From owner-chemistry@ccl.net Mon Mar 5 03:23:01 2007 From: "Ulrike Salzner salzner++fen.bilkent.edu.tr" To: CCL Subject: CCL: NH4NO3 Structure Message-Id: <-33729-070305021728-5341-6XIs3LqWxGf1ZimdIfkx+w::server.ccl.net> X-Original-From: Ulrike Salzner Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Mon, 05 Mar 2007 08:08:30 +0200 MIME-Version: 1.0 Sent to CCL by: Ulrike Salzner [salzner _ fen.bilkent.edu.tr] Dear Leh, Supposing that you get NH3 and HNO3, I think the answer is that you are not dealing with a molecule but with an ionic system. Ionic systems are stable in a crystal due to the lattice energy or in polar solvents as ion pairs. They are not stable in the gas phase and they dissociate homolyticly and not heterolyticly. This is what you have obtained. Just consider NaCl. The electron affinity of Cl is less than the ionization potential of sodium. Therfore electron transfer is unfavorable in the gas phase. Regards, Ulrike Salzner Young Leh youngleh * gmail.com schrieb: > Sent to CCL by: "Young Leh" [youngleh*|*gmail.com] > Dear CCLer, > > I have problem while optimizing the structure of NH4NO3. It looks like no matter what my initial structure is, the structure always ends up with CH3 & HNO3. Could somebody please provide me some help on this, a xyz or pdb file will greatly help? > > Thanks all > > Young Leh> > > > > > From owner-chemistry@ccl.net Mon Mar 5 09:50:01 2007 From: "Marcelo Zaldini zaldini-,-ufpe.br" To: CCL Subject: CCL: mopac NOREOR Message-Id: <-33730-070305094846-28733-wB81pc24DuBRxegz3oKD+Q[a]server.ccl.net> X-Original-From: "Marcelo Zaldini" Date: Mon, 5 Mar 2007 09:48:41 -0500 Sent to CCL by: "Marcelo Zaldini" [zaldini^^^ufpe.br] Dear CCLers, Is it possible to setup the mopac 6.10 to NOT reorient the molecular geometry before calculations, using keyword or even any change in source code ? The RE-ORIENTATION is normally used for symmetry purposes. In mopac93 manual, there is a keyword named NOREOR, but it doesn't work in mopac 6.10. Best Regards, Marcelo. From owner-chemistry@ccl.net Mon Mar 5 10:24:00 2007 From: "Patrick Pang skpang!A!ctimail.com" To: CCL Subject: CCL: Eyring equation for the transition state more stable than the reactant Message-Id: <-33731-070305095001-28868-PcTPJrlzvequagDd2H6MuQ,server.ccl.net> X-Original-From: "Patrick Pang" Date: Mon, 5 Mar 2007 09:49:57 -0500 Sent to CCL by: "Patrick Pang" [skpang|-|ctimail.com] Dear all, Is it possible to make use of Eyring equation to determine the rate constant for the reaction, whcih the transition state (TS) is more stable than the reactants (R), i.e. the energy of TS is lower than the R? This reaction coordinate is: R -- \ TS \ /--\ \__/ \ I \__ P Are there any textbooks and articles for reference? Regards, Patrick From owner-chemistry@ccl.net Mon Mar 5 11:27:00 2007 From: "Lucilla Angeli angeli2__student.unisi.it" To: CCL Subject: CCL: Sixth European Workshop in Drug Design Message-Id: <-33732-070305100904-6197-QEStQZF57K9BxvArRPoVIg=-=server.ccl.net> X-Original-From: Lucilla Angeli Content-transfer-encoding: 8BIT Content-type: text/plain; charset=UTF-8 Date: Mon, 05 Mar 2007 15:06:37 +0100 MIME-version: 1.0 Sent to CCL by: Lucilla Angeli [angeli2(a)student.unisi.it] University of Siena VI EWDD Sixth European Workshop in Drug Design June 03 - 10, 2007 - Certosa di Pontignano, Siena (Italy) The University of Siena is pleased to announce the sixth edition of its unique Workshop for researchers at Universities and in the Pharmaceutical Industry, to be held in Certosa di Pontignano, Siena, Italy, on June, 3th â€“ 10th 2007. The Sixth European Workshop in Drug Design will allow 65 participating scientists to work closely with 20 leading researchers from both drug industry and academic institutions in exploring solutions to concrete problems encountered in the drug design and discovery process. The goal of the Workshop is to help participants to collect, interpret and use experimental data to design new drugs using new methods of molecular modelling in conjunction with synthetic feasibility concepts and metabolic pathways. Interaction of these studies with strategies adopted in the Pharmaceutical Industries, such as high-throughput screening, will be explored. Each workshop topic will be considered in terms of individual tasks and their inter-relationships within the discovery cycle. The major topics will be the following: ligand/structure based drug design, in silico ADME - Tox and metabolism, design and screening of virtual libraries, molecular modelling methodologies, cheminformatics/bioinformatics and synthetic feasibility. These topics will be covered by lectures in the mornings. Further info at: www.unisi.it/EWDD To apply, please submit your name, address, affiliation, and primary area of research, along with a curriculum vitae, by fax or mail/E-mail to: Prof. Maurizio Botta, â€śSixth European Workshop in Drug Designâ€ť, UniversitĂ di Siena Dipartimento Farmaco Chimico Tecnologico Via Aldo Moro 2, I-53100 Siena, Italy Fax: +39(0)577 234333 mailto: ewdd%x%unisi.it Fee for participation (Euro 2,500.00) will include all meals and participation in social events and hotel accommodation in two-bed rooms for seven nights (some single rooms are also available, supplementary fee Euro 300.00). Some places are still available ******************************************** Maurizio Botta, Ph.D. Professor Head of Dip. Farmaco Chimico Tecnologico UniversitĂ degli Studi di Siena Via Aldo Moro 2 53100 Siena, Italy Tel. +39 0577 234306 mobile: +39 328 0091722 Fax. +39 0577 234333 ******************************************** From owner-chemistry@ccl.net Mon Mar 5 12:02:01 2007 From: "taye beyene beyene sene3095 .. yahoo.com" To: CCL Subject: CCL: Eyring equation for the transition state more stable than the reactant Message-Id: <-33733-070305114619-27617-yc3kdNZmuIAUo7L7frxFSw()server.ccl.net> X-Original-From: taye beyene beyene Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-61275820-1173113155=:14586" Date: Mon, 5 Mar 2007 08:45:55 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: taye beyene beyene [sene3095/./yahoo.com] --0-61275820-1173113155=:14586 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit I think it difficult to attain such an energy which makes the transition state product more stable than the reactants. If you have the access you can read the text book written by Eyring himself ( Chemical Kinetics) Thanks Taye "Patrick Pang skpang!A!ctimail.com" wrote: Sent to CCL by: "Patrick Pang" [skpang|-|ctimail.com] Dear all, Is it possible to make use of Eyring equation to determine the rate constant for the reaction, whcih the transition state (TS) is more stable than the reactants (R), i.e. the energy of TS is lower than the R? This reaction coordinate is: R -- \ TS \ /--\ \__/ \ I \__ P Are there any textbooks and articles for reference? Regards, Patrickhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- Sucker-punch spam with award-winning protection. Try the free Yahoo! Mail Beta. --0-61275820-1173113155=:14586 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit

I think it difficult to attain such an energy which makes the transition state product more stable than the reactants. If you have the access you can read the text book written by Eyring himself ( Chemical Kinetics)

Thanks

Taye
"Patrick Pang skpang!A!ctimail.com" <owner-chemistry~!~ccl.net> wrote:

Sent to CCL by: "Patrick Pang" [skpang|-|ctimail.com]
Dear all,

Is it possible to make use of Eyring equation to determine the rate constant for the reaction, whcih the transition state (TS) is more stable than the reactants (R), i.e. the energy of TS is lower than the R? This reaction coordinate is:
R
--
\ TS
\ /--\
\__/ \
I \__
P
Are there any textbooks and articles for reference?

Regards,

Patrick

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Try the free Yahoo! Mail Beta. --0-61275820-1173113155=:14586-- From owner-chemistry@ccl.net Mon Mar 5 17:57:01 2007 From: "Tom s Pe a Ruiz truiz!^!ujaen.es" To: CCL Subject: CCL: Concerning NBO bond orders Message-Id: <-33734-070305040328-29197-n7GvuWHlafkbL+ZVFjvEpw(-)server.ccl.net> X-Original-From: "Tom s Pe a Ruiz" Date: Mon, 5 Mar 2007 04:03:24 -0500 Sent to CCL by: "Tom s Pe a Ruiz" [truiz:_:ujaen.es] Hallo!! I'm studying a chemical reaction and trying to compare the modification of the bond orders among reactants, molecular complex and transition state. NBO provides a series of bond orders calculated under different assumptions. Which kind of bond orders could be more appropiate, Wiberg's indexes, atom-atom overlap NAO bond order, NLMO bond orders? Thanks Toms Toms Pea Ruiz Dpt of Physical and Analytical Chemistry University of Jan, Jan (Spain) Ph: +34 953212555 e-mail: truiz^ujaen.es From owner-chemistry@ccl.net Mon Mar 5 18:32:00 2007 From: "=?ISO-8859-1?Q?Tom=E1s_Pe=F1a_Ruiz?= truiz++ujaen.es" To: CCL Subject: CCL: Concerning NBO bond orders Message-Id: <-33735-070301110610-24044-z7sW5S1I8EsmP06e4T61SQ|a|server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Tom=E1s_Pe=F1a_Ruiz?= Content-Type: multipart/alternative; boundary="------------060707080203000104070305" Date: Thu, 01 Mar 2007 16:09:06 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Tom=E1s_Pe=F1a_Ruiz?= [truiz(_)ujaen.es] This is a multi-part message in MIME format. --------------060707080203000104070305 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Hallo!! I'm studying a chemical reaction and trying to compare the modification of the bond orders among reactants, molecular complex and transition state. NBO provides a series of bond orders calculated under different assumptions. Which kind of bond orders could be more appropiate, Wiberg's indexes, atom-atom overlap NAO bond order, NLMO bond orders? Thanks Tomás Konrad Hinsen hinsen!^!cnrs-orleans.fr wrote: >Sent to CCL by: "Konrad Hinsen" [hinsen]~[cnrs-orleans.fr] >On 28.02.2007, at 07:07, Pradipta Bandyopadhyay pradipta:iitg.ernet.in wrote: > > > >>Applying GNM to a protein (whose structure is a bit open), I found that in >>some regions B-factors obtained from calculation is different from >>experimental one (for the rest other regions these are close). This >>probably means using one gamma may not be enough. Does anyone know if >>there is any simple way to use more than one gamma in GNM (any other >>suggestion would be appreciated also)? >> >> > >It is certainly possible to use different gammas for the different interacting pairs, but I am not >aware of anyone having done so in a GNM. > >If you are reasonably sure that the experimental B factors are reliable, then my first suggestion >would be to try an elastic network model, i.e. a model taking into account the directions of atomic >displacements. This increases the number of coordinates in your system by a factor of three, but >that difference matters only for huge proteins. You gain in two points: > > 1) The description with three coordinates per C-alpha atom is in itself more precise and thus >more realistic. > > 2) The GNM potential is physically unrealistic in not being invariant under rotations. This >means that it penalizes global rotations (which you probably don't care about), but also rotational >domain motions which you may well have in your protein. > >There is also a wider choice of potential models that have been published for elastic network >models. The most widely used variety of elastic network models uses a force constant that depends >on the interatomic distance in the input configuration, nearby atom pairs interacting stronger than >more distant ones. In this family we find, in historical order: > > 1) A exp(-r^2) decrease with distance: > K Hinsen > Analysis of domain motions by approximate normal mode calculations > Proteins 33:417-429 (1998) > http://dirac.cnrs-orleans.fr/plone/publications/all-publications/H_1998 > > 2) A more complex function obtained from fitting to the Amber94 all-atom potential: > K Hinsen, A J Petrescu, S Dellerue, M C Bellissent-Funel, and G R Kneller > Harmonicity in slow protein dynamics > Chem. Phys. 261(1+2):25-37 (2000) > http://dirac.cnrs-orleans.fr/plone/publications/all-publications/Hinsen2000a > > 3) A step function: constant up to a cutoff distance, then zero (like for GNM): > A. R. Atilgan, S. R. Durell, R. L. Jernigan, M. C. Demirel, O. Keskin, and I. Bahar > Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model > Biophys. J. 80, 505515 (2001) > >The best model is probably the one described in 2). You can find a ready-to-use implementation in >the Molecular Modelling Toolkit (http://dirac.cnrs-orleans.fr/MMTK, it's called CalphaForceField >there). There is also a Web server that performs various normal-mode based calculations (including >B factors) using this model for any PDB file you submit; the address is > > http://www.bioinfo.no/tools/normalmodes > >I remember having seen a paper that modifies the elastic network model in choosing the force >constants in a more protein-specific way, but I don't have the reference at hand. > >Konrad. >-- >--------------------------------------------------------------------- >Konrad Hinsen >Centre de Biophysique Molculaire, CNRS Orlans >Synchrotron Soleil - Division Expriences >Saint Aubin - BP 48 >91192 Gif sur Yvette Cedex, France >Tel. +33-1 69 35 97 15 >E-Mail: hinsen||cnrs-orleans.fr >---------------------------------------------------------------------> > > > > > > --------------060707080203000104070305 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hallo!!

I'm studying a chemical reaction and trying to compare the modification of the bond orders among reactants, molecular complex and transition state. NBO provides a series of bond orders calculated under different assumptions. Which kind of bond orders could be more appropiate, Wiberg's indexes, atom-atom overlap NAO bond order, NLMO bond orders?

Thanks

Tomás

Konrad Hinsen hinsen!^!cnrs-orleans.fr wrote:

Sent to CCL by: "Konrad  Hinsen" [hinsen]~[cnrs-orleans.fr]
On 28.02.2007, at 07:07, Pradipta Bandyopadhyay pradipta:iitg.ernet.in wrote:

Applying GNM to a protein (whose structure is a bit open), I found that in
some regions B-factors obtained from calculation is different from
experimental one (for the rest other regions these are close). This
probably means using one gamma may not be enough. Does anyone know if
there is any simple way to use more than one gamma in GNM (any other
suggestion would be appreciated also)?

It is certainly possible to use different gammas for the different interacting pairs, but I am not
aware of anyone having done so in a GNM.

If you are reasonably sure that the experimental B factors are reliable, then my first suggestion
would be to try an elastic network model, i.e. a model taking into account the directions of atomic
displacements. This increases the number of coordinates in your system by a factor of three, but
that difference matters only for huge proteins. You gain in two points:

1) The description with three coordinates per C-alpha atom is in itself more precise and thus
more realistic.

2) The GNM potential is physically unrealistic in not being invariant under rotations. This
means that it penalizes global rotations (which you probably don't care about), but also rotational
domain motions which you may well have in your protein.

There is also a wider choice of potential models that have been published for elastic network
models. The most widely used variety of elastic network models uses a force constant that depends
on the interatomic distance in the input configuration, nearby atom pairs interacting stronger than
more distant ones. In this family we find, in historical order:

1) A exp(-r^2) decrease with distance:
K Hinsen
Analysis of domain motions by approximate normal mode calculations
Proteins 33:417-429 (1998)
http://dirac.cnrs-orleans.fr/plone/publications/all-publications/H_1998

2) A more complex function obtained from fitting to the Amber94 all-atom potential:
K Hinsen, A J Petrescu, S Dellerue, M C Bellissent-Funel, and G R Kneller
Harmonicity in slow protein dynamics
Chem. Phys. 261(1+2):25-37 (2000)
http://dirac.cnrs-orleans.fr/plone/publications/all-publications/Hinsen2000a

3) A step function: constant up to a cutoff distance, then zero (like for GNM):
A. R. Atilgan, S. R. Durell, R. L. Jernigan, M. C. Demirel, O. Keskin, and I. Bahar
Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model
Biophys. J. 80, 505515 (2001)

The best model is probably the one described in 2). You can find a ready-to-use implementation in
the Molecular Modelling Toolkit (http://dirac.cnrs-orleans.fr/MMTK, it's called CalphaForceField
there). There is also a Web server that performs various normal-mode based calculations (including
B factors) using this model for any PDB file you submit; the address is

http://www.bioinfo.no/tools/normalmodes

I remember having seen a paper that modifies the elastic network model in choosing the force
constants in a more protein-specific way, but I don't have the reference at hand.

Konrad.
--
---------------------------------------------------------------------
Konrad Hinsen
Centre de Biophysique Molculaire, CNRS Orlans
Synchrotron Soleil - Division Expriences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hinsen||cnrs-orleans.fr
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--------------060707080203000104070305-- From owner-chemistry@ccl.net Mon Mar 5 19:07:00 2007 From: "ugur akgun akgun_ugur!^!yahoo.com" To: CCL Subject: CCL: CO2 - parameter and topology Message-Id: <-33736-070305103631-26520-NDzRbiU7D4lrrX9PUFvgUA%x%server.ccl.net> X-Original-From: ugur akgun Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1005093307-1173108976=:41619" Date: Mon, 5 Mar 2007 07:36:16 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: ugur akgun [akgun_ugur__yahoo.com] --0-1005093307-1173108976=:41619 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit I am trying to find charmm parameter and topology files for CO2 ... I'd appreciate any help. cheers --------------------------------- Access over 1 million songs - Yahoo! Music Unlimited. --0-1005093307-1173108976=:41619 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit

I am trying to find charmm parameter and topology files for CO2 ...
I'd appreciate any help.
cheers

Access over 1 million songs - Yahoo! Music Unlimited. --0-1005093307-1173108976=:41619-- From owner-chemistry@ccl.net Mon Mar 5 19:43:01 2007 From: "ugur akgun akgun_ugur*yahoo.com" To: CCL Subject: CCL: CO2 - parameter and topology Message-Id: <-33737-070228174354-3965-Z3ucIv8sPnOVNXcMTRw03w|,|server.ccl.net> X-Original-From: ugur akgun Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-387684278-1172699013=:22807" Date: Wed, 28 Feb 2007 13:43:33 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: ugur akgun [akgun_ugur~!~yahoo.com] --0-387684278-1172699013=:22807 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit I am trying to find charmm parameter and topology files for CO2 ... I'd appreciate any help. cheers --------------------------------- Looking for earth-friendly autos? Browse Top Cars by "Green Rating" at Yahoo! Autos' Green Center. --0-387684278-1172699013=:22807 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit I am trying to find charmm parameter and topology files for CO2 ...
I'd appreciate any help.
cheers

Looking for earth-friendly autos?
Browse Top Cars by "Green Rating" at Yahoo! Autos' Green Center. --0-387684278-1172699013=:22807-- From owner-chemistry@ccl.net Mon Mar 5 20:17:00 2007 From: "Raphael A. Bauer raphael.bauer{:}charite.de" To: CCL Subject: CCL: Free Tool for conformer generation Message-Id: <-33738-070305121006-9346-95JepoXYlM8UaMVAoewMww+/-server.ccl.net> X-Original-From: "Raphael A. Bauer" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 05 Mar 2007 17:31:27 +0100 MIME-Version: 1.0 Sent to CCL by: "Raphael A. Bauer" [raphael.bauer,charite.de] Hi CC List, I am wondering if anybody of you knows a tool for the generation of conformers. Pretty much what Catalyst does. But - for my project I would need something "free" (open source) and scriptable (command line version maybe). Any recommendations for good tools? Many thanks in advance! Raphael From owner-chemistry@ccl.net Mon Mar 5 20:51:00 2007 From: "Bingxing Wang wangbx[#]dicp.ac.cn" To: CCL Subject: CCL:G: how to write this input file? Message-Id: <-33739-070305103743-27830-HYdNtXetJS2ps197Pd3RZA..server.ccl.net> X-Original-From: "Bingxing Wang" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="gb2312" Date: Mon, 5 Mar 2007 23:03:36 +0800 Mime-Version: 1.0 Sent to CCL by: "Bingxing Wang" [wangbx[-]dicp.ac.cn] Dear all ccler, In an article, it said,"The relativistic effective core potential (ECP) of the Los Alamos National Laboratory 2 ( LANL2)was used to describe the 60 core electrons of a Pt atom. The 5s, 5p, 5d, and 6s valence electrons of the Pt atom were described with split-valence (double-zeta) basis sets." G03 program is used. I want to know how to write the input file. Is it LanL2DZ basis set? Then how about the 5s,5p,5d, and 6s valence electrons? Any suggestion is helpful. Thanks a lot. ˇˇˇˇˇˇˇˇˇˇˇˇˇˇˇˇ ˇˇˇˇˇˇˇˇˇˇˇˇˇˇˇˇˇˇwangbx^_^dicp.ac.cn ˇˇˇˇˇˇˇˇˇˇˇˇˇˇˇˇˇˇˇˇ2007-03-05 From owner-chemistry@ccl.net Mon Mar 5 23:08:01 2007 From: "Brunsteiner, Michael micb(~)uic.edu" To: CCL Subject: CCL: Free Tool for conformer generation Message-Id: <-33740-070305224538-8916-0DuxoG6Ps6N+0SEu3wbymg . server.ccl.net> X-Original-From: "Brunsteiner, Michael" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 5 Mar 2007 20:45:23 -0600 (CST) MIME-Version: 1.0 Sent to CCL by: "Brunsteiner, Michael" [micb#,#uic.edu] On Mon, March 5, 2007 10:31, Raphael A. Bauer raphael.bauer{:}charite.de wrote: > > Sent to CCL by: "Raphael A. Bauer" [raphael.bauer,charite.de] > Hi CC List, > > I am wondering if anybody of you knows a tool for the generation of > conformers. Pretty much what Catalyst does. But - for my project I would > need something "free" (open source) and scriptable (command line version > maybe). > > Any recommendations for good tools? omega2 from openeye (www.eyesopen.com) its fast, quite versatile, and can (only) be used > from the command-line. for academia/non-profit its free. mic > Many thanks in advance! > > Raphael> > >