Content-Type: Multipart/Alternative; boundary="------------Boundary-00=_Y26TG6G0000000000000" Date: Thu, 1 Dec 2005 15:28:10 +0800 MIME-Version: 1.0 Sent to CCL by: "Zhao Yuan" [ccl-x-mail.sioc.ac.cn] --------------Boundary-00=_Y26TG6G0000000000000 Content-Type: Text/Plain; charset="gb2312" Content-Transfer-Encoding: quoted-printable Hi, CCLers!=0D Can anybody give me some information about the relationship between G= A parameters and the speed of calculation in gold(v.3.0)? It spent me abou= t 7 hours when using the following parameters to screening 1000 molecules:=0D =0D Score Function : GoldScore=0D GA parameter:=0D Population Size 100=0D Selection Pressure 1.125=0D No. of Operations 3000=0D No. of Islands 1=0D Niche Size 2=0D Migrate 0=0D Mutate 100=0D Crossover 100=0D =0D I know that ChemScore will be faster than GoldScore, however I also found that GoldScore gave better result than ChemScore in my system. So I need = to use GoldScore as my score function.=0D =0D I wanted to know how much these parameters meant to the speed.=0D =0D Best regards!=0D =0D Steven=0D =20 --------------Boundary-00=_Y26TG6G0000000000000 Content-Type: Text/HTML; charset="gb2312" Content-Transfer-Encoding: quoted-printable

Hi, CCLers!

Can anybody give me some information about the re= lationship between GA parameters and the speed of calculation in gol= d(v.3.0)? It spent me about 7 hours when using the following parame= ters to screening 1000 molecules:

Score Function : GoldScore

GA parameter:

Population Size       100
Selection= Pressure 1.125
No. of Operations    3000No. of Islands         &nb= sp; 1
Niche Size        =        2
Migrate   = ;            =       0

Mutate &n= bsp; 10= 0
Crossover = ; 100

I know that ChemScore will be faster than GoldScore, however I also = found that GoldScore gave better result than ChemScore in my system.= So I need to use GoldScore as my score function.

I wanted to know how much these parameters meant to the speed.

Best regards!

Steven

--------------Boundary-00=_Y26TG6G0000000000000-- From owner-chemistry@ccl.net Thu Dec 1 09:05:01 2005 From: "XunLei Ding dxl[-]ustc.edu.cn" To: CCL Subject: CCL:G: Ask for diffuse function for Lanl2dz in g03 Message-Id: <-30140-051201061153-25994-9ZtgIFAhCKB7QCadvm88KQ- -server.ccl.net> X-Original-From: "XunLei Ding" Content-Type: text/plain Date: Thu, 01 Dec 2005 18:05:05 +0800 Sent to CCL by: "XunLei Ding" [dxl- -ustc.edu.cn] Dear all, I want to do calculations on Ni using Gaussian03. I want to use Lanl2dz basis set with diffuse function for Ni atom. Does anybody know the coefficient? Thank you very much! Ding From owner-chemistry@ccl.net Thu Dec 1 11:08:00 2005 From: "Hugo Martiniano hugomartiniano_-_sapo.pt" To: CCL Subject: CCL: Solvation Enthalpy with PCM Message-Id: <-30141-051201110717-5876-7h+0ITqyyx1mi5cFVsm06A-.-server.ccl.net> X-Original-From: "Hugo Martiniano" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 1 Dec 2005 16:07:12 -0000 MIME-Version: 1.0 Sent to CCL by: "Hugo Martiniano" [hugomartiniano(_)sapo.pt] I would like to thank A. Klamt and P. Archirel for the replies to my question about solvation Enthalpy in PCM models. In a subsequent search of the literature I found that this question has already been addressed by Tomasi in the framework of the PCM model, to account for the enthalpy of cavity formation. Apparently he uses the thermal expansion coefficient of the solvent as the dR/dT term, so the problem of performing simulations to obtain it may be circumvented in a simple way. Once again thank you, Hugo -----Original Message----- > From: owner-chemistry*|*ccl.net [mailto:owner-chemistry*|*ccl.net] Sent: segunda-feira, 28 de Novembro de 2005 11:42 To: Martiniano, Hugo Subject: CCL: Solvation Enthalpy with PCM Sent to CCL by: "Pierre Archirel" [pierre.archirel---lcp.u-psud.fr] This is an answer to H. Martiniano: The question you address has been clearly discussed by Karplus: B. Roux, H.A. Yu, M. Karplus, J. Phys. Chem. 94 (1990) p. 4683. and can be answered qualitatively aith the help of the Born formula, giving the solvation FREE ENERGY of a spherical ion: DGsolv=-(q2/2R)(1-1/eps) where q is the charge, R the radius of the ion and eps the dielectric constant of the solvent. Now the solvation ENTHALPY requires the derivative of G with respect to temperature: DHsolv=DGsolv+T(dDGsolv/dT). This derivative has two terms: 1- an easy term with deps/dT, which is small and well known, at least for water. 2- a very difficult term with dR/dT, namely the variation of the cavity radius with temperature. Karplus gives an evaluation for Cl- in water and shows it is large. In principle it can be evaluated in molecular simulations, looking for the variation of the maximum of the solute-solvent radial distribution function g(r) with temperature. This seems impossible, due to the convergence requirement. Maybe other collegues will have other comments. P. Archirel, LCP, Orsay, Francehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml Before posting check wait time for next message at: http://www.ccl.nethttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Dec 1 14:17:00 2005 From: "nhung le nhung04hc^_^yahoo.com" To: CCL Subject: CCL: Help with effects of cation polarization in complex substances Message-Id: <-30142-051201224202-21622-CdhhrkCwzeqZgrFqLyiwUQ_._server.ccl.net> X-Original-From: nhung le Date: Mon, 28 Nov 2005 17:52:51 -0800 (PST) Sent to CCL by: nhung le [nhung04hc|yahoo.com] could u help me! i want to undersatand clearly effects of polarization of cation in complex substances .I don't know the reason why complex substances are strong if cations polarize strongly. Please ,tell me about impacts in polarization of cation and explaination (in chemistry) thanks for your help From owner-chemistry@ccl.net Thu Dec 1 14:52:00 2005 From: "steffen.renner+/-chemie.uni-frankfurt.de" To: CCL Subject: CCL: Open Babel 2.0 Released Message-Id: <-30143-051201224202-2901-jDoL6u4JXUPbRQxHQPLubw*server.ccl.net> X-Original-From: steffen.renner~~chemie.uni-frankfurt.de Date: Mon, 28 Nov 2005 17:34:37 +0100 Sent to CCL by: steffen.renner=chemie.uni-frankfurt.de You have to google fot iconv.dll and put it in the directory. After that the program does not ask for this dll anymore. However the program still does not convert files. In the gui version an error message is shown that the input file was not possible to be opened. Has anyone found a solution to this? Best regards Steffen Quoting "Zhao Yuan ccl a mail.sioc.ac.cn" : > Sent to CCL by: "Zhao Yuan" [ccl###mail.sioc.ac.cn] > > When I run Open Babel 2.0(windows version) command line in DOS windows, > it popped up a window with the warning "iconv.dll not found". I wondered > how to solve this problem. Thanks! > Steven From owner-chemistry@ccl.net Thu Dec 1 15:27:00 2005 From: "Kirkpatrick, James james.kirkpatrick:imperial.ac.uk" To: CCL Subject: CCL: question on molecular orbitals in CO and NO Message-Id: <-30144-051201224202-21623-KdzIrYpOt9ShTJchp6vsRw]![server.ccl.net> X-Original-From: "Kirkpatrick, James" Date: Wed, 30 Nov 2005 14:19:30 -0000 Sent to CCL by: "Kirkpatrick, James" [james.kirkpatrick:+:imperial.ac.uk] hi, In my opinion, this discussion is again revolving aroung the theme of what does one mean by reality in science. "Are MOs real, or just mathematical constructs?" in my opinion contains two sides to it: a) are wavefunctions "real" b) are the approximations in treating the wavefunction of a molecule as made up of MOs appropriate. As regards a) I feel that most people involved in QM would say, yes MOs are real in the sense that very fundamental "mathematical constructs", such as momentum or mass or Temperature are real. As regards b) I imagine that it all depends on cicumstances: how are the MOs calculated, what system are we looking at... I imagine most people on this list have a better idea as to when particular model chemistries are appropriate and how to interpret MOs in each of those. So the statement "PES gives information about how MOs interact", in my opinion is perfectly justified, with the caveats that b) holds for the particular problem at hand. james -----Original Message----- From: Noko Phala nphala[#]angloresearch.com = Sent: Wed 11/30/2005 1:17 PM To: Kirkpatrick, James Subject: CCL: question on molecular orbitals in CO and NO Sent to CCL by: "Noko Phala" [nphala~~angloresearch.com] Being able to explain photoelectron spectra in terms of MO theory is not proof for existence of orbitals/orbital interactions. But perhaps the Nobel Laureate is proposing that the predictive power of the orbital concept so great that it is hard to not thing they are real.. _________________________ Dr Noko Phala Process Research Anglo Research=20 PO Box 106 Crown Mines 2025 Republic of South Africa Tel: +27 (11) 377 4817 e-mail: nphala\a/angloresearch.com=20 From owner-chemistry@ccl.net Thu Dec 1 16:02:01 2005 From: "Geoffrey Hutchison grh25,,cornell.edu" To: CCL Subject: CCL: Open Babel 2.0 Released Message-Id: <-30145-051201155039-3360-nZvo4YgxuPBLulvEAcQ1hQ^_^server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Date: Thu, 1 Dec 2005 15:50:24 -0500 Mime-Version: 1.0 (Apple Message framework v746.2) Sent to CCL by: Geoffrey Hutchison [grh25:_:cornell.edu] > However the program still does not convert files. In the gui > version an error > message is shown that the input file was not possible to be opened. > Has anyone > found a solution to this? As discussed on the Open Babel mailing list (openbabel- discuss ~~ lists.sourceforge.net), we pulled the originally-released Windows GUI which had these problems. There is, in fact, an updated Windows executable as of this morning. http://openbabel.sourceforge.net/ From Chris Morley: > There is a revised compiled Windows version of OpenBabel 2.0.0 > available for download as openbabel-2.0.0winS.zip. > > This has both a GUI and a command line program, each built as a > standalone exe. > > Both programs look the same as before, except that the command line > version has slightly improved error messages, arising from it > being built with the latest MS compiler. Best regards, Geoff -- -Dr. Geoffrey Hutchison Cornell University, Department of Chemistry and Chemical Biology Abruña Group http://abruna.chem.cornell.edu/ From owner-chemistry@ccl.net Thu Dec 1 16:37:01 2005 From: "Gustavo Seabra gustavo.seabra**gmail.com" To: CCL Subject: CCL: Wikis and more... Message-Id: <-30146-051201162748-19944-mDuARxOM/hGAxZK2BlgRJg---server.ccl.net> X-Original-From: Gustavo Seabra Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 1 Dec 2005 15:37:04 -0500 MIME-Version: 1.0 Sent to CCL by: Gustavo Seabra [gustavo.seabra]^[gmail.com] Hi, For all that were interested in the recent discussion about Wiki, there's a special feature in the current (Dec 1 2005) edition of Nature that is very close to what was discussed here. Check that out: http://www.nature.com/nature/index.html -- --------------------------------------------------------------------------------------------- Gustavo Seabra Postdoctoral Associate Quantum Theory Project University of Florida Registered Linux user number 381680 Say NO! to software patents: http://www.nosoftwarepatents.com --------------------------------------------------------------------------------------------- If at first you don't succeed... ...skydiving is not for you. From owner-chemistry@ccl.net Thu Dec 1 17:12:00 2005 From: "Brian Salter-Duke b_duke]-[octa4.net.au" To: CCL Subject: CCL: question on molecular orbitals in CO and NO Message-Id: <-30147-051201162618-19191-Dnz12I81SPgCT0Ucq1T6JQ%server.ccl.net> X-Original-From: Brian Salter-Duke Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Fri, 2 Dec 2005 08:26:20 +1100 Mime-Version: 1.0 Sent to CCL by: Brian Salter-Duke [b_duke#octa4.net.au] On Thu, Dec 01, 2005 at 03:29:17PM -0500, Kirkpatrick, James james.kirkpatrick:imperial.ac.uk wrote: > Sent to CCL by: "Kirkpatrick, James" [james.kirkpatrick:+:imperial.ac.uk] > hi, > > In my opinion, this discussion is again revolving aroung the theme of > what does one mean by reality in science. > > "Are MOs real, or just mathematical constructs?" in my opinion contains > two sides to it: a) are wavefunctions "real" > b) are the approximations in treating the wavefunction of a molecule as > made up of MOs appropriate. > > As regards a) I feel that most people involved in QM would say, yes MOs > are real in the sense that very fundamental "mathematical constructs", > such as momentum or mass or Temperature are real. Well I, for one such person, do not think they are real. Mass, momentum and temperature are measurable in principle, or at least in certain circumstances. MOs are not observable. The canonical molecular orbitals we normally use can be subjected to a unitary transformation which changes the MOs and leaves the total wavefunction invariant. How can you observe such beasts that are not fixed. MOs are not real, but they are usefull. I am more prepared to consider total wave functions as real, even though we can only observe their square - the electron density. If you think MOs are real, are canonical MOs more real than localised MOs, even though they both give the same total wwave function. Or are they equally real? If so why are they different? > As regards b) I imagine that it all depends on cicumstances: how are the > MOs calculated, what system are we looking at... I imagine most people > on this list have a better idea as to when particular model chemistries > are appropriate and how to interpret MOs in each of those. Your question (b) is actually asking "How appropriate is the Hartree-Fock approximation?". > So the statement "PES gives information about how MOs interact", in my > opinion is perfectly justified, with the caveats that b) holds for the > particular problem at hand. PES gives information about ion states and not about MOs. MOs however can be used to approximate the ion states and help us to understand the PES. The statement "PES gives information about how MOs interact" is strictly not true, but it can be seen to be correct in a very loose way. (b) does not hold for PES. Koopmans theorem may give good predictions for the energies of the PES bands, but only if relaxation and correlation effects are cancelling. Such cancellation of course completely confuses the notion of PES actually telling you about the orbitals even if the orbital energies are good predictors of the ion state energies. Brian. > james > > > > -----Original Message----- > From: Noko Phala nphala[#]angloresearch.com = > Sent: Wed 11/30/2005 1:17 PM > To: Kirkpatrick, James > Subject: CCL: question on molecular orbitals in CO and NO > > Sent to CCL by: "Noko Phala" [nphala~~angloresearch.com] > Being able to explain photoelectron spectra in terms of MO theory is not > proof for existence of orbitals/orbital interactions. But perhaps the > Nobel Laureate is proposing that the predictive power of the orbital > concept so great that it is hard to not thing they are real.. > > _________________________ > Dr Noko Phala > Process Research > Anglo Research=20 > PO Box 106 Crown Mines 2025 > Republic of South Africa > Tel: +27 (11) 377 4817 > e-mail: nphala\a/angloresearch.com=20> > > -- Brian Salter-Duke (Brian Duke) b_duke:-:octa4.net.au Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher, Chem., Melbourne Univ. & Med. Chem., Monash Univ. From owner-chemistry@ccl.net Thu Dec 1 18:17:01 2005 From: "Joslyn Y Kravitz jyudenfr a umich.edu" To: CCL Subject: CCL: question on molecular orbitals in CO and NO Message-Id: <-30148-051201163848-24374-IknmhraDRfwvbOmEBWl+qw_+_server.ccl.net> X-Original-From: Joslyn Y Kravitz Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Thu, 1 Dec 2005 15:57:37 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: Joslyn Y Kravitz [jyudenfr[a]umich.edu] Didn't we just have this conversation in February? Not that it wasn't interesting but I seem to recall that it got rather heated and since we've recently had a bunch of heated debates on the list maybe now is not the time to do this again. Joslyn On Thu, 1 Dec 2005, Kirkpatrick, James james.kirkpatrick:imperial.ac.uk wrote: > Sent to CCL by: "Kirkpatrick, James" [james.kirkpatrick:+:imperial.ac.uk] > hi, > > In my opinion, this discussion is again revolving aroung the theme of > what does one mean by reality in science. > > "Are MOs real, or just mathematical constructs?" in my opinion contains > two sides to it: a) are wavefunctions "real" > b) are the approximations in treating the wavefunction of a molecule as > made up of MOs appropriate. > > As regards a) I feel that most people involved in QM would say, yes MOs > are real in the sense that very fundamental "mathematical constructs", > such as momentum or mass or Temperature are real. > As regards b) I imagine that it all depends on cicumstances: how are the > MOs calculated, what system are we looking at... I imagine most people > on this list have a better idea as to when particular model chemistries > are appropriate and how to interpret MOs in each of those. > > So the statement "PES gives information about how MOs interact", in my > opinion is perfectly justified, with the caveats that b) holds for the > particular problem at hand. > james > > > > -----Original Message----- > From: Noko Phala nphala[#]angloresearch.com = > Sent: Wed 11/30/2005 1:17 PM > To: Kirkpatrick, James > Subject: CCL: question on molecular orbitals in CO and NO > > Sent to CCL by: "Noko Phala" [nphala~~angloresearch.com] > Being able to explain photoelectron spectra in terms of MO theory is not > proof for existence of orbitals/orbital interactions. But perhaps the > Nobel Laureate is proposing that the predictive power of the orbital > concept so great that it is hard to not thing they are real.. > > _________________________ > Dr Noko Phala > Process Research > Anglo Research=20 > PO Box 106 Crown Mines 2025 > Republic of South Africa > Tel: +27 (11) 377 4817 > e-mail: nphala\a/angloresearch.com=20> > > > > > From owner-chemistry@ccl.net Thu Dec 1 21:45:00 2005 From: "Xiao Jianfeng xiaojf*_*mail.shcnc.ac.cn" To: CCL Subject: CCL: STRUCTURES TO SMILES Message-Id: <-30149-051201211018-14194-14cRVg3VsswlXGWSQOcnxw]^[server.ccl.net> X-Original-From: Xiao Jianfeng Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=GB2312 Date: Fri, 02 Dec 2005 09:17:32 +0800 MIME-Version: 1.0 Sent to CCL by: Xiao Jianfeng [xiaojf(-)mail.shcnc.ac.cn] Vladimir V. Zernov VZernov**asinex.com wrote: > Sent to CCL by: "Vladimir V. Zernov" [VZernov:-:asinex.com] > See http://frowns.sourceforge.net/examples/example4.py > specifically and > http://frowns.sourceforge.net/ > in general > > Install Python and have with above-mentioned example batch MOL/SDF -> SMILES convering > > Best, Vladimir > As far as I know, Frowns is no longer under development.