqr structure, or from molecular dynamics > simulations? The following papers should provide a reasonable introduction. [2] also cites a good bunch of previous studies in the area: [1] Simonson, Perahia, "Internal and interfacial dielectric properties of cytochrome c from molecular dynamics in aqueous solution", PNAS 92 (1995) 1082 [2] Ng, Vora, Krishnamurthy, Chung, "Estimating the dielectric constant of the channel protein and pore", Eur. Biophys. J. 37 (2008) 213. Have a nice day, Mikael J. http://www.iki.fi/~mpjohans/ ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.