From owner-chemistry@ccl.net Wed Sep 24 08:01:01 2008 From: "Roger Kevin Robinson r.robinson^-^imperial.ac.uk" To: CCL Subject: CCL: Referencing Reactions Latex ? Message-Id: <-37795-080924074943-11517-btZEx712FIYlRrOhPuXmyA()server.ccl.net> X-Original-From: Roger Kevin Robinson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 24 Sep 2008 11:33:17 +0100 MIME-Version: 1.0 Sent to CCL by: Roger Kevin Robinson [r.robinson!=!imperial.ac.uk] Dear CCL, Anyone got any ideas how you reference reactions in latex ? Say I want to write the reaction as such A+C->C+D (1) and later reference it as reaction (1) how do I do this presumably I need a \label{reaction1} and later write \ref{reaction1} But how do I stop it referencing the section ? Thanks Roger > > Sent to CCL by: Geoffrey Hutchison [geoffh * pitt.edu] > I'm currently writing a paper which involves "inverse design" -- new > molecular structures which are optimal solutions for a particular > property. > > I'm aware of a number of attempts in this area, including data mining, > "inverse QSAR," combinatorial libraries, and some types of genetic > algorithms. What I'm interested is some of the new "alchemical" QM > methods, like Weitao Yang and David Beratan at Duke. These methods can > refine molecular structures by changing atomic composition. > > I remember hearing about a few other such methods, but can't seem to > find them now via Google, Web of Science, etc. > > I'll be happy to summarize articles/references to the list afterwards. > > Thanks very much! > -Geoff > > --- > Prof. Geoffrey Hutchison > Department of Chemistry, University of Pittsburgh > 219 Parkman Avenue, Pittsburgh, PA 15260 > http://hutchison.chem.pitt.edu/ > (412) 648-0492http://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > From owner-chemistry@ccl.net Wed Sep 24 09:47:00 2008 From: "Mikael Johansson mpjohans[-]chem.au.dk" To: CCL Subject: CCL: Heme parameters Message-Id: <-37796-080924094619-29458-WH5Ot1LEgx23bcA5RJ0LNw---server.ccl.net> X-Original-From: Mikael Johansson Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Wed, 24 Sep 2008 15:46:01 +0200 MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mpjohans]![chem.au.dk] Hello Mahesh and All! On Fri, 19 Sep 2008, Mahesh Sundararajan wrote: > I am unable to find MM heme parameters using OPLS-aa force field. In addition to the answers already provided, you might find the following articles of interest. They mainly focus on charge parameterisation of haems (the default charges of a specific force field can arguably be considered quite suboptimal): Autenrieth, Tajkhorshid, Baudry, Luthey-Schulten, "Classical force field parameters for the heme prosthetic group of cytochrome c", JCC 2004, http://dx.doi.org/10.1002/jcc.20079 Fadda, Chakrabarti, Pomes, "Acidity of a Cu-Bound Histidine in the Binuclear Center of Cytochrome c Oxidase", JPCB 2005, http://dx.doi.org/10.1021/jp052734%2B Quenneville, Popovic, Stuchebrukhov, "Combined DFT and electrostatics study of the proton pumping mechanism in cytochrome c oxidase", BBA 2006, http://dx.doi.org/10.1016/j.bbabio.2005.12.003 Favia, Cavalli, Masetti, Carotti, Recanatini, "Three-dimensional model of the human aromatase enzyme and density functional parameterization of the iron-containing protoporphyrin IX for a molecular dynamics study of heme-cysteinato cytochromes", Proteins 2006, http://dx.doi.org/10.1002/prot.20829 Johansson, Kaila, Laakkonen, "Charge parameterization of the metal centers in cytochrome c oxidase", JCC 2008, http://dx.doi.org/10.1002/jcc.20835 Have a nice day, Mikael J. http://www.iki.fi/~mpjohans From owner-chemistry@ccl.net Wed Sep 24 10:22:00 2008 From: "Tristan Youngs t.youngs[a]qub.ac.uk" To: CCL Subject: CCL: Referencing Reactions Latex ? Message-Id: <-37797-080924091554-25967-3s7dA6s3iGvgVW68U3wihw_-_server.ccl.net> X-Original-From: Tristan Youngs Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 24 Sep 2008 13:39:32 +0100 Mime-Version: 1.0 Sent to CCL by: Tristan Youngs [t.youngs|qub.ac.uk] Take a look at the bpchem package: http://www.ctan.org/tex-archive/help/Catalogue/entries/bpchem.html Should do everything you need and then some. Tris. On Wed, 2008-09-24 at 11:33 +0100, Roger Kevin Robinson r.robinson^-^imperial.ac.uk wrote: > Sent to CCL by: Roger Kevin Robinson [r.robinson!=!imperial.ac.uk] > Dear CCL, > > Anyone got any ideas how you reference reactions in latex ? > > Say I want to write the reaction as such > > A+C->C+D (1) > > and later reference it as reaction (1) > > how do I do this presumably I need a \label{reaction1} and later write > \ref{reaction1} > > But how do I stop it referencing the section ? > > Thanks Roger > > > > > Sent to CCL by: Geoffrey Hutchison [geoffh * pitt.edu] > > I'm currently writing a paper which involves "inverse design" -- new > > molecular structures which are optimal solutions for a particular > > property. > > > > I'm aware of a number of attempts in this area, including data mining, > > "inverse QSAR," combinatorial libraries, and some types of genetic > > algorithms. What I'm interested is some of the new "alchemical" QM > > methods, like Weitao Yang and David Beratan at Duke. These methods can > > refine molecular structures by changing atomic composition. > > > > I remember hearing about a few other such methods, but can't seem to > > find them now via Google, Web of Science, etc. > > > > I'll be happy to summarize articles/references to the list afterwards. > > > > Thanks very much! > > -Geoff > > > > --- > > Prof. Geoffrey Hutchison > > Department of Chemistry, University of Pittsburgh > > 219 Parkman Avenue, Pittsburgh, PA 15260 > > http://hutchison.chem.pitt.edu/ > > (412) 648-0492http://www.ccl.net/chemistry/sub_unsub.shtml> > > Job: http://www.ccl.net/jobsConferences: > > http://server.ccl.net/chemistry/announcements/conferences/> > -- Dr T. Youngs (t.youngs*o*qub.ac.uk) Atomistic Simulation Centre Old Physics Building Queens University Belfast Belfast, BT7 1NN, N.I. From owner-chemistry@ccl.net Wed Sep 24 11:32:01 2008 From: "Marcel Swart marcel.swart+*+icrea.es" To: CCL Subject: CCL: Heme parameters Message-Id: <-37798-080924110157-16414-zDlhMGIWwsZYukEW8qS/4Q_-_server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary=Apple-Mail-23--851847993 Date: Wed, 24 Sep 2008 17:01:27 +0200 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Marcel Swart [marcel.swart]^[icrea.es] --Apple-Mail-23--851847993 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; delsp=yes; format=flowed And don't forget this one: J Comput Chem 26: 818 =96 826, 2005 New AMBER Force Field Parameters of Heme Iron for Cytochrome P450s Determined by Quantum Chemical Calculations of Simplified Models AKIFUMI ODA, NORIYUKI YAMAOTSU, SHUICHI HIRONO On Sep 24, 2008, at 3:46 PM, Mikael Johansson mpjohans[-]chem.au.dk =20 wrote: > > Sent to CCL by: Mikael Johansson [mpjohans]![chem.au.dk] > > Hello Mahesh and All! > > On Fri, 19 Sep 2008, Mahesh Sundararajan wrote: > >> I am unable to find MM heme parameters using OPLS-aa force field. > > In addition to the answers already provided, you might find the =20 > following articles of interest. They mainly focus on charge =20 > parameterisation of haems (the default charges of a specific force =20 > field can arguably be considered quite suboptimal): > > Autenrieth, Tajkhorshid, Baudry, Luthey-Schulten, "Classical force =20 > field parameters for the heme prosthetic group of cytochrome c", =20 > JCC 2004, http://dx.doi.org/10.1002/jcc.20079 > > Fadda, Chakrabarti, Pomes, "Acidity of a Cu-Bound Histidine in the =20 > Binuclear Center of Cytochrome c Oxidase", JPCB 2005, http://=20 > dx.doi.org/10.1021/jp052734%2B > > Quenneville, Popovic, Stuchebrukhov, "Combined DFT and =20 > electrostatics study of the proton pumping mechanism in cytochrome =20 > c oxidase", BBA 2006, http://dx.doi.org/10.1016/j.bbabio.2005.12.003 > > Favia, Cavalli, Masetti, Carotti, Recanatini, "Three-dimensional =20 > model of the human aromatase enzyme and density functional =20 > parameterization of the iron-containing protoporphyrin IX for a =20 > molecular dynamics study of heme-cysteinato cytochromes", Proteins =20 > 2006, http://dx.doi.org/10.1002/prot.20829 > > Johansson, Kaila, Laakkonen, "Charge parameterization of the metal =20 > centers in cytochrome c oxidase", JCC 2008, http://dx.doi.org/=20 > 10.1002/jcc.20835 > > Have a nice day, > Mikael J. > http://www.iki.fi/~mpjohans =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D dr. Marcel Swart ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Parc Cient=EDfic i Tecnol=F2gic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) tel +34-972-183240 fax +34-972-183241 e-mail marcel.swart||icrea.es marcel.swart||udg.edu web http://www.icrea.es/pag.asp?id=3DMarcel.Swart http://iqc.udg.edu/~marcel =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D --Apple-Mail-23--851847993 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=WINDOWS-1252 And don't forget this one:

J Comput Chem 26: 818 = =96 826, 2005

New AMBER Force Field = Parameters of Heme Iron for=A0
Cytochrome P450s Determined by = Quantum Chemical=A0
Calculations of Simplified = Models

AKIFUMI ODA, NORIYUKI YAMAOTSU, = SHUICHI HIRONO

On Sep 24, = 2008, at 3:46 PM, Mikael Johansson mpjohans[-]chem.au.dk wrote:


Sent to = CCL by: Mikael Johansson [mpjohans]![chem.au.dk]

Hello = Mahesh and All!

On Fri, 19 Sep 2008, Mahesh Sundararajan = wrote:

=
I am unable to find MM heme = parameters using OPLS-aa force field.

In = addition to the answers already provided, you might find the following = articles of interest. They mainly focus on charge parameterisation of = haems (the default charges of a specific force field can arguably be = considered quite suboptimal):

Autenrieth, Tajkhorshid, Baudry, = Luthey-Schulten, "Classical force field parameters for the heme = prosthetic group of cytochrome c", JCC 2004, http://dx.doi.org/10.1002/jcc= .20079

Fadda, Chakrabarti, Pomes, "Acidity of a Cu-Bound = Histidine in the Binuclear Center of Cytochrome c Oxidase", JPCB 2005, = http://dx.doi.org/10.1021/j= p052734%2B

Quenneville, Popovic, Stuchebrukhov, "Combined DFT = and electrostatics study of the proton pumping mechanism in cytochrome c = oxidase", BBA 2006, http://dx.doi.org/= 10.1016/j.bbabio.2005.12.003

Favia, Cavalli, Masetti, = Carotti, Recanatini, "Three-dimensional model of the human aromatase = enzyme and density functional parameterization of the iron-containing = protoporphyrin IX for a molecular dynamics study of heme-cysteinato = cytochromes", Proteins 2006, http://dx.doi.org/10.1002/pr= ot.20829

Johansson, Kaila, Laakkonen, "Charge = parameterization of the metal centers in cytochrome c oxidase", JCC = 2008, http://dx.doi.org/10.1002/jcc= .20835

Have a nice day,
=A0 =A0 Mikael J.
=

dr. Marcel = Swart

ICREA = researcher=A0at
Institut de Qu=EDmica = Computacional
Universitat de = Girona

Parc Cient=EDfic i = Tecnol=F2gic
Pic de Peguera = 15
Catalunya = (Spain)

tel
http://iqc.udg.edu/~marcel<= /span>



= --Apple-Mail-23--851847993-- From owner-chemistry@ccl.net Wed Sep 24 12:14:00 2008 From: "Rudolf Herrmann rudolf.herrmann,,physik.uni-augsburg.de" To: CCL Subject: CCL: Referencing Reactions Latex ? Message-Id: <-37799-080924103850-32028-3N+Rz/PhseLY8N3FOGsKWg=server.ccl.net> X-Original-From: "Rudolf Herrmann" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 24 Sep 2008 15:56:45 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: "Rudolf Herrmann" [rudolf.herrmann]![physik.uni-augsburg.de] Hello, > > Sent to CCL by: Roger Kevin Robinson [r.robinson!=!imperial.ac.uk] > Dear CCL, > > Anyone got any ideas how you reference reactions in latex ? > > Say I want to write the reaction as such > > A+C->C+D (1) > > and later reference it as reaction (1) > maybe you are looking for something like the package "chemcompounds"? you can find it on CTAN under macros/latex/contrib/chemcompounds Hope this helps Rudolf. Rudolf Herrmann Institut für Physik Universität Augsburg From owner-chemistry@ccl.net Wed Sep 24 14:57:00 2008 From: "Mariusz Radon mariusz.radon*gmail.com" To: CCL Subject: CCL: Referencing Reactions Latex ? Message-Id: <-37800-080924142142-10893-yglsWpol044Hqvb4SsgMYA(!)server.ccl.net> X-Original-From: Mariusz Radon Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 24 Sep 2008 20:21:23 +0200 MIME-Version: 1.0 Sent to CCL by: Mariusz Radon [mariusz.radon:_:gmail.com] Roger Kevin Robinson r.robinson^-^imperial.ac.uk wrote: > Anyone got any ideas how you reference reactions in latex ? > Say I want to write the reaction as such > > A+C->C+D (1) > > and later reference it as reaction (1) > > how do I do this presumably I need a \label{reaction1} and later write > \ref{reaction1} > > But how do I stop it referencing the section ? > Hi Roger: The `mhchem' package might be useful. It is as simple as: \ce{A + B2X4 -> C + D+} (as in the exaple above: you even don't need to specify sub/superscripts explicitly in typical cases). Why not to treat reactions as ordinary mathematical equations (\begin{equation}\label{reaction1} ... \end{equation})? You will than take advantage of automatic numbering and referencing, which is what you want. Or eventually, you can create a simple, custom environment `reaction' based on the environment `equation' (use \newenvironment). best regards, Mariusz Radon From owner-chemistry@ccl.net Wed Sep 24 15:35:01 2008 From: "Mikael Johansson mpjohans+*+chem.au.dk" To: CCL Subject: CCL: Referencing Reactions Latex ? Message-Id: <-37801-080924153107-6460-lnM1EnECSBBk3RTC52WvaQ---server.ccl.net> X-Original-From: Mikael Johansson Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed" Date: Wed, 24 Sep 2008 21:30:49 +0200 MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mpjohans:+:chem.au.dk] Hello Roger and All! On Wed, 24 Sep 2008 Roger Kevin Robinson wrote: > Anyone got any ideas how you reference reactions in latex ? > Say I want to write the reaction as such > A+C->C+D (1) > and later reference it as reaction (1) If you just have a \label command in the middle of the text, it will =20 refer to the section number. To get it to refer to something else, you =20 need to have the label inside some other environment that is numbered =20 (like a figure or equation). The already mentioned packages probably do what you need, but if you =20 don't need anything too fancy, you could perhaps use the equation =20 environment which by default numbers things consecutively without =20 section numbers (this can be changed too). So something like: """ \begin{equation} \label{myreaction} \mathrm{ A_2 + C^{2+} \rightarrow C + D^{2+} } \end{equation} Reaction (\ref{myreaction}) is my favourite! """ Of course, if you also have numbered equations, this might not be what =20 you want. Have a nice day, Mikael J. http://www.iki.fi/~mpjohans ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.