From owner-chemistry@ccl.net Mon Feb 6 05:12:00 2006 From: "Ben Sattelle ben.sattelle-#-postgrad.manchester.ac.uk" To: CCL Subject: CCL: Aquous electrochemistry Message-Id: <-30788-060206050909-21200-K7+Wqw5IaQWIEMvqqgcs8Q]_[server.ccl.net> X-Original-From: Ben Sattelle Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15 Date: Mon, 6 Feb 2006 10:08:57 +0000 MIME-Version: 1.0 Sent to CCL by: Ben Sattelle [ben.sattelle~~postgrad.manchester.ac.uk] hi, i too would be interested in summary. sorry, no experience with single ions. the following may or may not be of interest to you. recently adapted the method of lewis et al., j. chem. ed (2004), 81(4):596-604, to calculate aqueous gibbs free energies and reduction potentials for two-electron transfer of 20 C7/C8/C9 substituted flavins (~30 atoms) using DFT and the SCRF PCM solvation model at the B3LYP/6-311++G(d,p)//B3LYP/6-311+G(d,p) level of theory. maximum, minimum and mean unsigned deviations from experimental values were 38, 1 and 15 mV. respectively. similar errors to contemporary analagous reports. the performance of several continuum solvation models for this type of calculation were recently compared by Takano & Houk, j. chem. theory. comput. (2005), 1:70-77. have a stack of further refs. for calculation of aqueous redox potentials of organic molecules using DFT & SCRF calculations if you are interested, cheers, ben. > Hi There, > Is anyone aware of successes in reproducing some of the tabulated redox > potentials of electrochemical reactions that ar elisted i standard > electrochemical tables, especiall those involving single ions? e.g. Cu > --> Cu2+(aq) + 2e-. The key issue that I need coment on here is the > selection of appropriate solvation models. I doubt if continuum models > would require inclusion of at least the first shell of water molecules, > as these are strongly bound. As a starting point I am trying to > reproduce the experimental value of the 'reference' reaction 2H+ +2e = > H2. Even this appears tricky. > > Thanks in advance, > > Noko Phala, Anglo Research > ________________________________________________________________________ > Check Out the new free AIM(R) Mail -- 2 GB of storage and > industry-leading spam and email virus protection.------------------------------------------------------------ Mr B.M. Sattelle, Room B8, Jackson's Mill, School of Chemical Engineering and Analytical Science (CEAS), The University of Manchester, PO Box 88, Sackville Street, Manchester, M60 1QD, UK. Tel: [+44] (0)161 306 8857 http://neon.ce.umist.ac.uk/ http://www.manchester.ac.uk/ceas ------------------------------------------------------------ From owner-chemistry@ccl.net Mon Feb 6 07:45:01 2006 From: "Timm Lankau TimmLankau-x-gmx.de" To: CCL Subject: CCL:G: normalization of wave functions in Guassian Message-Id: <-30789-060206050803-21123-bHKOgb5KkySlL43BIev/Cw()server.ccl.net> X-Original-From: Timm Lankau Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Date: Mon, 6 Feb 2006 17:07:50 +0800 Mime-Version: 1.0 (Apple Message framework v623) Sent to CCL by: Timm Lankau [TimmLankau(-)gmx.de] Dear CCL members, is there a fast and easy way to get a printout of the normalization constants of the used basis functions within the Gaussian 03 output? Any answer or hint to this problem is very much appreciated. Thanks a lot. Best wishes, Timm From owner-chemistry@ccl.net Mon Feb 6 08:20:01 2006 From: "Marius Retegan retegan.marius-#-gmail.com" To: CCL Subject: CCL: ONIOM for transition metal complex: more Message-Id: <-30790-060206072210-18367-zRDhu+S/BYBhzYHTE+Ufnw^_^server.ccl.net> X-Original-From: Marius Retegan Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 6 Feb 2006 12:56:55 +0100 MIME-Version: 1.0 Sent to CCL by: Marius Retegan [retegan.marius]![gmail.com] Sorry, but I've forgot to specify something regarding my first question. I want to make a ONIOM(B3LYP/genecp:UFF) on a W complex. For the W I want to use lanl2dz and for the other atoms 6-31g. Thank you From owner-chemistry@ccl.net Mon Feb 6 08:55:01 2006 From: "Jose Gascon jose.gascon a yale.edu" To: CCL Subject: CCL:G: working with charges Message-Id: <-30791-060206041427-17181-Ea4Sq7G4rMZEo+GmGI/yVA.@.server.ccl.net> X-Original-From: Jose Gascon Content-Type: multipart/alternative; boundary="------------070000090809060501030609" Date: Mon, 06 Feb 2006 02:42:01 -0500 MIME-Version: 1.0 Sent to CCL by: Jose Gascon [jose.gascon_+_yale.edu] --------------070000090809060501030609 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear George, The first principles self-consistent solution will take care of that, for such simple system, you don't have to worry about how the charge is distributed. It will come up right (within the limits of the theory level). The reason why you need to define the total charge is simply because the program needs to know what is the total number of electrons. There are certain cases however, in which it is necessary to define oxidation states. For instance, when you have more than one metal atom with open shells, such as Mn(IV), or Fe(III). In that case oxidation state is specified via the initial guess, and one needs to make sure that the spin states are preserved along the calculation. But this is certainly not a problem with oligopeptides. Also, you can always check the resulting charge distribution via the population analysis, mulliken and ESP (pop=esp). Hope this helps, Jose. -- Jose A. Gascon - Postdoctoral Associate http://xbeams.chem.yale.edu/~batista/jose/Jose.html Department of Chemistry - (203)432-5911; jose.gascon * yale.edu Yale University P.O. Box 208107 New Haven, CT 06520-8107. George V Papamokos me00109]_[cc.uoi.gr wrote: >Sent to CCL by: "George V Papamokos" [me00109###cc.uoi.gr] >Dear cclers, >Iam currently working with charged oligopeptides. These peptides are multiply charged (positive and negative charges) resulting to a total charge either positive or negative. >in the input of gaussian software i can give the total charge of the molecule but how do I know that this is distributed as it should be? >For example, an oxygen is connected with a single bond with a carbon atom and it carries a -1 charge. Two nitrogens are also connencted with two other Carbon atoms and they carry a +1 charge each. Total charge -1. I declare the total charge in the first lines of the input (1 1 ) but how do I know that the charges are correctly distributed to the proper atoms? >Is it just a matter of bond distances? > > > >Thank you in advance. > >George Papamokos> > > > > --------------070000090809060501030609 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear George,
The first principles self-consistent solution will take care of that, for such simple system, you don't have to worry about how the charge is distributed. It will come up right (within the limits of the theory level). The reason why you need to define the total charge is simply because the program needs to know what is the total number of electrons. There are certain cases however, in which it is necessary to define oxidation states. For instance, when you have more than one metal atom with open shells, such as Mn(IV), or Fe(III). In that case oxidation state is specified via the initial guess, and one needs to make sure that the spin states are preserved along the calculation. But this is certainly not a problem with oligopeptides.

Also, you can always check the  resulting charge distribution via the population analysis, mulliken and ESP (pop=esp). 
Hope this helps,
                        Jose.
--
Jose A. Gascon - Postdoctoral Associate
http://xbeams.chem.yale.edu/~batista/jose/Jose.html
Department of Chemistry - (203)432-5911; jose.gascon * yale.edu
Yale University
P.O. Box 208107
New Haven, CT 06520-8107.
 

George V Papamokos me00109]_[cc.uoi.gr wrote:
Sent to CCL by: "George V Papamokos" [me00109###cc.uoi.gr]
Dear cclers,
Iam currently working with charged oligopeptides. These peptides are multiply charged  (positive and negative charges) resulting to a total charge either positive or negative. 
in the input of gaussian software i can give the total charge of the molecule but how do I know that this is distributed as it should be?
For example, an oxygen is connected with a single bond with a carbon atom and it carries a -1 charge. Two nitrogens are also connencted with two other  Carbon atoms and they  carry a +1 charge each. Total charge -1. I declare the total charge in the first lines of the input (1 1 ) but how do I know that the charges are correctly distributed to the proper atoms?
Is it just a matter of bond distances?



Thank you in advance.

George PapamokosE-mail to subscribers: CHEMISTRY * ccl.net or use:
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--------------070000090809060501030609-- From owner-chemistry@ccl.net Mon Feb 6 09:30:00 2006 From: "Toomas Tamm tt-ccl() kky.ttu.ee" To: CCL Subject: CCL: Aquous electrochemistry Message-Id: <-30792-060206071612-18145-VIGG9D0YaIO6PlWNpvW6TA[#]server.ccl.net> X-Original-From: Toomas Tamm Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Mon, 6 Feb 2006 13:19:55 +0200 Mime-Version: 1.0 Sent to CCL by: Toomas Tamm [tt-ccl ~~ kky.ttu.ee] On Sun, Feb 05, 2006 at 10:34:34AM -0500, nokophala.-*-.aim.com wrote: > Sent to CCL by: nokophala++aim.com > > Hi There, > Is anyone aware of successes in reproducing some of the tabulated redox > potentials of electrochemical reactions that ar elisted i standard > electrochemical tables, especiall those involving single ions? e.g. Cu > --> Cu2+(aq) + 2e-. The key issue that I need coment on here is the For a series of octahedral complexes we did just that a couple of years ago: Merle Uudsemaa and Toomas Tamm Journal of Physical Chemistry A, 107, 9997-10003 (2003). > selection of appropriate solvation models. I doubt if continuum models > would require inclusion of at least the first shell of water molecules, > as these are strongly bound. As a starting point I am trying to > reproduce the experimental value of the 'reference' reaction 2H+ +2e = > H2. Even this appears tricky. We did have to include a couple of empirical data points (in particular, the 2H+/H2 standard potential value is from experiment) and the second solvation shell, and the results are still far from spectacular (0.3 volts average error). We continue to work on the model, and it seems that a static model like the one we used does not probably lead to much better accuracy. I also draw anyone's attention trying to do anything similar to the inaccuracies in the tabulated potentials which we also discuss in our paper. If one looks into the experimental literature on the topic, it becomes evident that the seemingly trivial redox potentials involving two aqueous ions are actually hard to determine with any reasonable precision and there are some question marks around the existence of some species (eg Co3+) in "pure" form in aqueous solution at all. -- Toomas Tamm e-mail: tt-ccl-*-kky.ttu.ee Chair of Inorganic Chemistry voice: INT+372-620-2810 Tallinn University of Technology fax: INT+372-620-2828 Ehitajate tee 5, EE-19086 Tallinn, Estonia http://www.kk.ttu.ee/toomas/ From owner-chemistry@ccl.net Mon Feb 6 10:05:16 2006 From: "Marius Retegan retegan.marius[#]gmail.com" To: CCL Subject: CCL:G: ONIOM for transition metal complex Message-Id: <-30793-060206072504-18510-WmjhO1gXdqcNI6R0gik6bw.@.server.ccl.net> X-Original-From: Marius Retegan Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 6 Feb 2006 12:30:17 +0100 MIME-Version: 1.0 Sent to CCL by: Marius Retegan [retegan.marius!=!gmail.com] Hello I have a few quick question: 1. Is possible to do a ONIOM calculation with Gaussian 03 for a tunsten complex using lanl2dz for tungsten and 6-31g for the other atoms (C,O,H,P)? 2. Is the connectivity of major importance in a ONIOM(B3LYP/lanl2dz:UFF) calculation on a protein? Thank you very much. Marius From owner-chemistry@ccl.net Mon Feb 6 11:16:00 2006 From: "Val Gillet v.gillet!^!sheffield.ac.uk" To: CCL Subject: CCL: Short course on Chemoinformatics Message-Id: <-30794-060206110857-11499-uqKt9B64Rg2rLqynQJclAw..server.ccl.net> X-Original-From: "Val Gillet" Sent to CCL by: "Val Gillet" [v.gillet .. sheffield.ac.uk] "A Practical Introduction to Chemoinformatics" June 27th-30th 2006 The University of Sheffield will be hosting the above short course which is supported by the Chemical Structure Association Trust and the Molecular Graphics and Modelling Society. This intensive short course provides an introduction to the major aspects of Chemoinformatics, with particular emphasis on applications in modern drug discovery. The course will comprise a mixture of hands-on workshops, lectures, and informal discussions. Please note that places on the course are limited. For further details see: http://cisrg.shef.ac.uk/ci_course or contact Val Gillet (v.gillet{:}sheffield.ac.uk) From owner-chemistry@ccl.net Mon Feb 6 12:13:00 2006 From: "Jim Kress ccl_nospam..kressworks.com" To: CCL Subject: CCL: Aquous electrochemistry Message-Id: <-30795-060206115239-8691-UdeME4FFagwTagvkHB4xAw%server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 6 Feb 2006 11:52:35 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam#kressworks.com] Here's an interesting link: http://comp.chem.umn.edu/netstep/2000/february/9truhcram.html Jim > -----Original Message----- > From: nokophala.!^!.aim.com [mailto:owner-chemistry!^!ccl.net] > Sent: Sunday, February 05, 2006 10:22 AM > To: Kress, Jim > Subject: CCL: Aquous electrochemistry > > Sent to CCL by: nokophala++aim.com > > Hi There, > Is anyone aware of successes in reproducing some of the > tabulated redox potentials of electrochemical reactions that > ar elisted i standard electrochemical tables, especiall those > involving single ions? e.g. Cu > --> Cu2+(aq) + 2e-. The key issue that I need coment on here is the > selection of appropriate solvation models. I doubt if > continuum models would require inclusion of at least the > first shell of water molecules, as these are strongly bound. > As a starting point I am trying to reproduce the experimental > value of the 'reference' reaction 2H+ +2e = H2. Even this > appears tricky. > > Thanks in advance, > > Noko Phala, Anglo Research > ______________________________________________________________ > __________ > Check Out the new free AIM(R) Mail -- 2 GB of storage and > industry-leading spam and email virus protection. > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, > please change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > > From owner-chemistry@ccl.net Mon Feb 6 14:54:01 2006 From: "Goedele Roos groos[]vub.ac.be" To: CCL Subject: CCL: Aquous electrochemistry Message-Id: <-30796-060206145016-24036-x/nhc8QIb0PEcUYV3iR/SA^^^server.ccl.net> X-Original-From: Goedele Roos Date: Mon, 6 Feb 2006 20:50:03 +0100 (CET) Sent to CCL by: Goedele Roos [groos^-^vub.ac.be] Yes, the first solvatation shell is important, see Uudsemaa, M., Tamm, T., J. Phys. Chem. A 2003, 107, 9997. or see: M. Namazian, Siahrostami, s., Noorbala, M. R., Coote, m. L., J. Mol. Struct.: Theochem, 759,(2006), 245. or: Shamsipur, M., Alizadeh, Arshadi, S., J. Mol. Struct.: Theochem, 758, (2005), 71 also a very good paper Dutton, A., S., Fukuto, J. M., Kendall, N. H., J. Inorg. Chem. 2005, 44, 4024. Baik, M.-H., Friesner, A. J. Phys. Chem. A 2002, 106, 7407. Patterson, E, Cramer, C., Truhlar, D, JACS, 123 (2001) 2025. Greetz, Goedele >Sent to CCL by: "Jim Kress" [ccl_nospam#kressworks.com] >Here's an interesting link: > >http://comp.chem.umn.edu/netstep/2000/february/9truhcram.html > > >Jim > >> -----Original Message----- >> From: nokophala. ~ .aim.com [mailto:owner-chemistry ~ ccl.net] >> Sent: Sunday, February 05, 2006 10:22 AM >> To: Kress, Jim >> Subject: CCL: Aquous electrochemistry >> >> Sent to CCL by: nokophala++aim.com >> >> Hi There, >> Is anyone aware of successes in reproducing some of the >> tabulated redox potentials of electrochemical reactions that >> ar elisted i standard electrochemical tables, especiall those >> involving single ions? e.g. Cu >> --> Cu2+(aq) + 2e-. The key issue that I need coment on here is the >> selection of appropriate solvation models. I doubt if >> continuum models would require inclusion of at least the >> first shell of water molecules, as these are strongly bound. >> As a starting point I am trying to reproduce the experimental >> value of the 'reference' reaction 2H+ +2e = H2. Even this >> appears tricky. >> >> Thanks in advance, >> >> Noko Phala, Anglo Research >> ______________________________________________________________ >> __________ >> Check Out the new free AIM(R) Mail -- 2 GB of storage and >> industry-leading spam and email virus protection. >> >> >> >> -= This is automatically added to each message by the mailing >> script =- >> To recover the email address of the author of the message, >> please change> Conferences: >> http://server.ccl.net/chemistry/announcements/conferences/ >> >> Search Messages: http://www.ccl.net/htdig (login: ccl, >> Password: search)> >> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ >> -+-+-+-+-+> > > > 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 Mon Feb 6 16:33:01 2006 From: "Samuel Flores samuel.flores~~yale.edu" To: CCL Subject: CCL: puzzling tinker pdbxyz problem Message-Id: <-30797-060206150438-30281-BSDSlnEqxCT3EIxdhbCpRw*o*server.ccl.net> X-Original-From: "Samuel Flores" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Mon, 6 Feb 2006 14:23:33 -0500 MIME-Version: 1.0 Sent to CCL by: "Samuel Flores" [samuel.flores.^.yale.edu] Hi guys, I wonder if anyone can help me with a problem I'm having. The pdbxyz program is producing .xyz files that the program 'dynamic' later has trouble with. It does fine when the atom names are single letter with charges (e.g. 'H', 'C', 'O-' ..) but fails when the names are longer than that (e.g. 'CT3', etc). I have no idea why it translates the demo files perfectly, but not any other files. In fact, if I move the demo files out of their directory, they are mistranslated also! It's almost as if there exists a 'ghost' file somewhere that is needed for proper translation. Can anyone help? Thanks Sam Samuel Flores Graduate Student Gerstein Lab Office: Bass 437 266 Whitney Avenue New Haven, CT 06520 203.432.5405 Home: 28 Pearl Street New Haven, CT 06511 cell: 203.747.2682 -----Original Message----- > From: owner-chemistry^ccl.net [mailto:owner-chemistry^ccl.net] Sent: Monday, February 06, 2006 12:19 PM To: Flores, Samuel Subject: CCL: Aquous electrochemistry Sent to CCL by: "Jim Kress" [ccl_nospam#kressworks.com] Here's an interesting link: http://comp.chem.umn.edu/netstep/2000/february/9truhcram.html Jim > -----Original Message----- > From: nokophala. ~ .aim.com [mailto:owner-chemistry ~ ccl.net] > Sent: Sunday, February 05, 2006 10:22 AM > To: Kress, Jim > Subject: CCL: Aquous electrochemistry > > Sent to CCL by: nokophala++aim.com > > Hi There, > Is anyone aware of successes in reproducing some of the > tabulated redox potentials of electrochemical reactions that > ar elisted i standard electrochemical tables, especiall those > involving single ions? e.g. Cu > --> Cu2+(aq) + 2e-. The key issue that I need coment on here is the > selection of appropriate solvation models. I doubt if > continuum models would require inclusion of at least the > first shell of water molecules, as these are strongly bound. > As a starting point I am trying to reproduce the experimental > value of the 'reference' reaction 2H+ +2e = H2. Even this > appears tricky. > > Thanks in advance, > > Noko Phala, Anglo Research > ______________________________________________________________ > __________ > Check Out the new free AIM(R) Mail -- 2 GB of storage and > industry-leading spam and email virus protection. > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, > please change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Feb 6 18:55:00 2006 From: "Yingbin Ge yingbin.ge:-:gmail.com" To: CCL Subject: CCL: frozen core orbitals using Aces2 Message-Id: <-30798-060206185414-19156-VhHFY1DZjbVXN/y0zzwM2A[#]server.ccl.net> X-Original-From: Yingbin Ge Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 6 Feb 2006 17:54:11 -0600 MIME-Version: 1.0 Sent to CCL by: Yingbin Ge [yingbin.ge|-|gmail.com] Hi, I've run a few MP2 and CCSD(T) calculations using Aces2. It seems that Aces2 has no option of freezing core orbitals when computing the correlation energies at the MP2 and CCSD(T) levels of theory, or does it? Is there anyway to freeze the core orbitals for CCSD(T) calculations using Aces? Thanks! -- Yingbin Ge, Ph. D. 207 Spedding Hall, Ames Lab, Iowa State university Ames, IA 50011 (Office Phone: 515-294-0540) -- Yingbin Ge, Ph. D. 207 Spedding Hall, Ames Lab, Iowa State university Ames, IA 50011 (Office Phone: 515-294-0540) From owner-chemistry@ccl.net Mon Feb 6 19:30:01 2006 From: "Yingbin Ge yingbin.ge%a%gmail.com" To: CCL Subject: CCL: ACES Message-Id: <-30799-060206185141-19047-DVMxo+VvKt/9Yf3LRP6dkQ-,-server.ccl.net> X-Original-From: Yingbin Ge Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 6 Feb 2006 17:51:36 -0600 MIME-Version: 1.0 Sent to CCL by: Yingbin Ge [yingbin.ge()gmail.com] Hi, I've run a few MP2 and CCSD(T) calculations using Aces2. It seems that Aces2 has no option of freezing core orbitals when computing the correlation energies at the MP2 and CCSD(T) levels of theory, or does it? Is there anyway to freeze the core orbitals for CCSD(T) calculations using Aces? Thanks! -- Yingbin Ge, Ph. D. 207 Spedding Hall, Ames Lab, Iowa State university Ames, IA 50011 (Office Phone: 515-294-0540) From owner-chemistry@ccl.net Mon Feb 6 21:22:01 2006 From: "Gustavo Mercier gamercier _ yahoo.com" To: CCL Subject: CCL: puzzling tinker pdbxyz problem Message-Id: <-30800-060206210941-7141-tatV8gHZNRGipFY09pUyTA()server.ccl.net> X-Original-From: Gustavo Mercier Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-665419101-1139274567=:20273" Date: Mon, 6 Feb 2006 17:09:27 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Gustavo Mercier [gamercier .. yahoo.com] --0-665419101-1139274567=:20273 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi! Tinker uses the file with extension "key" to define a parameter file and this is used in the translation. These are presumed to be in the same directory: "dat" and "key" with output "log" for most programs obviously pdbxyz generates "pdb" and "xyz" files instead of using "dat" and "log". Hope this helps! Bye GMercier, MD,PhD gamercier__yahoo.com "Samuel Flores samuel.flores~~yale.edu" wrote: Sent to CCL by: "Samuel Flores" [samuel.flores.__.yale.edu] Hi guys, I wonder if anyone can help me with a problem I'm having. The pdbxyz program is producing .xyz files that the program 'dynamic' later has trouble with. It does fine when the atom names are single letter with charges (e.g. 'H', 'C', 'O-' ..) but fails when the names are longer than that (e.g. 'CT3', etc). I have no idea why it translates the demo files perfectly, but not any other files. In fact, if I move the demo files out of their directory, they are mistranslated also! It's almost as if there exists a 'ghost' file somewhere that is needed for proper translation. Can anyone help? Thanks Sam Samuel Flores Graduate Student Gerstein Lab Office: Bass 437 266 Whitney Avenue New Haven, CT 06520 203.432.5405 Home: 28 Pearl Street New Haven, CT 06511 cell: 203.747.2682 -----Original Message----- > From: owner-chemistry|-|ccl.net [mailto:owner-chemistry|-|ccl.net] Sent: Monday, February 06, 2006 12:19 PM To: Flores, Samuel Subject: CCL: Aquous electrochemistry Sent to CCL by: "Jim Kress" [ccl_nospam#kressworks.com] Here's an interesting link: http://comp.chem.umn.edu/netstep/2000/february/9truhcram.html Jim > -----Original Message----- > From: nokophala. ~ .aim.com [mailto:owner-chemistry ~ ccl.net] > Sent: Sunday, February 05, 2006 10:22 AM > To: Kress, Jim > Subject: CCL: Aquous electrochemistry > > Sent to CCL by: nokophala++aim.com > > Hi There, > Is anyone aware of successes in reproducing some of the > tabulated redox potentials of electrochemical reactions that > ar elisted i standard electrochemical tables, especiall those > involving single ions? e.g. Cu > --> Cu2+(aq) + 2e-. The key issue that I need coment on here is the > selection of appropriate solvation models. I doubt if > continuum models would require inclusion of at least the > first shell of water molecules, as these are strongly bound. > As a starting point I am trying to reproduce the experimental > value of the 'reference' reaction 2H+ +2e = H2. Even this > appears tricky. > > Thanks in advance, > > Noko Phala, Anglo Research > ______________________________________________________________ > __________ > Check Out the new free AIM(R) Mail -- 2 GB of storage and > industry-leading spam and email virus protection. > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, > please change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+http://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-- Gustavo A. Mercier, Jr. MD,PhD Baylor University Medical Center Radiology American Radiology Associates 712 N. Washington, Suite 101 Dallas, TX 75246 214-826-8822 214-826-9792 fax gamercier__yahoo.com --0-665419101-1139274567=:20273 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hi!
 
Tinker uses the file with extension "key" to define a parameter file and this is used in the translation. These are presumed to be in the same directory: "dat" and "key" with output "log" for most programs obviously pdbxyz generates "pdb" and "xyz" files instead of using "dat" and "log".
 
Hope this helps!
Bye
GMercier, MD,PhD
gamercier__yahoo.com

"Samuel Flores samuel.flores~~yale.edu" <owner-chemistry__ccl.net> wrote:
Sent to CCL by: "Samuel Flores" [samuel.flores.__.yale.edu]
Hi guys,

I wonder if anyone can help me with a problem I'm having. The pdbxyz
program is producing .xyz files that the program 'dynamic' later has trouble
with. It does fine when the atom names are single letter with charges (e.g.
'H', 'C', 'O-' ..) but fails when the names are longer than that (e.g.
'CT3', etc).

I have no idea why it translates the demo files perfectly, but not any other
files. In fact, if I move the demo files out of their directory, they are
mistranslated also! It's almost as if there exists a 'ghost' file somewhere
that is needed for proper translation.

Can anyone help?

Thanks

Sam



Samuel Flores
Graduate Student
Gerstein Lab

Office:
Bass 437
266 Whitney Avenue
New Haven, CT 06520
203.432.5405

Home:
28 Pearl Street
New Haven, CT 06511
cell: 203.747.2682

-----Original Message-----
> From: owner-chemistry|-|ccl.net [mailto:owner-chemistry|-|ccl.net]
Sent: Monday, February 06, 2006 12:19 PM
To: Flores, Samuel
Subject: CCL: Aquous electrochemistry

Sent to CCL by: "Jim Kress" [ccl_nospam#kressworks.com]
Here's an interesting link:

http://comp.chem.umn.edu/netstep/2000/february/9truhcram.html


Jim

> -----Original Message-----
> From: nokophala. ~ .aim.com [mailto:owner-chemistry ~ ccl.net]
> Sent: Sunday, February 05, 2006 10:22 AM
> To: Kress, Jim
> Subject: CCL: Aquous electrochemistry
>
> Sent to CCL by: nokophala++aim.com
>
> Hi There,
> Is anyone aware of successes in reproducing some of the
> tabulated redox potentials of electrochemical reactions that
> ar elisted i standard electrochemical tables, especiall those
> involving single ions? e.g. Cu
> --> Cu2+(aq) + 2e-. The key issue that I need coment on here is the
> selection of appropriate solvation models. I doubt if
> continuum models would require inclusion of at least the
> first shell of water molecules, as these are strongly bound.
> As a starting point I am trying to reproduce the experimental
> value of the 'reference' reaction 2H+ +2e = H2. Even this
> appears tricky.
>
> Thanks in advance,
>
> Noko Phala, Anglo Research
> ______________________________________________________________
> __________
> Check Out the new free AIM(R) Mail -- 2 GB of storage and
> industry-leading spam and email virus protection.
>
>
>
> -= This is automatically added to each message by the mailing
> script =-
> To recover the email address of the author of the message,
> please change> Conferences:
> http://server.ccl.net/chemistry/announcements/conferences/
>
> Search Messages: http://www.ccl.net/htdig (login: ccl,
> Password: search)>
> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
> -+-+-+-+-+http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/chemistry/sub_unsub.shtml
http://www.ccl.net/spammers.txt






--
Gustavo A. Mercier, Jr. MD,PhD
Baylor University Medical Center
Radiology
American Radiology Associates
712 N. Washington, Suite 101
Dallas, TX 75246
214-826-8822
 --0-665419101-1139274567=:20273-- From owner-chemistry@ccl.net Mon Feb 6 21:57:06 2006 From: "Crawford, Daniel crawdad]![vt.edu" To: CCL Subject: CCL: ACES Message-Id: <-30801-060206185414-12345-9P5A8PsTgh2xd7Zn/liw3Q]^[server.ccl.net> X-Original-From: "Crawford, Daniel" Date: Mon, 6 Feb 2006 20:48:19 -0500 MIME-Version: 1.0 Sent to CCL by: "Crawford, Daniel" [crawdad,vt.edu] [The MS "winmail.dat" attachment removed by jkl*ccl.net] Use the "DROP_MO" keyword to freeze core orbitals. For example, if you want to freeze the lowest three orbitals (ordered by energy), you would set: DROP_MO=1>3 -Daniel -----Original Message----- From: Yingbin Ge yingbin.ge%a%gmail.com [mailto:owner-chemistry*ccl.net] Sent: Mon 2006-02-06 19:49 To: Crawford, Daniel Subject: CCL: ACES =20 Sent to CCL by: Yingbin Ge [yingbin.ge()gmail.com] Hi, I've run a few MP2 and CCSD(T) calculations using Aces2. It seems that Aces2 has no option of freezing core orbitals when computing the correlation energies at the MP2 and CCSD(T) levels of theory, or does it? Is there anyway to freeze the core orbitals for CCSD(T) calculations = using Aces? Thanks! -- Yingbin Ge, Ph. D. 207 Spedding Hall, Ames Lab, Iowa State university Ames, IA 50011 (Office Phone: 515-294-0540) From owner-chemistry@ccl.net Mon Feb 6 22:50:01 2006 From: "William F. Polik polik~~hope.edu" To: CCL Subject: CCL: frozen core orbitals using Aces2 Message-Id: <-30802-060206223229-16431-Syki4vbhKk85DmoW2h2ghQ*o*server.ccl.net> X-Original-From: "William F. Polik" Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Mon, 06 Feb 2006 21:17:20 -0500 Mime-Version: 1.0 Sent to CCL by: "William F. Polik" [polik!A!hope.edu] At 07:07 PM 2/6/2006, you wrote: >I've run a few MP2 and CCSD(T) calculations using Aces2. >It seems that Aces2 has no option of freezing core orbitals when >computing the correlation energies at the MP2 and CCSD(T) levels of >theory, or does it? > >Is there anyway to freeze the core orbitals for CCSD(T) calculations >using Aces? Use the "DROPMO" job control directive to control the number of core orbitals you wish to "freeze," i.e., exclude from the post-SCF calculation. Will Polik ================================ Dr. William F. Polik Hofma Professor of Chemistry Department of Chemistry Hope College 35 East 12th Street Holland, MI 49422-9000 USA polik^_^hope.edu http://www.chem.hope.edu/~polik tel: (616) 395-7639 fax: (616) 395-7118 ================================