From owner-chemistry@ccl.net Thu Feb 23 04:40:00 2006 From: "Michel Petitjean ptitjean-#-itodys.jussieu.fr" To: CCL Subject: CCL: superimposing molecules Message-Id: <-30980-060223043709-27558-oJDNZm1yIwwxLvXxTR0HOA,+,server.ccl.net> X-Original-From: Michel Petitjean Date: Thu, 23 Feb 2006 10:36:52 +0100 (MET) Sent to CCL by: Michel Petitjean [ptitjean!^!itodys.jussieu.fr] To: Subject: CCL: Re: superimposing molecules CSR does not run under Windows but an implementation may be run via the webserver http://bioserv.rpbs.jussieu.fr/Help/3DMSS.html Two input files may be opened, and the output coordinates are saved in PDB format. Michel Petitjean, Email: petitjean],[itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean],[ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html Sent to CCL by: "RICHARD JILL WOOD" [rwoodphd^_^msn.com]: > Hi all, > > Is there a free program out there that runs under Windows and will allow one > to open two pdb files simultaneously, superimpose one on the other easily, > and then save the coordinates of the molecule that has been moved? > > Thanks in advance, > Richard From owner-chemistry@ccl.net Thu Feb 23 05:14:01 2006 From: "John Bushnell bushnell _ chem.ucsb.edu" To: CCL Subject: CCL: G3B3 Atomization Energy Methane Message-Id: <-30981-060223043844-27807-A1V0LDS90VlU5goCAQdmbg{}server.ccl.net> X-Original-From: John Bushnell Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Thu, 23 Feb 2006 01:38:37 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: John Bushnell [bushnell],[chem.ucsb.edu] So the ZPE of methane is approximately equal to the singlet/triplet splitting in atomic carbon. What a coincidence! Also, I guess I was a little confused. The enthalpy of formation involves the difference in energy going from graphite and H2 gas to methane gas. But you also refer to the atomization energy, which is what you are calculating below. I wonder what all goes into the reported experimental value for the enthalpy of atomization. They're certainly not mixing triplet carbon and doublet hydrogen. :-) I can see how to measure (experimentally) enthalpies starting from graphite, but I wonder how this is related to atomic triplet carbon? - John On Wed, 22 Feb 2006, Pablo F. Salazar Pablo.Salazar#%#chemail.tamu.edu wrote: > Sent to CCL by: "Pablo F. Salazar" [Pablo.Salazar||chemail.tamu.edu] > It is not fortuitous, it is actually much better: > > Apparently the singlet was used instead of the triplet for C. > Also notice that the data from the log file at 0K and the G3(0K), already > contains the ZPE correction . Thus, with the following energies at 0K: > H -0.501087 > C -37.82845 > CH4 -40.458277, > the atomization energy for methane at 0K is: > (-37.82845+4*-0.501087)- -40.458277 = 1642.20 kJ/mol > in perfect agreement with the experiment at 0K(1642.27 kJ/mol). > > For the atomization energy for methane at 298K, you must use the corrections > listed in the log file. So the energy of a molecule (or a atom) at 298K > would be: > > H -0.498727 > C -37.82609 > CH4 -40.454469 > > and the atomization energy for methane at 298K is: > (-37.82609+4*-0.498727)- -40.454469 = 1663.2 kJ/mol > also in perfect agreement with the experiment at 0K(1663.3 kJ/mol). > > > Pablo F Salazar > Department Chemical Engineering > 3122 TAMU > College Station, TX 77843-3122 > Phone 979-862-1329 > > > -----Original Message----- >> From: "John Bushnell bushnell,+,chem.ucsb.edu" > To: "Salazar, Pablo Felix " > Date: Mon, 20 Feb 2006 19:43:34 -0500 > Subject: CCL: G3B3 Atomization Energy Methane > > Sent to CCL by: John Bushnell [bushnell**chem.ucsb.edu] > I'm not at all familiar with the "G3B3" method, but right off hand > I would think that this is very good agreement with experiment. > You show an error of 13 kJ/mol at zero K. But the calculation involves > the difference of some very large numbers. The difference of only > 3 kJ/mol at 298 K seems fortuitously small in fact. If enthalpies > of formation could be routinely calculated to this accuracy, we > wouldn't have to do so many experiments. :-) > > Just my offhand impression... > > - John > > On Mon, 20 Feb 2006, Roger Kevin Robinson r.robinson .. imperial.ac.uk wrote: > >> Sent to CCL by: Roger Kevin Robinson [r.robinson,,imperial.ac.uk] >> Hi, >> >> I've asked about this before but i still seem to be having some >> trouble. Im just using Methane as an example. >> >> Using G3B3 methods. >> >> At 298K I get >> >> Name G3-Energy(G3B3) ZPE >> >> C -37.778738 >> >> H -0.499671 >> >> CH4 -40.455401 0.043410 >> >> Using this values to calculate Atomization Energy >> >> = (-37.778738 + 4* -0.499671) - -40.455401 - 0.043410= 0.634569 = >> 1666.06091 kJ/mol >> >> this fits in well with an experimental value of 1663.3 >> >> to calculate Enthalpy of formation you need the atomization Energy at 0K >> as far as im aware. >> >> Right at 0K >> >> >> Name G3(0K) - (G3B3) ZPE >> >> C -37.780154 >> >> H -0.501087 >> >> CH4 -40.458277 0.043410 >> >> = ( -37.780154 +4 * -0.499671) - -40.455401 - 0.043410 = 0.630365 = >> 1655.02331. >> >> But the experimental value is 1642.27 >> >> Does any one know where im making the mistake ? >> >> Thanks > From owner-chemistry@ccl.net Thu Feb 23 05:50:01 2006 From: "Peter Bladon cbas25.:.strath.ac.uk" To: CCL Subject: CCL: superimposing molecules Message-Id: <-30982-060222223501-25320-D93sDSvgnmaRqVcRXGbfVA .. server.ccl.net> X-Original-From: Peter Bladon Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Thu, 23 Feb 2006 02:34:57 +0000 MIME-Version: 1.0 Sent to CCL by: Peter Bladon [cbas25-x-strath.ac.uk] Dear Richard Jill Wood, Yes Interchem-pc will do what you want. It is free to Academics etc. Available from Interprobe Chemical Services. I am afraid that the website and download site are down at the moment, but I hope that they will be up and running soon. Peter Bladon RICHARD JILL WOOD rwoodphd/amsn.com wrote: > Sent to CCL by: "RICHARD JILL WOOD" [rwoodphd^_^msn.com] > > Hi all, > > Is there a free program out there that runs under Windows and will allow one > to open two pdb files simultaneously, superimpose one on the other easily, > and then save the coordinates of the molecule that has been moved? > > Thanks in advance, > Richard > > _________________________________________________________________ > Don’t just search. Find. Check out the new MSN Search! > http://search.msn.click-url.com/go/onm00200636ave/direct/01/> > > > From owner-chemistry@ccl.net Thu Feb 23 06:24:02 2006 From: "CCL CCL computationalchemist{}gmail.com" To: CCL Subject: CCL:G: Molecular Orbitals in Turbomole Message-Id: <-30983-060223055010-8344-1SMmjSR6vkaPLadYLEu52Q(!)server.ccl.net> X-Original-From: "CCL CCL" Content-Type: multipart/alternative; boundary="----=_Part_19272_10235735.1140690356073" Date: Thu, 23 Feb 2006 10:25:56 +0000 MIME-Version: 1.0 Sent to CCL by: "CCL CCL" [computationalchemist:gmail.com] ------=_Part_19272_10235735.1140690356073 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear CCLers, I'm novice to computational chemistry and learning TURBOMOLE and Gaussian. In Gaussian I could find the contribution of each atomic orbital to the molecular orbital listed below the eigen values of the molecular orbital. But in TURBOMOLE i couldn't find the % of atomic orbital contribution. I'may have missed that somewhere. 1) Could any one help me to point out to know about the atomic orbital contribution to Molecular orbitals in Turbomole. 2) Since i'm new i would like to do some simple exercises in these package= s and anyone who has the set of experiments for practising could help me by pointing those exercises. Thanks and regards, Dr. Sanjay ------=_Part_19272_10235735.1140690356073 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
Dear CCLers,
 
I'm novice to computational chemistry and learning TURBOMOLE= and Gaussian. In Gaussian I could find the contribution of each atomic orb= ital to the molecular orbital listed below the eigen values of the molecula= r orbital. But in TURBOMOLE i couldn't find the % of  atomic orbital c= ontribution. I'may have missed that somewhere.=20
 
 1) Could any one help me to point out to know about the atomic o= rbital contribution to Molecular orbitals in Turbomole.
 
 2) Since i'm new i would like to do some simple exercises in the= se packages and anyone who has the set of experiments for practising could = help me by pointing those exercises.
 
Thanks and regards,
Dr. Sanjay

 
------=_Part_19272_10235735.1140690356073-- From owner-chemistry@ccl.net Thu Feb 23 07:08:00 2006 From: "Goedele Roos groos^-^vub.ac.be" To: CCL Subject: CCL: dreiding force field Message-Id: <-30984-060223070631-22878-Hn8UzV3N3uiBa2JvLbsOYA{}server.ccl.net> X-Original-From: Goedele Roos Date: Thu, 23 Feb 2006 13:06:20 +0100 (CET) Sent to CCL by: Goedele Roos [groos^^^vub.ac.be] Dear all, Who has some experience with the dreiding force field applied on biosystems. Does it perform reasonable? Best regards Goedele Drs. Goedele Roos Dienst Algemene Chemie (ALGC) Vrije Universiteit Brussel (VUB) Pleinlaan 2 B-1050 Brussels Tel: 0032-2-629 35 16 Fax: 0032-2-629 33 17 From owner-chemistry@ccl.net Thu Feb 23 09:53:00 2006 From: "=?iso-8859-1?Q?Carlos_C=E1rdenas?= car.cardenas_._uandresbello.edu" To: CCL Subject: CCL: Electronic Part of MEP Message-Id: <-30985-060222171033-13556-yc3kdNZmuIAUo7L7frxFSw^_^server.ccl.net> X-Original-From: =?iso-8859-1?Q?Carlos_C=E1rdenas?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Wed, 22 Feb 2006 18:11:36 -0300 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-1?Q?Carlos_C=E1rdenas?= [car.cardenas{:}uandresbello.edu] Dear all Anybody know how to calculate the electronic part of molecular electrostatic potential with any standart package (Gauusian,ADF,NWchem...)? I would not programig, if is not extrictly necessary. Best for all, Carlos Cárdenas From owner-chemistry@ccl.net Thu Feb 23 10:28:01 2006 From: "Pierre Mignon pmignon-$-vub.ac.be" To: CCL Subject: CCL:G: Electronic Part of MEP Message-Id: <-30986-060223102529-26181-rH58G18zdzVO3h5Jyc7j/w*|*server.ccl.net> X-Original-From: Pierre Mignon Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="ISO-8859-1" Date: Thu, 23 Feb 2006 16:25:18 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: Pierre Mignon [pmignon#vub.ac.be] Dear, With Gaussian it is quite simple. Use the keyword prop=potential and iop(6/17=2) then at the end specify the points where you want the values to be calculated. Regards, Pierre. >Sent to CCL by: =?iso-8859-1?Q?Carlos_C=E1rdenas?= [car.cardenas{:}uandresbello.edu] > >Dear all > >Anybody know how to calculate the electronic part of molecular electrostatic >potential with any standart package (Gauusian,ADF,NWchem...)? I would not >programig, if is not extrictly necessary. > >Best for all, > >Carlos Cárdenas> > > > Mignon Pierre PhD Free University of Brussel (VUB) Dienst Algemene Chemie (ALGC) Pleinlaan, 2 1050 Brussels Belgium Tel + 32 2 629 35 80 Fax + 32 2 629 33 17 e-mail pmignon**vub.ac.be From owner-chemistry@ccl.net Thu Feb 23 11:03:00 2006 From: "Baris Binay binayba!^!itu.edu.tr" To: CCL Subject: CCL: PDB Data Bank Message-Id: <-30987-060223090927-26605-i/kYX1HdDDEHy/gHqWB0Fw,server.ccl.net> X-Original-From: "Baris Binay" Date: Thu, 23 Feb 2006 09:09:26 -0500 Sent to CCL by: "Baris Binay" [binayba[A]itu.edu.tr] Hi, I would like to learn if there is an effective way of searching the desired structures (in fact the coordinates) in the PDB database. I would also appreciate if you could suggest additional references and or databases about the listed structures (coordinates) below: All the structures (coordinates) needed are for the Lactate Dehydrogenase (LDH) from Bacillus stearothermophilus: LDH alone, LDH + NAD, LDH + lactate, LDH + inhibitor, LDH + pyruvate, LDH+NADH Thanks a lot for any help or suggestion Baris Binay binayba]_[itu.edu.tr From owner-chemistry@ccl.net Thu Feb 23 11:58:01 2006 From: "chemical reactivity chemreac : vub.ac.be" To: CCL Subject: CCL: Chemical Reacivity, Brussel, Brussels, Apr. 5-7, '06 - FINAL PROGRAM Message-Id: <-30988-060223102529-12345-1Vm6nZXJwozuJQTnTjbHNQ,+,server.ccl.net> X-Original-From: "chemical reactivity" Date: Thu, 23 Feb 2006 15:04:58 +0100 Sent to CCL by: "chemical reactivity" [chemreac(0)vub.ac.be] Dear Colleague, A Three Day International Symposium will be held on (Theoretical Aspects of) f "Chemical Reactivity", at the Vrije Universiteit Brussel, Brussels, Belgium, from April 5 to 7, 2006. This Symposium is organized under the auspices of the Fund for Scientific Research Flanders and the International Solvay Institutes for Physics and Chemistry. The aim of the conference is to give the audience an impression of theoretical aspects of chemical reactivity, as it can now be studied starting from the electronic structure of atoms, molecules,... using a variety of quantum mechanical methodologies. Both more fundamental and applied aspects (wave function vs. DFT reactivity descriptors, dynamics, aromaticity, organic and inorganic reactions, biosystems, zeolites, ...) will be addressed. For this purpose 13 internationally renowned speakers will deliver invited talks (40 minutes each) on various approaches/applications. Contributed lectures will be given by selected number of foreign participants and representatives of a number of Belgian research groups. A poster session will give ample space and time for presentation of research results by all other participants. The invited speakers (all confirmed) are: P. W. Ayers (McMaster University Hamilton, Ontario, Canada) P. K. Chattaraj (Indian Institute of Technology, Kharagpur, India) D. A. Dixon (The University of Alabama, Tuscaloosa, USA) W. Domcke (Lehrstuhl für Theoretische Chemie, Garching, Germany) P. W. Fowler (University of Sheffield, Sheffield, UK) J. Hutter (Universität Zürich, Zürich, Switzerland) J.M.L. Martin (Weizmann Institute of Science, Rechovot, Israel) R. G. Parr (University of North Carolina, Chapel Hill, USA) U. Röthlisberger (Ecole Polytechnique Federale, Lausanne,Switzerland) M. Solà (Universitat de Girona, Girona, Spain) M. Sprik (University of Cambridge, United Kingdom) R.A. van Santen (Eindhoven Technical University,The Netherlands ) P. von Rague Schleyer ( University of Georgia, Athens, USA) The final program including the titles of all invited and contributed lectures is now available at the conference website http://www.vub.ac.be/chemicalreactivity/ Moreover, some slots are still available for poster presentations so it is still possible to both register for the conference and submit an abstract for a poster presentation. The final deadline is March 10, 2006. Looking forward to meet you in Brussels, With very best regards, Paul Geerlings Chair of the Organizing Committee Prof. P. GEERLINGS Free University of Brussels Faculty of Sciences Department of General Chemistry (ALGC) Pleinlaan 2 1050 Brussels Belgium Tel. : +32.2.629.33.14 Fax. : +32.2.629.33.17 From owner-chemistry@ccl.net Thu Feb 23 13:27:00 2006 From: "Ivanciuc, Ovidiu I. oiivanci{:}utmb.edu" To: CCL Subject: CCL: PDB Data Bank Message-Id: <-30989-060223132530-15766-IyYvZceRebjWImuKK6BqgQ ~ server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." Content-Class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="Windows-1252" Date: Thu, 23 Feb 2006 12:25:18 -0600 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci(_)utmb.edu] >>I would like to learn if there is an effective way >> of searching the desired structures (in fact the coordinates) >> in the PDB database If you know the sequence of the protein you are looking for, just use a BLAST search in PDB, http://www.ncbi.nlm.nih.gov/BLAST/ If you want to find PDB structures from a certain protein class, then just use the search function from PDB, http://www.rcsb.org/pdb/ Regards, Ovidiu From owner-chemistry@ccl.net Thu Feb 23 16:33:00 2006 From: "Jeff Nauss jnauss###accelrys.com" To: CCL Subject: CCL: dreiding force field Message-Id: <-30990-060223162845-18188-QWK3VOPT87CDVAjjVg7Yjg+/-server.ccl.net> X-Original-From: Jeff Nauss Content-Type: multipart/alternative; boundary="=_alternative 0071C24A8825711E_=" Date: Thu, 23 Feb 2006 12:42:28 -0800 MIME-Version: 1.0 Sent to CCL by: Jeff Nauss [jnauss * accelrys.com] This is a multipart message in MIME format. --=_alternative 0071C24A8825711E_= Content-Type: text/plain; charset="US-ASCII" owner-chemistry---ccl.net wrote on 02/23/2006 04:08:09 AM: > Sent to CCL by: Goedele Roos [groos^^^vub.ac.be] > Dear all, > Who has some experience with the dreiding force field applied on > biosystems. Does it perform reasonable? I would say that Dreiding is not a good quality force field to use on biological systems. It is better suited for small molecules such as ligands where typing and parameterization are issues with other force fields. Basically Dreiding will type without error pretty much any molecule. But the geometries you get may be suspect. A more quantitative assessment of force field performance (including Dreiding) can be found in the following references: Gundertofte et al. J. Comp. Chem. 1996, 17:429-49 Pettersson & Liljefors Rev. Comp. Chem. 1996, 9:167-90 Nicklaus, J. Comp. Chem. 1997, 18:1056-60 Halgren, J. Comp. Chem. 1999, 20:730-748 Jeff -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121-4779 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/training --=_alternative 0071C24A8825711E_= Content-Type: text/html; charset="US-ASCII"
owner-chemistry---ccl.net wrote on 02/23/2006 04:08:09 AM:

> Sent to CCL by: Goedele Roos [groos^^^vub.ac.be]
> Dear all,
> Who has some experience with the dreiding force field applied on
> biosystems. Does it perform reasonable?
I would say that Dreiding is not a good quality force field to use on biological systems.  It is better suited for small molecules such as ligands where typing and parameterization are issues with other force fields.  Basically Dreiding will type without error pretty much any molecule.  But the geometries you get may be suspect.

A more quantitative assessment of force field performance (including Dreiding) can be found in the following references:
Gundertofte et al. J. Comp. Chem. 1996, 17:429-49
Pettersson & Liljefors Rev. Comp. Chem. 1996, 9:167-90
Nicklaus, J. Comp. Chem. 1997, 18:1056-60
Halgren, J. Comp. Chem. 1999, 20:730-748

Jeff
--
Jeffrey L. Nauss, Ph.D.
Lead Training Scientist
Accelrys
10188 Telesis Court, Suite 100
San Diego, CA 92121-4779

Phone: +1-858-799-5555
Fax: +1-858-799-5100
http://www.accelrys.com/training
 --=_alternative 0071C24A8825711E_=-- From owner-chemistry@ccl.net Thu Feb 23 17:07:02 2006 From: "Qadir Timerghazin qadir.timerghazin=-=cermm.concordia.ca" To: CCL Subject: CCL: protein docking including prosthetic groups Message-Id: <-30991-060223164340-25105-02uYUYMEdxl9IV8LaaCfyw{=}server.ccl.net> X-Original-From: "Qadir Timerghazin" Date: Thu, 23 Feb 2006 16:43:39 -0500 Sent to CCL by: "Qadir Timerghazin" [qadir.timerghazin~~cermm.concordia.ca] Dear CCLers, I need to model a docking between two proteins, both have either prosthetic groups and/or metal ions. I tried several algorithms/program suites, but they all remove everything but standard aminoacid residues before starting the actual docking. Does anybody know any docking method which can treat prosthetic groups and metal ions or, at least, a publication where prosthetic group-containing proteins were successfully docked? Thanks, Qadir ****************************************************** Qadir K. Timerghazin Centre for Research in Molecular Modeling (CERMM) Concordia University Richard J. Renaud Science Complex 7141 Sherbrooke St.West Montral, Qubec, CANADA H4B 1R6 Phone: (514) 848 2424 x3336 Email: Qadir.Timerghazin-$-CERMM.Concordia.CA ****************************************************** From owner-chemistry@ccl.net Thu Feb 23 17:42:00 2006 From: "Pablo F. Salazar Pablo.Salazar_-_chemail.tamu.edu" To: CCL Subject: CCL: G3B3 Atomization Energy Methane Message-Id: <-30992-060223162643-18075-YIzPsXUCRRjaPgWDQtxaYw---server.ccl.net> X-Original-From: "Pablo F. Salazar" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="UTF-8" Date: Thu, 23 Feb 2006 15:26:20 -0600 MIME-Version: 1.0 Sent to CCL by: "Pablo F. Salazar" [Pablo.Salazar]*[chemail.tamu.edu] You can do either of the two (T is some accessible temperature, eg. 298 K) 1) you get theoretically results at 0 K and then correct them to T. or 2) you get the experimental values at T then correct them to 0 K In both cases the corrections are a mixture of theoretically and experimentally obtained values, thus the comparisons theory-experiment are not strictly between purely theoretical neither and purely experimental data. This explains why the errors should be similar at both 0 and T. Pablo F Salazar Department Chemical Engineering 3122 TAMU College Station, TX 77843-3122 Phone 979-862-1329 -----Original Message----- > From: "John Bushnell bushnell _ chem.ucsb.edu" To: "Salazar, Pablo Felix " Date: Thu, 23 Feb 2006 05:21:57 -0500 Subject: CCL: G3B3 Atomization Energy Methane Sent to CCL by: John Bushnell [bushnell],[chem.ucsb.edu] So the ZPE of methane is approximately equal to the singlet/triplet splitting in atomic carbon. What a coincidence! Also, I guess I was a little confused. The enthalpy of formation involves the difference in energy going from graphite and H2 gas to methane gas. But you also refer to the atomization energy, which is what you are calculating below. I wonder what all goes into the reported experimental value for the enthalpy of atomization. They're certainly not mixing triplet carbon and doublet hydrogen. :-) I can see how to measure (experimentally) enthalpies starting from graphite, but I wonder how this is related to atomic triplet carbon? - John On Wed, 22 Feb 2006, Pablo F. Salazar Pablo.Salazar#%#chemail.tamu.edu wrote: > Sent to CCL by: "Pablo F. Salazar" [Pablo.Salazar||chemail.tamu.edu] > It is not fortuitous, it is actually much better: > > Apparently the singlet was used instead of the triplet for C. > Also notice that the data from the log file at 0K and the G3(0K), already > contains the ZPE correction . Thus, with the following energies at 0K: > H -0.501087 > C -37.82845 > CH4 -40.458277, > the atomization energy for methane at 0K is: > (-37.82845+4*-0.501087)- -40.458277 = 1642.20 kJ/mol > in perfect agreement with the experiment at 0K(1642.27 kJ/mol). > > For the atomization energy for methane at 298K, you must use the corrections > listed in the log file. So the energy of a molecule (or a atom) at 298K > would be: > > H -0.498727 > C -37.82609 > CH4 -40.454469 > > and the atomization energy for methane at 298K is: > (-37.82609+4*-0.498727)- -40.454469 = 1663.2 kJ/mol > also in perfect agreement with the experiment at 0K(1663.3 kJ/mol). > > > Pablo F Salazar > Department Chemical Engineering > 3122 TAMU > College Station, TX 77843-3122 > Phone 979-862-1329 > > > -----Original Message----- >> From: "John Bushnell bushnell,+,chem.ucsb.edu" > To: "Salazar, Pablo Felix " > Date: Mon, 20 Feb 2006 19:43:34 -0500 > Subject: CCL: G3B3 Atomization Energy Methane > > Sent to CCL by: John Bushnell [bushnell**chem.ucsb.edu] > I'm not at all familiar with the "G3B3" method, but right off hand > I would think that this is very good agreement with experiment. > You show an error of 13 kJ/mol at zero K. But the calculation involves > the difference of some very large numbers. The difference of only > 3 kJ/mol at 298 K seems fortuitously small in fact. If enthalpies > of formation could be routinely calculated to this accuracy, we > wouldn't have to do so many experiments. :-) > > Just my offhand impression... > > - John > > On Mon, 20 Feb 2006, Roger Kevin Robinson r.robinson .. imperial.ac.uk wrote: > >> Sent to CCL by: Roger Kevin Robinson [r.robinson,,imperial.ac.uk] >> Hi, >> >> I've asked about this before but i still seem to be having some >> trouble. Im just using Methane as an example. >> >> Using G3B3 methods. >> >> At 298K I get >> >> Name G3-Energy(G3B3) ZPE >> >> C -37.778738 >> >> H -0.499671 >> >> CH4 -40.455401 0.043410 >> >> Using this values to calculate Atomization Energy >> >> = (-37.778738 + 4* -0.499671) - -40.455401 - 0.043410= 0.634569 = >> 1666.06091 kJ/mol >> >> this fits in well with an experimental value of 1663.3 >> >> to calculate Enthalpy of formation you need the atomization Energy at 0K >> as far as im aware. >> >> Right at 0K >> >> >> Name G3(0K) - (G3B3) ZPE >> >> C -37.780154 >> >> H -0.501087 >> >> CH4 -40.458277 0.043410 >> >> = ( -37.780154 +4 * -0.499671) - -40.455401 - 0.043410 = 0.630365 = >> 1655.02331. >> >> But the experimental value is 1642.27 >> >> Does any one know where im making the mistake ? >> >> Thankshttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Feb 23 18:43:00 2006 From: "Christopher Fuhrman fuhrman+*+creol.ucf.edu" To: CCL Subject: CCL: PDB Data Bank Message-Id: <-30993-060223154547-14928-fYLLEjtS+sTzOsJaCZ8uDA(!)server.ccl.net> X-Original-From: "Christopher Fuhrman" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=US-ASCII Date: Thu, 23 Feb 2006 15:04:12 -0500 Mime-Version: 1.0 Sent to CCL by: "Christopher Fuhrman" [fuhrman * creol.ucf.edu] Do you mean to search the files themselves? You could probably download a snapshot or get a DVD of all the file, then search them using your own app. regards, Kit Kit Fuhrman Masters Student Molecular Biology and Microbiology fuhrman-#-mail.ucf.edu >>> owner-chemistry-#-ccl.net 02/23/06 1:53 PM >>> Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci(_)utmb.edu] >>I would like to learn if there is an effective way >> of searching the desired structures (in fact the coordinates) >> in the PDB database If you know the sequence of the protein you are looking for, just use a BLAST search in PDB, http://www.ncbi.nlm.nih.gov/BLAST/ If you want to find PDB structures from a certain protein class, then just use the search function from PDB, http://www.rcsb.org/pdb/ Regards, Ovidiuhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt