From owner-chemistry@ccl.net Wed Aug 29 05:32:01 2007 From: "Yangsoo Kim vsmember() gmail.com" To: CCL Subject: CCL:G: To: Thermochemical calculations from Gaussian output file Message-Id: <-35043-070829041156-7575-Qw0ZmFsuct8Yi8MCTfh6OQ-$-server.ccl.net> X-Original-From: "Yangsoo Kim" Content-Type: multipart/alternative; boundary="----=_Part_192_32542444.1188371185045" Date: Wed, 29 Aug 2007 16:06:25 +0900 MIME-Version: 1.0 Sent to CCL by: "Yangsoo Kim" [vsmember(!)gmail.com] ------=_Part_192_32542444.1188371185045 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear CCL users Thank you for your reply. I would like to extract thermodynamic properties from gaussian03 output. MOLTRAN program is suitable for my purpose. However I cannot access the website. (http://ichem.unn.runnet.ru/tcg/) If anyone have information (file or manual) about MOLTRAN program, please send me an e-mail... And I have another question. I'm running gaussian03 on AMD X2 (Dual Core) with Linux 64bit OS. I'm wondering it is possible to install gaussian03 (rev D.02) on Intel Core2Quad (Quad Core) with Linux 64bit OS. If it is possible, what is the best combinations of CPU and Mainboard? Thank you very much for any suggestion, Yangsoo Kim 2007/8/28, Ol Ga eurisco1^^^pochta.ru : > > > Sent to CCL by: "Ol Ga" [eurisco1() pochta.ru] > To: Thermochemical calculations from Gaussian output file > > MOLTRAN - a program for molecular structure construction and > visualization, vibrations animation, and thermodynamic calculations > http://ichem.unn.runnet.ru/tcg/ > (FREE !!!) > 5. Calculation of thermodynamic properties: > - internal energy > - enthalpy > - entropy > - Gibbs free energy > - heat capacities (Cv and Cp) > - calculation of partition functions (statsums) for the thermodynamic > and/or kinetic studies > - calculation translational, rotational, and vibrational contributions > - manual setting temperature and pressure > - calculation of thermodynamic properties in manually defined temperature > ranges > 6. Taking into account the internal rotation contributions into the > thermodynamics using the different approximations for calculation of > internal rotation contributions > 7. Automatic estimation of the rotation barrier heights using the Fourier > transformation of the calculated potentials.> > > > ------=_Part_192_32542444.1188371185045 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline

Dear CCL users

Thank you for your reply.

I would like to extract thermodynamic properties from gaussian03 output.

MOLTRAN program is suitable for my purpose. However I cannot access the website. (http://ichem.unn.runnet.ru/tcg/)
If anyone have information (file or manual) about MOLTRAN program, please send me an e-mail...


And I have another question.
I'm running gaussian03 on AMD X2 (Dual Core) with Linux 64bit OS.
I'm wondering it is possible to install gaussian03 (rev D.02) on Intel Core2Quad (Quad Core) with Linux 64bit OS.
If it is possible, what is the best combinations of CPU and Mainboard?

Thank you very much for any suggestion,

Yangsoo Kim

2007/8/28, Ol Ga eurisco1^^^pochta.ru <owner-chemistry/./ccl.net>:

Sent to CCL by: "Ol  Ga" [eurisco1() pochta.ru]
To: Thermochemical calculations from Gaussian output file

MOLTRAN - a program for molecular structure construction and visualization, vibrations animation, and thermodynamic calculations
http://ichem.unn.runnet.ru/tcg/
(FREE !!!)
5. Calculation of thermodynamic properties:
- internal energy
- enthalpy
- entropy
- Gibbs free energy
- heat capacities (Cv and Cp)
- calculation of partition functions (statsums) for the thermodynamic and/or kinetic studies
- calculation translational, rotational, and vibrational contributions
- manual setting temperature and pressure
- calculation of thermodynamic properties in manually defined temperature ranges
6. Taking into account the internal rotation contributions into the thermodynamics using the different approximations for calculation of internal rotation contributions
7.  Automatic estimation of the rotation barrier heights using the Fourier transformation of the calculated potentials.



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------=_Part_192_32542444.1188371185045-- From owner-chemistry@ccl.net Wed Aug 29 06:14:00 2007 From: "Rene Thomsen rt_+_molegro.com" To: CCL Subject: CCL: Molegro releases Molegro Virtual Docker 2007 v2.2.5 Message-Id: <-35044-070829060751-20498-nUxkbFmo0qo53BW4pJ/AZw(-)server.ccl.net> X-Original-From: "Rene Thomsen" Date: Wed, 29 Aug 2007 06:07:47 -0400 Sent to CCL by: "Rene Thomsen" [rt()molegro.com] Aarhus, Denmark, August 29th, 2007 - Molegro is pleased to announce a new release of Molegro Virtual Docker, an integrated platform for predicting protein-ligand interactions available for Windows, Linux, and Mac OS X. Molegro Virtual Docker offers high-quality docking based on a novel optimization technique combined with a user interface experience focusing on usability and productivity. New features in version 2.2.5: * 'Split Bond' context menu command. * Cavity Dialog: It is now possible to include ligands and cofactors as target molecules and to specify a minimum/maximum volume. * New features added to Data Analyzer (e.g. coloring of spreadsheet rows and of 2D/3D plots, Dataset Finder, support for subsets, jitter option for 2D/3D plots). * Pose Organizer: It is now possible to specify the threshold (in angstrom) for the 'Show distant residues' option. * Misc. bug fixes (see Release Notes for details). To download a trial version, please visit our company website at: http://www.molegro.com. For more information contact: Rene Thomsen, CEO Molegro Hoegh-Guldbergs Gade 10, Bldg. 1090 DK-8000 Aarhus Denmark E-mail: rt+*+molegro.com Phone: (+45) 89 42 31 65 About Molegro Molegro is a Danish company founded in 2005. Our company concentrates on developing high-performance drug discovery solutions leading to a faster drug-development process. Our goal is to provide scientifically superior products focusing on both state-of-the-art algorithms and an intuitive graphical user interface experience. From owner-chemistry@ccl.net Wed Aug 29 08:34:00 2007 From: "=?ISO-8859-1?Q?Sina_T=FCreli?= sinatureli{}gmail.com" To: CCL Subject: CCL: Placing RM1 parameters to PM3 Message-Id: <-35045-070829082608-522-I9k0TlgvhHkWJmFztNg5VQ,+,server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?Sina_T=FCreli?=" Content-Type: multipart/alternative; boundary="----=_Part_631_17114330.1188390352821" Date: Wed, 29 Aug 2007 15:25:52 +0300 MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?Sina_T=FCreli?=" [sinatureli{}gmail.com] ------=_Part_631_17114330.1188390352821 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Or in another point of view, will adding MG parameters into a RM1 or AM1 parameters file work? On 8/29/07, Sina T reli sinatureli%x%gmail.com wrote: > > > Sent to CCL by: "Sina T reli" [sinatureli],[gmail.com] > Greetings, > > I am working with biomolecules using spartan 04 and I would like to update > my se methods to RM1 which has been shown to perform better for certain > types of biomolecules (one is partially which I am working on). I have seen > people replacing parameters in AM1 with those in RM1. But since the molecule > I am working with contains MG, I need to use the PM3 method. I am wondering, > will just replacing the paramters in PM3 with those in RM1 is likely to > produce a good result? Because all the replacements I have seen is between > AM1-RM1 > > Thanks, > Sina> > > > ------=_Part_631_17114330.1188390352821 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Or in another point of view, will adding MG parameters into a RM1 or AM1 parameters file work?

On 8/29/07, Sina T reli sinatureli%x%gmail.com < owner-chemistry#ccl.net> wrote:

Sent to CCL by: "Sina  T  reli" [sinatureli],[ gmail.com]
Greetings,

I am working with biomolecules using spartan 04 and I would like to update my se methods to RM1 which has been shown to perform better for certain types of biomolecules (one is partially which I am working on). I have seen people replacing parameters in AM1 with those in RM1. But since the molecule I am working with contains MG, I need to use the PM3 method. I am wondering, will just replacing the paramters in PM3 with those in RM1 is likely to produce a good result? Because all the replacements I have seen is between AM1-RM1

Thanks,
Sina



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------=_Part_631_17114330.1188390352821-- From owner-chemistry@ccl.net Wed Aug 29 10:16:01 2007 From: "Zeyar Aung azeyar:i2r.a-star.edu.sg" To: CCL Subject: CCL: PubChem substructure fingerprint Message-Id: <-35046-070829101310-21246-LcGpFIc45uGYSkfShCiqtw[a]server.ccl.net> X-Original-From: "Zeyar Aung" Date: Wed, 29 Aug 2007 10:13:05 -0400 Sent to CCL by: "Zeyar Aung" [azeyar|,|i2r.a-star.edu.sg] Hi All, Is anyone of you familiar with PubChem substructure fingerprint? According to the manual, it is an 880-bit string with 32-bit length indicator (so, totally 912 bits). In SDF format, it is encoded with base64 (i.e. 6 bits = 1 char). But, when I study the actual SDF files in PubChem, the string length is 154 chars (without 2 padding chars). 154 * 6 = 924 bits. Why there is a 12 bit (924 - 912) difference? Could somebody kindly explain? Thank you very much for your time. Best regards, Zeyar =========================================== Zeyar Aung, Ph.D. Research Fellow Data Mining Department Institute for Infocomm Research, Singapore =========================================== (Pls excuse me if you receive this email twice) From owner-chemistry@ccl.net Wed Aug 29 10:57:01 2007 From: "John McKelvey jmmckel-$-gmail.com" To: CCL Subject: CCL: Placing RM1 parameters to PM3 Message-Id: <-35047-070829100608-20694-dptICmaajcF4SbQRZJHVMA]-[server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_1465_31011155.1188395933457" Date: Wed, 29 Aug 2007 09:58:53 -0400 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel+/-gmail.com] ------=_Part_1465_31011155.1188395933457 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline One should be careful replacing a single element's parameters from one parameter set with that from another. I do not know if it is possible to replace parameetrs in Spartan. On the other hand, academeic researchers can get the latest MOPAC from Jimm= y Stewart for no cost, and this contains RM1, and is _extremely_ efficient. [google "MRMOPAC" ] Cheers, John McKelvey On 8/29/07, Sina T=FCreli sinatureli{}gmail.com wrote: > > Or in another point of view, will adding MG parameters into a RM1 or AM1 > parameters file work? > > On 8/29/07, Sina T reli sinatureli%x%gmail.com < owner-chemistry]^[ccl.ne= t> > wrote: > > > > > > Sent to CCL by: "Sina T reli" [sinatureli],[ gmail.com] > > Greetings, > > > > I am working with biomolecules using spartan 04 and I would like to > > update my se methods to RM1 which has been shown to perform better for > > certain types of biomolecules (one is partially which I am working on).= I > > have seen people replacing parameters in AM1 with those in RM1. But sin= ce > > the molecule I am working with contains MG, I need to use the PM3 metho= d. I > > am wondering, will just replacing the paramters in PM3 with those in RM= 1 is > > likely to produce a good result? Because all the replacements I have se= en is > > between AM1-RM1 > > > > Thanks, > > Sina > > > > > > > > > > E-mail to subscribers: CHEMISTRY]^[ccl.net o= r use:> > > > E-mail to administrators: CHEMISTRY-REQUEST]^[ccl.netor use> > > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > > search) > > > > > > > > RTFI: > > http://www.ccl.net/chemistry/aboutccl/instructions/ > > > > > > > > > > > ------=_Part_1465_31011155.1188395933457 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline One should be careful replacing a single element's parameters from one = parameter set with that from another.  I do not know if it is possible= to replace parameetrs in Spartan. 

On the other hand, academe= ic researchers can get the latest MOPAC from Jimmy Stewart for no cost, and= this contains RM1, and is _extremely_ efficient. [google "MRMOPAC&quo= t; ]

Cheers,

John McKelvey

On 8/29/07, Sina T=FCreli sinatureli{}gmail= .com <owner-chemistry**ccl= .net > wrote:
Or in another point of view, will adding MG parameters into a RM1 or A= M1 parameters file work?

On 8/29/07, Sina T reli sinatureli%x%gmail.com < owner-chemistry]^[ccl.net> wrote:

Sent to CCL by: "Sina  T&n= bsp; reli" [sinatureli],[ gmail.com]
Greetings,

I am worki= ng with biomolecules using spartan 04 and I would like to update my se meth= ods to RM1 which has been shown to perform better for certain types of biom= olecules (one is partially which I am working on). I have seen people repla= cing parameters in AM1 with those in RM1. But since the molecule I am worki= ng with contains MG, I need to use the PM3 method. I am wondering, will jus= t replacing the paramters in PM3 with those in RM1 is likely to produce a g= ood result? Because all the replacements I have seen is between AM1-RM1

Thanks,
Sina




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   = ;   

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Job: http://www.ccl.net/job= s
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<= br>


------=_Part_1465_31011155.1188395933457-- From owner-chemistry@ccl.net Wed Aug 29 11:26:00 2007 From: "Michel Petitjean ptitjean++itodys.jussieu.fr" To: CCL Subject: CCL: 3D: smallest size computation Message-Id: <-35048-070829110608-5153-YvWiwD45C6nk6neX3ft9LQ##server.ccl.net> X-Original-From: Michel Petitjean Date: Wed, 29 Aug 2007 17:05:57 +0200 (MEST) Sent to CCL by: Michel Petitjean [ptitjean%itodys.jussieu.fr] To: chemistry]![ccl.net Subj: 3D: smallest size computation Computing the largest size of a set (i.e. its diameter) is easy. Computing its smallest size is a bit more difficult. Now it is done in RADI2, available for free on: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html I hope it helps. Thanks. Michel Petitjean, Email: petitjean]![itodys.jussieu.fr ITODYS (CNRS, UMR 7086) 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html From owner-chemistry@ccl.net Wed Aug 29 12:00:01 2007 From: "=?ISO-8859-1?Q?Sina_T=FCreli?= sinatureli..gmail.com" To: CCL Subject: CCL: Placing RM1 parameters to PM3 Message-Id: <-35049-070829115341-9660-D01zSfnM0pHk4dq0iERBgw{=}server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?Sina_T=FCreli?=" Content-Type: multipart/alternative; boundary="----=_Part_1513_11060433.1188402812894" Date: Wed, 29 Aug 2007 18:53:32 +0300 MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?Sina_T=FCreli?=" [sinatureli=gmail.com] ------=_Part_1513_11060433.1188402812894 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Thanks for the advice, I have found this http://gepard.bioinformatik.uni-saarland.de/people/hutter/mgam1.html which is a work to place a MG parameter in AM1 (so I suppose it should work with RM1). I have found the files that are used for giving the paramteres i= n spartan. I am now replacing them all to see if they give good results. On the other hand can mopac do geometry optimizations? Thanks... On 8/29/07, John McKelvey jmmckel-$-gmail.com wrote: > > One should be careful replacing a single element's parameters from one > parameter set with that from another. I do not know if it is possible to > replace parameetrs in Spartan. > > On the other hand, academeic researchers can get the latest MOPAC from > Jimmy Stewart for no cost, and this contains RM1, and is _extremely_ > efficient. [google "MRMOPAC" ] > > Cheers, > > John McKelvey > > On 8/29/07, Sina T=FCreli sinatureli{}gmail.com > wrote: > > > > Or in another point of view, will adding MG parameters into a RM1 or AM= 1 > > parameters file work? > > > > On 8/29/07, Sina T reli sinatureli%x%gmail.com > > > wrote: > > > > > > > > > Sent to CCL by: "Sina T reli" [sinatureli],[ gmail.com] > > > Greetings, > > > > > > I am working with biomolecules using spartan 04 and I would like to > > > update my se methods to RM1 which has been shown to perform better fo= r > > > certain types of biomolecules (one is partially which I am working on= ). I > > > have seen people replacing parameters in AM1 with those in RM1. But s= ince > > > the molecule I am working with contains MG, I need to use the PM3 met= hod. I > > > am wondering, will just replacing the paramters in PM3 with those in = RM1 is > > > likely to produce a good result? Because all the replacements I have = seen is > > > between AM1-RM1 > > > > > > Thanks, > > > Sina > > > > > > > > > > > > > > > E-mail to subscribers: CHEMISTRY]^[ccl.net or use:> > > > > > E-mail to administrators: CHEMISTRY-REQUEST]^[ccl.netor use> > > > > Conferences: http://server.ccl.net/chemistry/announcements/conference= s/ > > > > > > > > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > > > search) > > > > > > > > > > > > RTFI: > > > http://www.ccl.net/chemistry/aboutccl/instructions/ > > > > > > > > > > > > > > > > > > ------=_Part_1513_11060433.1188402812894 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Thanks for the advice, I have found this

http://gepard.bioinfo= rmatik.uni-saarland.de/people/hutter/mgam1.html

which is a work = to place a MG parameter in AM1 (so I suppose it should work with RM1). I ha= ve found the files that are used for giving the paramteres in spartan. I am= now replacing them all to see if they give good results.
 

On the other hand can mopac do geometry optimizations? Th= anks...

On 8/29/07, John McKelvey jmmckel-$-gmail.c= om <owner-chemistry ~ ccl.net= > wrote:
One should be careful replacing a single element's parameters from one= parameter set with that from another.  I do not know if it is possibl= e to replace parameetrs in Spartan. =20

On the other hand, academeic researchers can get the latest MOPAC f= rom Jimmy Stewart for no cost, and this contains RM1, and is _extremely_ ef= ficient. [google "MRMOPAC" ]

Cheers,

John McKelvey

On 8/29/07, Sina T=FCreli= sinatureli{}gmail.com < owner-chemistry%a%ccl.net > wrote:
Or in another point of view, will adding MG p= arameters into a RM1 or AM1 parameters file work?

On 8/29/0= 7, Sina T reli sinatureli%x%gmail.com <= ; owner-chemistry]^[ccl.net> wrote:

Sent to CCL by: = "Sina  T  reli" [sinatureli],[ gmail.com]
Greetings,

I am worki= ng with biomolecules using spartan 04 and I would like to update my se meth= ods to RM1 which has been shown to perform better for certain types of biom= olecules (one is partially which I am working on). I have seen people repla= cing parameters in AM1 with those in RM1. But since the molecule I am worki= ng with contains MG, I need to use the PM3 method. I am wondering, will jus= t replacing the paramters in PM3 with those in RM1 is likely to produce a g= ood result? Because all the replacements I have seen is between AM1-RM1

Thanks,
Sina




E-mail to subscribers: CHEMISTRY]^[ccl.net or use:
&n= bsp;      http://www.ccl.= net/cgi-bin/ccl/send_ccl_message

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   = ;   

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Search Messages: http://ww= w.ccl.net/htdig  (login: ccl, Password: search)

 =      

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<= br>



------=_Part_1513_11060433.1188402812894-- From owner-chemistry@ccl.net Wed Aug 29 15:34:01 2007 From: "Gustavo Seabra gustavo.seabra*_*gmail.com" To: CCL Subject: CCL: Placing RM1 parameters to PM3 Message-Id: <-35050-070829151819-10640-0/2ZtoV6qg2bZ6M3hfeuig::server.ccl.net> X-Original-From: "Gustavo Seabra" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 29 Aug 2007 14:17:53 -0400 MIME-Version: 1.0 Sent to CCL by: "Gustavo Seabra" [gustavo.seabra()gmail.com] On 8/29/07, Sina Türeli sinatureli..gmail.com wrote: > Thanks for the advice, I have found this > > http://gepard.bioinformatik.uni-saarland.de/people/hutter/mgam1.html > > which is a work to place a MG parameter in AM1 (so I suppose it should work > with RM1). I have found the files that are used for giving the paramteres in > spartan. I am now replacing them all to see if they give good results. Just a note... RM1 is a "re-parametrization" of AM1, as is PM3. In the end, it is a different semi-empirical method and, in principle, John McKelvey's advice is still valid here. > On the other hand can mopac do geometry optimizations? Thanks... It should... Gustavo. From owner-chemistry@ccl.net Wed Aug 29 16:09:00 2007 From: "Kaci Tizi_Ouzou kaci.tiziouzou~!~gmail.com" To: CCL Subject: CCL: Heterogeneous catalysis in Gaussian Message-Id: <-35051-070829005749-11670-yhdQNg4IxEhWVa6CEtgGMg-$-server.ccl.net> X-Original-From: "Kaci Tizi_Ouzou" Content-Type: multipart/alternative; boundary="----=_Part_127132_8349496.1188359737666" Date: Tue, 28 Aug 2007 21:55:37 -0600 MIME-Version: 1.0 Sent to CCL by: "Kaci Tizi_Ouzou" [kaci.tiziouzou^^gmail.com] ------=_Part_127132_8349496.1188359737666 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Greetings all, I am currently working on a problem in which I intend to model a chemical reaction (oxydation of CO) catalysed by TiO2. At this point I wonder what is the usual procedure to model the catalyst. This is what I think to do, but I am willing to explore other routes: [1] Optimize CO alone [2] Optimize TiO2 alone. In this case, I will consider a single cell of TiO2. The problem will of course be how to include the crystal effect. I hear that VASP or ABINIT use plane wave basis sets which takes care of the crystal effect. ANY COMMENTS? [3] Approach a CO molecule and use a scan to determine the TS. In this case, I use the cluster (super cluster) methodology. "CO + TiO2" is my cluster. [4] Question: Once I have the TS, can I say that E(TS) = E(CO) + E(TiO2) + E(Ads). Here I am quite lost. Anyhow, if anybody can suggest a reference describing in some detail this type of calculations, it'll be greatly appreciated. Thanks all, Kass ------=_Part_127132_8349496.1188359737666 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Greetings all,
 
I am currently working on a problem in which I intend to model a chemical reaction (oxydation of CO) catalysed by TiO2. At this point I wonder what is the usual procedure to model the catalyst. This is what I think to do, but I am willing to explore other routes:
 
 
[1] Optimize CO alone
 
[2] Optimize TiO2 alone. In this case, I will consider a single cell of TiO2. The problem will of course be how to include the crystal effect. I hear that VASP or ABINIT use plane wave basis sets which takes care of the crystal effect. ANY COMMENTS?
 
[3] Approach a CO molecule and use a scan to determine the TS. In this case, I use the cluster (super cluster) methodology. "CO + TiO2" is my cluster.
 
[4] Question: Once I have the TS, can I say that E(TS) = E(CO) + E(TiO2) + E(Ads). Here I am quite lost.
 
Anyhow, if anybody can suggest a reference describing in some detail this type of calculations, it'll be greatly appreciated.
 
 
Thanks all,
 
 
Kass
------=_Part_127132_8349496.1188359737666-- From owner-chemistry@ccl.net Wed Aug 29 16:47:00 2007 From: "=?ISO-8859-1?Q?Sina_T=FCreli?= sinatureli/a\gmail.com" To: CCL Subject: CCL: Placing RM1 parameters to PM3 Message-Id: <-35052-070829163011-1462-4RlLy+AQbCub5wbwZT6Myw^^^server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?Sina_T=FCreli?=" Content-Type: multipart/alternative; boundary="----=_Part_2658_22910588.1188419401317" Date: Wed, 29 Aug 2007 23:30:01 +0300 MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?Sina_T=FCreli?=" [sinatureli*_*gmail.com] ------=_Part_2658_22910588.1188419401317 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline But I think the difference is (as someone told me) the equations in RM1 and AM1 are the same where is in PM3 there are some differences. Onyl problem here is that those MG parameters I found were generated with AM1 parameters which also include interractions with the "old" N parameters. But still substitutin those MG parameters into RM1 seems to give good results. On 8/29/07, Gustavo Seabra gustavo.seabra*_*gmail.com < owner-chemistry=ccl.net> wrote: > > > Sent to CCL by: "Gustavo Seabra" [gustavo.seabra()gmail.com] > On 8/29/07, Sina T=FCreli sinatureli..gmail.com > wrote: > > Thanks for the advice, I have found this > > > > http://gepard.bioinformatik.uni-saarland.de/people/hutter/mgam1.html > > > > which is a work to place a MG parameter in AM1 (so I suppose it should > work > > with RM1). I have found the files that are used for giving the > paramteres in > > spartan. I am now replacing them all to see if they give good results. > > Just a note... RM1 is a "re-parametrization" of AM1, as is PM3. In the > end, it is a different semi-empirical method and, in principle, John > McKelvey's advice is still valid here. > > > On the other hand can mopac do geometry optimizations? Thanks... > > It should... > > Gustavo. > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > > ------=_Part_2658_22910588.1188419401317 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline But I think the difference is (as someone told me) the equations in RM1 and= AM1 are the same where is in PM3 there are some differences. Onyl problem = here is that those MG parameters I found were generated with AM1 parameters= which also include interractions with the "old" N parameters. Bu= t still substitutin those MG parameters into RM1 seems to give good results= .=20

On 8/29/07, Gustavo Seabra gustavo.seabra*_*gmail.com < owner-chemistry=ccl.net> wrote:

Sent to CCL by: "Gustavo Seabra" [gustavo.seabra()gmail.com]<= br>On 8/29/07, Sina T=FCreli sinatureli..gmail.com <owner-chemistry:_: ccl.net> wrote:
> Thanks for the advice, I have found this
>
> http://gepard.bioinformatik.uni-saarland.de/people/h= utter/mgam1.html
>
> which is a work to place a MG parameter in AM1 (so I s= uppose it should work
> with RM1). I have found the files that are used for giving the par= amteres in
> spartan. I am now replacing them all to see if they give= good results.

Just a note... RM1 is a "re-parametrization"= ; of AM1, as is PM3. In the
end, it is a different semi-empirical method and, in principle, JohnMcKelvey's advice is still valid here.

> On the other hand c= an mopac do geometry optimizations? Thanks...

It should...

Gustavo.



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------=_Part_2658_22910588.1188419401317-- From owner-chemistry@ccl.net Wed Aug 29 17:19:00 2007 From: "Phillips, James M. PhillipsJ:_:umkc.edu" To: CCL Subject: CCL:G: Heterogeneous catalysis in Gaussian Message-Id: <-35053-070829165848-31978-sdWDIW5jxXn3yC6Wm7XuWQ _ server.ccl.net> X-Original-From: "Phillips, James M." Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C7EA7A.DEC4D651" Date: Wed, 29 Aug 2007 15:26:24 -0500 MIME-Version: 1.0 Sent to CCL by: "Phillips, James M." [PhillipsJ#,#umkc.edu] This is a multi-part message in MIME format. ------_=_NextPart_001_01C7EA7A.DEC4D651 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Kass: Take a look at S. Yang, James M. Phillips, L. Ouyang, "Density-functional calculations of a (1x1) and a (1x3) supported gold system: Au/TiO3/Mo(112)." Physical Review B 74, 1 (2006). Regards, Jim Phillips =20 ________________________________ > From: owner-chemistry{:}ccl.net [mailto:owner-chemistry{:}ccl.net]=20 Sent: Tuesday, August 28, 2007 10:56 PM To: Phillips, James M. Subject: CCL: Heterogeneous catalysis in Gaussian =20 Greetings all, =20 I am currently working on a problem in which I intend to model a chemical reaction (oxydation of CO) catalysed by TiO2. At this point I wonder what is the usual procedure to model the catalyst. This is what I think to do, but I am willing to explore other routes:=20 =20 =20 [1] Optimize CO alone =20 [2] Optimize TiO2 alone. In this case, I will consider a single cell of TiO2. The problem will of course be how to include the crystal effect. I hear that VASP or ABINIT use plane wave basis sets which takes care of the crystal effect. ANY COMMENTS?=20 =20 [3] Approach a CO molecule and use a scan to determine the TS. In this case, I use the cluster (super cluster) methodology. "CO + TiO2" is my cluster.=20 =20 [4] Question: Once I have the TS, can I say that E(TS) =3D E(CO) + = E(TiO2) + E(Ads). Here I am quite lost. =20 Anyhow, if anybody can suggest a reference describing in some detail this type of calculations, it'll be greatly appreciated.=20 =20 =20 Thanks all, =20 =20 Kass ------_=_NextPart_001_01C7EA7A.DEC4D651 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Kass: Take a look at S. Yang, James M. = Phillips, L. Ouyang, “Density-functional calculations of a (1x1) and a (1x3) = supported gold system: Au/TiO3/Mo(112).” Physical Review B 74, 1 (2006).

Regards, Jim = Phillips

 

From: owner-chemistry{:}ccl.net [mailto:owner-chemistry{:}ccl.net]
Sent: Tuesday, August 28, = 2007 10:56 PM
To: Phillips, James M.
Subject: CCL: = Heterogeneous catalysis in Gaussian

 

Greetings all,

 

I am currently working on a problem in which I intend to model a chemical reaction (oxydation of CO) catalysed by TiO2. At this = point I wonder what is the usual procedure to model the catalyst. This is what I = think to do, but I am willing to explore other routes: =

 

 

[1] Optimize CO alone

 

[2] Optimize TiO2 alone. In this case, I will consider a single = cell of TiO2. The problem will of course be how to include the crystal effect. I = hear that VASP or ABINIT use plane wave basis sets which takes care of the = crystal effect. ANY COMMENTS?

 

[3] Approach a CO molecule and use a scan to determine the TS. = In this case, I use the cluster (super cluster) methodology. "CO + = TiO2" is my cluster.

 

[4] Question: Once I have the TS, can I say that E(TS) =3D E(CO) = + E(TiO2) + E(Ads). Here I am quite lost.

 

Anyhow, if anybody can suggest a reference describing in some = detail this type of calculations, it'll be greatly appreciated. =

 

 

Thanks all,

 

 

Kass

------_=_NextPart_001_01C7EA7A.DEC4D651-- From owner-chemistry@ccl.net Wed Aug 29 18:23:01 2007 From: "Igor Filippov Contr igorf-.-helix.nih.gov" To: CCL Subject: CCL: PubChem substructure fingerprint Message-Id: <-35054-070829181757-16672-CZncSMxwDil3ibb1JSYTmQ]|[server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 29 Aug 2007 18:17:47 -0400 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf~!~helix.nih.gov] My guess would be it is because 924 bits is an integer number of 7-bit "characters". 912 is not. Cheers, Igor On Wed, 2007-08-29 at 10:13 -0400, Zeyar Aung azeyar:i2r.a-star.edu.sg wrote: > Sent to CCL by: "Zeyar Aung" [azeyar|,|i2r.a-star.edu.sg] > Hi All, > > Is anyone of you familiar with PubChem substructure fingerprint? > > According to the manual, it is an 880-bit string with 32-bit length indicator (so, totally 912 bits). > In SDF format, it is encoded with base64 (i.e. 6 bits = 1 char). > > But, when I study the actual SDF files in PubChem, the string length is 154 chars (without 2 padding chars). 154 * 6 = 924 bits. > > Why there is a 12 bit (924 - 912) difference? Could somebody kindly explain? > > Thank you very much for your time. > > Best regards, > Zeyar > > =========================================== > Zeyar Aung, Ph.D. > Research Fellow > Data Mining Department > Institute for Infocomm Research, Singapore > =========================================== > > (Pls excuse me if you receive this email twice)-- Igor Filippov [Contr]