From owner-chemistry@ccl.net Sat Dec 2 01:18:00 2006 From: "N. Sukumar nagams]=[rpi.edu" To: CCL Subject: CCL: A philosophical question Message-Id: <-33152-061202000119-25972-SBgfL4AAwvdLnfLZmnNIzQ##server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Sat, 02 Dec 2006 0:01:13 -0500 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams%a%rpi.edu] ==============Original message text=============== On Fri, 01 Dec 2006 22:33:12 EST "Eric Scerri scerri**chem.ucla.edu" wrote: Sent to CCL by: Eric Scerri [scerri-$-chem.ucla.edu] Thanks for your posting but I have no idea of what you are getting at and how it might relate to the questions I asked! eric scerri ===========End of original message text=========== Eric, Sorry, I was perhaps too terse; let me explain... the properties of O2 and H2 are only marginally related to that of H2O because of the different bonding environments. But O in C2H5OH is very close to O in CH3OH; so if you know the properties of the atomtype O in some alcohol, you can to a good approximation obtain the properties of O in some other alcohol. We say the atomtypes of O in alcohols are very nearly the same, but different from the phenolic O atomtypes and VERY different from the nitro O atomtypes or that in O=O. Deriving the properties of water or ethanol knowing the properties of O=O or that of NaCl knowing those of Na and Cl2 is very difficult. In principle this should be possible from ab initio quantum mechanics, but as you have argued elsewhere, it questionable whether this program can be accomplished truly ab initio to any desired accuracy. What I am saying instead is that knowing the properties of the atom types alcohol O, methyl H and methylene H, one can get those of any homologous series alcohol to a good accuracy. If the atoms are virial fragments, as defined by Bader, the properties of the atoms can simply be summed up to give the properties of any molecule containing those atom types. This is the basis of QSAR/QSPR, as implemented in our Transferable Atom Equivalent recombination approach in the RECON algorithm: http://www.chem.rpi.edu/chemweb/recondoc/ http://reccr.chem.rpi.edu/ I hope this helps clarify my earlier statements somewhat, without relapsing too much into advertisement mode! You asked "to what extent can the resulting properties of compounds be predicted ab initio from current physical theory from a knowledge of the properties of the contributing elements?" My answer is that the properties of compounds can be predicted (to good approximation) from those of the CONSTITUENT ATOM TYPES. I think it is an important distiction in practice, as well as philosophically. You have phrased your questions in reductionist terms, but I am pointedly refraining from falling into the reductionist trap by emphasizing that an atom type is the combination of the element AND its bonding environment! Best regards, Dr. N. Sukumar Rensselaer Exploratory Center for Cheminformatics Research Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute From owner-chemistry@ccl.net Sat Dec 2 04:08:00 2006 From: "Eric Scerri scerri a chem.ucla.edu" To: CCL Subject: CCL: Table of Contents/ Foundations of Chemistry/ latest issue Message-Id: <-33153-061201172839-26008-pxddVOXg1jmtpLm7AUlJ8w|-|server.ccl.net> X-Original-From: Eric Scerri Content-Type: multipart/alternative; boundary=Apple-Mail-16--125827412 Date: Fri, 1 Dec 2006 14:34:09 -0800 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Eric Scerri [scerri(0)chem.ucla.edu] --Apple-Mail-16--125827412 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Foundations of Chemistry, volume 8 Number 3, 2006. http://www.springerlink.com/content/t62k711k77p0/? p=457a721c0cb74360945d618876d2b7ff&pi=0 Editorial 24, Eric Scerri Chemical Elements and the Problem of Universals, Mark Sharlow Chhromium Photophysics - A Prototypical Case History, Leslier Forster Another Scientific Practice Separating Chemistry from Physics: Thought Experiments, Rodney Snooks Some Philosophical Influences on Ilya Prigogine's Statistical Mechanics, Joseph Earley Commentary on Allen and Knight's Response to the Lowdin Challenge (concerning the n + l rule), Eric Scerri Book Review of D.H. Rouvray and R.B. King's "The Periodic Table: Into the 21st Century", by John Bloor and Eugen Schwarz Book Review of John Buckingham's "Chasing the Molecule" by Richard Pagni ------------------------------------------------------------------------ ------------------------------------------------------------ The Periodic Table: Its Story and Its Significance, by Eric Scerri, Oxford University Press, 2006. ------------------------------------------------------------------------ ----------------------------------------------------------- Dr. Eric Scerri, Department of Chemistry & Biochemistry, UCLA, Los Angeles, CA 90095-1569 E-mail scerri ~ chem.ucla.edu Tel: 310 206 7443 UCLA faculty web page: http://www.chem.ucla.edu/dept/Faculty/scerri/ Editor of Foundations of Chemistry, http://www.springer.com/sgw/cda/frontpage/0,11855,4-40399-70-35545882- detailsPage%253Djournal%257CmostViewedArticles%257CmostViewedArticles, 00.html International Society for the Philosophy of Chemistry, http://ispc.sas.upenn.edu/ --Apple-Mail-16--125827412 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1

Foundations of Chemistry, volume 8 Number 3, = 2006.

http://www.springerlink.com/content/t62k711k7= 7p0/?p=3D457a721c0cb74360945d618876d2b7ff&pi=3D0



Editorial 24, Eric Scerri

Chemical Elements and the Problem of Universals, = Mark = Sharlow

Chhromium Photophysics - A Prototypical Case History,=A0= Leslier = Forster

Another Scientific Practice Separating Chemistry from = Physics: Thought Experiments,=A0 Rodney = Snooks

Some Philosophical Influences on Ilya Prigogine's = Statistical Mechanics,=A0 Joseph Earley

Commentary on Allen and Knight's Response to the = Lowdin Challenge (concerning the n + l rule), Eric = Scerri

Book Review of D.H. Rouvray and R.B. King's "The = Periodic Table: Into the 21st Century", by=A0John Bloor and Eugen = Schwarz

Book Review of John Buckingham's "Chasing the = Molecule" by Richard Pagni




The Periodic Table: Its Story and Its Significance, by = Eric Scerri, Oxford University Press, = 2006.
---------------------------------------------------= --------------------------------------------------------------------------= ------

Dr. = Eric Scerri,
Department of Chemistry & = Biochemistry,
UCLA,
Los Angeles,
CA = 90095-1569

E-mail scerri ~ chem.ucla.edu
Te= l: 310 206 7443

UCLA faculty web page:=A0=A0=A0http://www.chem.ucl= a.edu/dept/Faculty/scerri/

Editor of = Foundations of Chemistry,
http://www.springer.com/sgw/cda/frontpage/0,11855,4-40399-70-3554= 5882-detailsPage%253Djournal%257CmostViewedArticles%257CmostViewedArticles= ,00.html

International Society for the = Philosophy of Chemistry,
http://ispc.sas.upenn.edu/

















= --Apple-Mail-16--125827412-- From owner-chemistry@ccl.net Sat Dec 2 05:16:00 2006 From: "FyD fyd*u-picardie.fr" To: CCL Subject: CCL: Amino Acid in Amber Message-Id: <-33154-061202042818-18220-fAk8N7SQ+Ho41dsU/oCgAQ~!~server.ccl.net> X-Original-From: FyD Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Sat, 02 Dec 2006 09:20:21 +0100 MIME-Version: 1.0 Sent to CCL by: FyD [fyd:u-picardie.fr] Quoting "Yubo Fan yubofan(a)mail.chem.tamu.edu" : > I got problems to generate correct geometries for amino acids using = > AMBER. I mean I can generate correct structures for amono acid residues, = > including N-terminal, C-terminal and mid ones, BUT NOT a single amino = > acid such as alanine itself. Is there any way to generate the initial = > files for single amino acids from Amber force field? Thanks in advance. I do not see where is the problem, just derive the charge values for your single amino-acid as any other small molecules. You can use R.E.D. http://www.u-picardie.fr/labo/lbpd/RED/ And you have many examples of charge derivation in http://www.u-picardie.fr/labo/lbpd/REDDB/ for small molecule or N-terminal, C-terminal and central fragments... regards, Francois From owner-chemistry@ccl.net Sat Dec 2 10:35:00 2006 From: "lior itzhaki lior.itzhaki[-]gmail.com" To: CCL Subject: CCL: electrons' density Message-Id: <-33155-061201092522-3499-7f5UexbUjJCdVpAc8aNnWw^^^server.ccl.net> X-Original-From: "lior itzhaki" Content-Type: multipart/alternative; boundary="----=_Part_677_4287756.1164982710004" Date: Fri, 1 Dec 2006 16:18:30 +0200 MIME-Version: 1.0 Sent to CCL by: "lior itzhaki" [lior.itzhaki^_^gmail.com] ------=_Part_677_4287756.1164982710004 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear CCLers, I'm doing AB-initio calculation on a linear molecule (poly-acetylene). Can anyone tell me how can I get the electrons' density as a function of the distance from the main axis of the molecule? Thank you lior ------=_Part_677_4287756.1164982710004 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Dear CCLers,

 
I'm doing AB-initio calculation on a linear molecule (poly-acetylene).
Can anyone tell me how can I get the electrons' density as a function of the distance from the main axis of the molecule?
 
Thank you
lior
 ------=_Part_677_4287756.1164982710004-- From owner-chemistry@ccl.net Sat Dec 2 11:09:00 2006 From: "M. L. Dodson mldodson+*+houston.rr.com" To: CCL Subject: CCL: GROMACS installation on Mac-OS Message-Id: <-33156-061202103135-23534-8y1/taWEwLu+kXS5+pwLug:-:server.ccl.net> X-Original-From: "M. L. Dodson" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Sat, 2 Dec 2006 09:31:27 -0600 MIME-Version: 1.0 Sent to CCL by: "M. L. Dodson" [mldodson:houston.rr.com] Summary for the list archive. The cause of the behavior observed by Ibrahim M. Moustafa seems to be the GROMACS use of the path to the executable file to determine the location of the GROMACS library directory. For reference see the definition of the function void CopyRight(FILE *out,char *szProgram) in src/gmxlib/copyrite.c in the GROMACS source code. please email me if you want a more complete explanation. Bud Dodson On Friday 01 December 2006 19:03, John Bushnell bushnell[-]chem.ucsb.edu wrote: > Sent to CCL by: John Bushnell [bushnell..:..chem.ucsb.edu] > > First of all: I have never used GROMACS, and have extremely little > experience using MacOS. But this does sound strange. > > The first thing I would do is use the "which" command to make > absolutely sure that you are running the command that you think > you are via your path. Like this: > > which pdb2gmx > > Just a guess, but this is always a good thing to check before > chasing down ghosts... > > - John > > On Thu, 30 Nov 2006, Ibrahim M. Moustafa I.moustafa*o*psu.edu wrote: > > Sent to CCL by: "Ibrahim M. Moustafa" [I.moustafa^-^psu.edu] > > > > Yea, it segfaults only when I don't type the whole path name and this > > is what is puzzling me! > > Whether is it is a bug or something else faulty....I can't tell! > > > > If you get the chance to install GROMOCS on MacOS and managed to > > get around this, plz let me know! > > > > Kind regards, > > Ibrahim > > > > At 02:59 PM 11/30/2006, you wrote: > >> Sent to CCL by: "M. L. Dodson" [mldodson{=}houston.rr.com] > >> On Thursday 30 November 2006 11:40, Ibrahim M. Moustafa > >> I.moustafa##psu.edu > >> > >> wrote: > >>> Sent to CCL by: "Ibrahim M. Moustafa" [I.moustafa**psu.edu] > >>> > >>> Hi, > >>> > >>> Thanks Dodson for your reply. Actually, the $GMSBIN was already > >>> sitting in the $PATH prentenv confirmed that. > >>> As for the Segmentation fault error, it could be as you suggested! > >>> but if so, how does this related to the way I type the command? > >>> For the time being, I'm aliasing all the commands in $GMSBIN and it > >>> is working (at least for the demo)!. > >>> > >>> As for Amber, unfortunately, I don't have access to download it > >>> for the time being....same for Charmm. > >> > >> Hmmm... I Guess I misunderstood you about the segfault. Do you > >> mean it segfaults only when you DO NOT type the whole path name? > >> Or the other way around? In either case, I do not understand why > >> it should make any difference unless the pdb2gmx program is using > >> its argv[0] (executable file name) variable for some purpose. I > >> will shut up now as I know very little about GROMACS itself. I > >> was just answering with general Unix information. Segfaults can > >> happen for many different reasons. My suggestion was based on an > >> earlier installation of GROMACS on (Intel) FreeBSD where I had the > >> precision mismatch problem. > >> > >> If you still can not get it to work after other people put in > >> their 2 cents, let me know, and I will try to install GROMACS on > >> my iBook G4 to see if I can debug the problem. Should be really > >> funny to measure how much longer simulations take on the iBook :-) > >> > >> Both AMBER and CHARMM cost $$ as well (but are well worth it if > >> you qualify for the academic prices). > >> > >> Bud Dodson > >> > >>> thanks for your time and help, > >>> > >>> Ibrahim > >>> > >>> At 08:53 PM 11/29/2006, you wrote: > >>>> Sent to CCL by: "M. L. Dodson" [mldodson^houston.rr.com] > >>>> On Wednesday 29 November 2006 16:30, Ibrahim M. Moustafa > >>>> ria2(a)psu.edu > >>>> > >>>> wrote: > >>>>> Sent to CCL by: "Ibrahim M. Moustafa" [ria2|a|psu.edu] > >>>>> Hi everybody, > >>>>> > >>>>> Thanks Rick for your advice; but actually my Xcode was recently > >>>>> updated! I'm kind of figured out what was the problem which is: > >>>>> after installation and setting the variables I got an error message > >>>>> "Segmentation fault" when trying to issue any command...or trying > >>>>> the demo tutorial! > >>>>> It appeared that my installation was fine (even my compilation > >>>>> was alright......in fact compilation resulted in a code that is > >>>>> much faster than the provided binary for Mac-OSX). > >>>>> I found the whole path is required to issue GROMACS' command to run > >>>>> any program; although, the variable $GMXBIN is already set in my > >>>>> .cshrc file. This has solved the problem, but still I don't > >>>>> understand why I can't run the programs (e.g. pdb2gmx) by just > >>>>> typing "pdb2gmx" in the xterm rather than typing "$GMXBIN/pdb2gmx" > >>>>> to make it working!! I'm not sure if this is a an OS problem or > >>>>> GROMACS problem! or something obvious that I'm missing! Any advice > >>>>> would be appreciated. > >>>>> > >>>>> I haven't heard any comments regarding TINKER vs GROMACS as a > >>>>> modelling package! wish I can hear from someone though! > >>>>> > >>>>> thanks, > >>>>> Ibrahim > >>>> > >>>> Try issuing the command > >>>> > >>>> printenv PATH > >>>> > >>>> and look to see if the $GMXBIN directory is in your path. The > >>>> behavior you describe indicates it is probably not there. Fix > >>>> your .cshrc to include it, and your "full path problem" should go > >>>> away. The seg fault problem may indicate that your have some > >>>> component(s) compiled for single precision and other components > >>>> compiled for double precision. On FreeBSD (at least on Intel > >>>> architectures), this can be confusing at times. GROMACS gets a > >>>> lot of its speed by running in single precision, whereas most > >>>> other MD packages are compiled for double precision. In > >>>> particular, make sure the compiled precisions match for your > >>>> GROMACS and FFTW installations. > >>>> > >>>> As to your TINKER vs GROMACS question, I prefer AMBER and namd :-) > >>>> > >>>> Bud Dodson > >>>> > >>>>> At 12:22 AM 11/28/2006, you wrote: > >>>>>> Sent to CCL by: Rick Venable [venabler(_)nhlbi.nih.gov] > >>>>>> There can be issues with the gcc and g77 versions under MacOS X; > >>>>>> in particular, if you've kept up to date with OS patches, you may > >>>>>> need to download a newer version of the Xcode tools from the Apple > >>>>>> Developer site. > >>>>>> > >>>>>> I had some problems compiling CHARMM until I updated my Xcode > >>>>>> tools. > >>>>>> > >>>>>> -- > >>>>>> Rick Venable 29/500 > >>>>>> Membrane Biophysics Section > >>>>>> NIH/NHLBI Lab. of Computational Biology > >>>>>> Bethesda, MD 20892-8014 U.S.A. > >>>>>> (301) 496-1905 venabler AT nhlbi*nih*gov > >>>>>> > >>>>>>> Sent to CCL by: "Ibrahim M. Moustafa" [ria2!=!psu.edu] > >>>>>>> > >>>>>>> I have a limited experience in Molecular modelling of protein > >>>>>>> structures; I'd love to expand my experience in that direction. > >>>>>>> So, I have few questions for people with more experience in the > >>>>>>> field. I wanted to install GROMACS package on my Mac-OS 10.4 > >>>>>>> according to the instructions on the GROMACS website. > >>>>>>> First, I installed the FFTW source as instructed in the README > >>>>>>> file. Then, I installed the GROMACS binary for the MacOS-X 10.4. > >>>>>>> However, it did not work! I tried the examples provided with the > >>>>>>> package but I got "Segmentation faults"....nothing in the output. > >>>>>>> Just a blank pages while the script is running interactively. > >>>>>>> I tried to build the package myself from the source code; but > >>>>>>> again I got the same error message when running the examples' > >>>>>>> scripts! Presumably, my installation was not successful! > >>>>>>> even running the command pdb2gmx gives that error message > >>>>>>> "Segmentation fault"!!!-- > >>>> > >>>> M. L. Dodson > >>>> Email: mldodson-at-houston-dot-rr-dot-com > >>>> Phone: eight_three_two-56_three-386_one-- > >> > >> M. L. Dodson > >> Email: mldodson-at-houston-dot-rr-dot-com > >> Phone: eight_three_two-56_three-386_one-- M. L. Dodson Email: mldodson-at-houston-dot-rr-dot-com Phone: eight_three_two-56_three-386_one From owner-chemistry@ccl.net Sat Dec 2 12:21:00 2006 From: "Anselm.Horn()chemie.uni-erlangen.de" To: CCL Subject: CCL:G: electrons' density Message-Id: <-33157-061202121918-24008-6On9GW8xymOeXjwl1Ej80Q ~~ server.ccl.net> X-Original-From: Anselm.Horn|*|chemie.uni-erlangen.de Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Sat, 2 Dec 2006 18:19:13 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: Anselm.Horn[a]chemie.uni-erlangen.de Hi, > I'm doing AB-initio calculation on a linear molecule (poly-acetylene). > Can anyone tell me how can I get the electrons' density as a function of > the > distance from the main axis of the molecule? if you use Gaussian, you could e.g. use the tool 'cubegen' on a formatted checkpoint file to compute the density at some points in space specified via the input-stream, and write the output to a formatted file. See the manual for details of the invocation. Regards, Anselm From owner-chemistry@ccl.net Sat Dec 2 17:13:01 2006 From: "errol lewars elewars{:}trentu.ca" To: CCL Subject: CCL: pka calculation with Spartan 04 Message-Id: <-33158-061202131956-7701-Bx7LHZKrYplRh97PuYnusA:+:server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sat, 02 Dec 2006 12:27:38 -0500 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars~~trentu.ca] 2006 Dec 2 Hello, Using Spartan, I have plotted experimental pKa's vs. the maximally positive charge on the van der Waals surface (the ESP at the bluest place, with ESP mapped onto the surface), for a series of carboxylic acids. The correlation coefficient was good, and enables one to venture a prediction for an experimentally unknown pKa. I do not know if this would work for a series of related nitrogen compounds. E. Lewars ========= Eric Hu list.eric]![gmail.com wrote: >Sent to CCL by: "Eric Hu" [list.eric-,-gmail.com] >Hi, > >I wonder if anyone has performed any pka calculations with Spartan. I >would like to know the procedure and performance for heterocyclic >compounds containing nitrogen if possible. Thanks. > >BTW, the wavefunction's customer service is probably one of the worst >in my opinion. > >-Eric> > > > > From owner-chemistry@ccl.net Sat Dec 2 22:28:00 2006 From: "Carl LeBlond carl.leblond[]iup.edu" To: CCL Subject: CCL:G: Diradicaloid Transition State Message-Id: <-33159-061202191850-19141-1J0ATu9zCQCMGWp+EdaQ+g(0)server.ccl.net> X-Original-From: "Carl LeBlond" Date: Sat, 2 Dec 2006 19:18:49 -0500 Sent to CCL by: "Carl LeBlond" [carl.leblond|-|iup.edu] I am trying to reproduce some work from the literature. It is the isomerization of vinylcyclopropanes which has been shown to proceed through a diradicaloid transiton state. The authors indicate they find the transition state using HF UB3LYP/6-31G* in Gaussian 94. I have tried everything to reproduce this transiton structure with no avail. I have tried GAMESS, Gaussian03 and Spartan all do not converge on the transition structure when using UHF. In GAMESS I can get RHF to work however the energy is a good bit lower than that of the UHF reported. I have tried UHF and ROHF, as singlets and triplets (and for kicks as a doublet). I have optimized many transition structures in the past (although only RHF) and i understand how important the initial guess is and some of the other intricacies (i.e. start with good hessian etc). The authors state in a reference "Transition structures initially obtained by a closed-shell wavefunction, proved to be UHF unstable. Upon release of the spin restriction constraint, they collapsed to the UB3LYP geometries." I must be missing something here. How do I release the spin restriction constraint? Doesn't release of the spin restiction constraint just mean UHF? Thank you. Carl