From owner-chemistry@ccl.net Tue Nov 14 02:05:01 2006 From: "T-Tsuru[-]coral t-tsuru[-]coral.dti.ne.jp" To: CCL Subject: CCL: MMFF94 for H-Bonding and vdW-Bonding Message-Id: <-33023-061114015939-21058-H2tDo0J4uG/vD7Wq03cdew],[server.ccl.net> X-Original-From: "T-Tsuru,,coral" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="Windows-1252"; reply-type=response Date: Tue, 14 Nov 2006 15:59:30 +0900 MIME-Version: 1.0 Sent to CCL by: "T-Tsuru+*+coral" [t-tsuru+*+coral.dti.ne.jp] Hello, CCLers. I'm a novice of Merck Molecular Force Field (MMFF94). I would especially like to know its structural accuracy for hydrogen bonding and van der Waals bonding (for example - comparing with MP2/6-31(d) optimization.) I think one Halgren's paper describes van der Waals bond: "Merck Molecular Force Field. II. MMFF94 van der Waals and Electrostatic Parameters for Intermolecular Interactions," J. Comp. Chem. 17, 520-552. But I don't know other papers. If you know the papers which include those descriptions, please recommend to me. Sincerely yours, ---------------------------------------------------- Telkuni Tsuru t-tsuru##coral.dti.ne.jp Bunshi Gijyutu From owner-chemistry@ccl.net Tue Nov 14 03:30:00 2006 From: "=?gb2312?B?Y2Ns?= ccl**mail.sioc.ac.cn" To: CCL Subject: CCL: =?gb2312?B?UmU6IENDTDogTU1GRjk0IGZvciBILUJvbmRpbmcgYW5kIHZkVy1Cb24=?= =?gb2312?B?ZGluZw==?= Message-Id: <-33024-061114032104-18446-EjjkVOMaJJhYl8vZB4KiOw]^[server.ccl.net> X-Original-From: "=?gb2312?B?Y2Ns?=" Content-Type: Multipart/Alternative; boundary="Boundary-=_BTpYvZDDOtPKeHzpJgqOoHIvRszb" Date: Tue, 14 Nov 2006 16:17:52 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: "=?gb2312?B?Y2Ns?=" [ccl#mail.sioc.ac.cn] --Boundary-=_BTpYvZDDOtPKeHzpJgqOoHIvRszb Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: base64 VGhlcmUgaXMgYW4gYXJ0aWNsZSBhYm91dCBNTUZGOTQgZm9yY2UgZmllbGQuIEhvcGUgaXQg Y2FuIGhlbHAgeW91Lg0KICJNZXJjayBNb2xlY3VsYXIgRm9yY2UgRmllbGQuIEkuIEJhc2lz 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--Boundary-=_BTpYvZDDOtPKeHzpJgqOoHIvRszb-- From owner-chemistry@ccl.net Tue Nov 14 08:33:00 2006 From: "Robert W. Gora robert.gora|*|pwr.wroc.pl" To: CCL Subject: CCL: Interaction energy of the trimer Message-Id: <-33025-061114052557-19006-KmlbA1Dz8ImavUYPt6hYmg*|*server.ccl.net> X-Original-From: "Robert W. Gora" Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Tue, 14 Nov 2006 10:33:30 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: "Robert W. Gora" [robert.gora\a/pwr.wroc.pl] Hi, >> Is there any straightforward way of calculating this energy? What about the counterpoise method? >> > In priniciple, if you use the whole basis for all 7 calculations above > you will get a good estimate of the BSSE-free three-body term. Simply > start from the geometry of the trimer and set to "ghost" all atoms > except those of the subsystem you are calculating each time. There is > another hierarchical approach for counterpoise that is more involved and > requieres more extra calculations. I'd suggest to use the simpler one > unless you're interested in seeing how the third fragment affects the > BSSE extent of the other two. In fact there's a lot of counterpoise schemes for many body systems ... and there's absolutely no theoretical justification of their 'correctness' :) See article of Mierzwicki et al. (CHEMICAL PHYSICS LETTERS 380 (5-6): 654-664 OCT 28 2003) for review and references cited therein. Regards, Robert - Robert W. Gora -----------------(^^ ^^ `)--- Wroclaw Univ. of Technology, Wyspianskiego 27, 50-370 Wroclaw, Poland tel: +48(71)3204076, fax: +48(71)3203364, http://ichfit.ch.pwr.wroc.pl ------------------------------------------------------------------------ From owner-chemistry@ccl.net Tue Nov 14 09:08:00 2006 From: "ioana..gw-chimie.math.unibuc.ro" To: CCL Subject: CCL: computing NMR structures Message-Id: <-33026-061114063024-27318-9p+OCi4bxVM16jdexBAppA!A!server.ccl.net> X-Original-From: ioana|a|gw-chimie.math.unibuc.ro Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Tue, 14 Nov 2006 12:52:25 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: ioana+/-gw-chimie.math.unibuc.ro Hi, Could anyone suggest a freeware for Windows to compute NMR structures of biomolecules in solution from NOESY interproton distances and 3J coupling constants? Thank You in advance! Best regards, Ioana Stanculescu From owner-chemistry@ccl.net Tue Nov 14 09:43:00 2006 From: "Robert W. Gora robert.gora||pwr.wroc.pl" To: CCL Subject: CCL: Interaction energy of the trimer Message-Id: <-33027-061114052558-19024-yktIAxP8K/EbrbL+qlxBpw=-=server.ccl.net> X-Original-From: "Robert W. Gora" Content-Type: MULTIPART/MIXED; BOUNDARY="295466499-1993141489-1163496123=:25718" Date: Tue, 14 Nov 2006 10:22:03 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: "Robert W. Gora" [robert.gora^^^pwr.wroc.pl] This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. --295466499-1993141489-1163496123=:25718 Content-Type: TEXT/PLAIN; charset=ISO-8859-2; format=flowed Content-Transfer-Encoding: QUOTED-PRINTABLE Dear CCLers, I've implemented many-body interaction energy partitioning scheme in GAMESS= =2E It's an optional add-on module available for GAMESS (US) ab initio quantum chemistry package. It performs hybrid variational-perturbational interactio= n energy decomposition scheme. See references 1-10 for details. The present implementation was described in references 11-13. Modified gamess source files can be downloaded from (http://ar.ch.pwr.wroc.pl/course/view.php?id=3D19). I'll provide the passwo= rd to any one interested, but please note that the prospective user of EDS should= obtain a valid license for GAMESS from the Gordon research group. A site license f= or GAMESS is available at no cost to both academic and industrial users. Kindest regards, Robert G=F3ra References 1. Gutowski, M.; van Duijneveldt, F.B.; Chalasinski, G.; and Piela, L.;= Mol. Phys. 1987, 61, 233. 2. Sokalski, W.A.; Roszak, S.; Pecul, K.; Chem. Phys. Lett. 1988, 153, = 153. 3. Cybulski, S.M.; Chalasinski, G.; Moszynski, R.; J. Chem. Phys. 1990,= 92, 4357. 4. Chalasinski, G.; Szczesniak, M.M.; Mol. Phys. 1988, 63, 205. 5. Chalasinski, G.; Szczesniak, M.M.; Chem. Rev. 1994, 94, 1723. 6. Jeziorski, B.; Bulski, M.; Piela, L.; Int. J. Quant. Chem. 1976, 10,= 281. 7. Gutowski, M.; Piela, L.; Mol. Phys. 1988, 64, 943. 8. Jeziorski, B.; van Hemert, M.C.; Mol. Phys. 1976, 31, 713. 9. Cybulski, S.M.; Burcl, R.; Chalasinski, G.; Szczesniak, M.M.; J. Che= m. Phys. 1995, 103, 10116. 10. Moszynski, R.; Rybak, S.; Cybulski, S.; Chalasinski, G.; Chem. Phys.= Lett. 1990, 166, 609. 11. Gora, R.W.; Bartkowiak, W.; Roszak, S.; Leszczynski J.; J. Chem. Phy= s. 2002, 117, 1031. 12. Gora, R.W.; Bartkowiak, W.; Roszak, S.; Leszczynski J.; J. Chem. Phy= s. 2004, 120, 2802. 13. Gora, R.W.; Sokalski, W.A.; Leszczynski, J.; Pett, V.; J. Phys. Chem= =2E B 2005, 109, 2027. On Mon, 13 Nov 2006, errol lewars elewars*_*trentu.ca wrote: > Sent to CCL by: errol lewars [elewars|*|trentu.ca] > 2006 Nov 13 > > You may wish to look at this paper on the C2H4...H2O...C2H4 H-bonded > ternary complex: > M G K Thompson, E G Lewars, J M Parnis, J Phys Chem, 2005, 109(42), 9499. > > E. Lewars > =3D=3D=3D=3D=3D=3D > > > Mateusz Witkowski big_mateo*_*inbox.com wrote: > >> Sent to CCL by: Mateusz Witkowski [big_mateo(~)inbox.com] >> Dear CCLers, >> >> Can anyone of you suggest the way of calculating the interaction energy = between two molecules that is assisted by the third one? I would like to a= ssess the effect of an additional water molecule or ion on the interaction = energy. >> >> I'm aware of the following scheme: Eabc =3D Eab + Eac + Ebc + E3 (the su= m of pairwise contributions + three-body term), but dont't exactly know how= to calculate E3. >> Is there any straightforward way of calculating this energy? What about = the counterpoise method? >> >> I will appreciate your comments. >> Thanks, >> Mateo> >> >> >> >> > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > > > - Robert W. Gora -----------------(^^ ^^ `)--- Wroclaw Univ. of Technology, Wyspianskiego 27, 50-370 Wroclaw, Poland tel: +48(71)3204076, fax: +48(71)3203364, http://ichfit.ch.pwr.wroc.pl ------------------------------------------------------------------------ --295466499-1993141489-1163496123=:25718-- From owner-chemistry@ccl.net Tue Nov 14 10:17:01 2006 From: "Gonzalo Jimenez Oses gonzalo.jimenez ~ dq.unirioja.es" To: CCL Subject: CCL:G: Bond orders through AIM theory Message-Id: <-33028-061114085304-19517-yj41I0he3mUeXjdJN4yGkQ() server.ccl.net> X-Original-From: "Gonzalo Jimenez Oses" Date: Tue, 14 Nov 2006 08:53:04 -0500 Sent to CCL by: "Gonzalo Jimenez Oses" [gonzalo.jimenez.:.dq.unirioja.es] Hi, I wonder if there is any straightforward way to calculate (covalent) bond orders using the AIMPAC software. I have used EXTREME and PROAIM a couple of times, and I havent find these parameters explicitly in the outputs. Of course, the old implementation in G98 crashes during the numerical integration...and AIM2000 is not available for me at this moment. Thanks in advance. Best regards, Gonzalo From owner-chemistry@ccl.net Tue Nov 14 10:52:00 2006 From: "TJ O Donnell tjo/./acm.org" To: CCL Subject: CCL: QEMU Message-Id: <-33029-061113212316-19666-brVKYB9LK4i9T6Vu71IvQQ*|*server.ccl.net> X-Original-From: "TJ O'Donnell" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 13 Nov 2006 17:44:37 -0800 MIME-Version: 1.0 Sent to CCL by: "TJ O'Donnell" [tjo/./acm.org] I've used VMWare extensively and find it to be an excellent product. I would not recommend the free version, especially since the full version costs only about $185. The disk I/O can be slow, but it is relatively easy to configure VMWare to use a raw disk partition, in which case it is much more efficient with I/O. In other words, the linux you install in VMWare formats the disk partition itself, avoiding overlaying the linux file system into a NTFS (or other) file. TJ O'Donnell http://www.gnova.com Jerome Kieffer jerome.Kieffer-#-terre-adelie.org wrote: > Sent to CCL by: Jerome Kieffer [jerome.Kieffer:_:terre-adelie.org] > On Mon, 13 Nov 2006 13:35:19 -0500 > "John McKelvey jmmckel[#]attglobal.net" wrote: > >> Sent to CCL by: John McKelvey [jmmckel!^!attglobal.net] >> My apologies if I was too loose in my statement.. Perhaps I should have >> referred to QEMU is an open source code for allowing multiple OS's to be >> run on a given machine in a fashion similar to VMware. > > Qemu is not the same fashion as VMWare as it does the CPU emulation (ie > very slow but can run x86 code on ppc). Well it is possible to > accelerate it using a kqemu patched linux kernel but this works only > for emulating x86 code on x86 computers. The speed is almost the same > as vmware with acceleration. > >> For those who >> might have tried it I would appreciate having your opinions as to ease >> of use, application code execution relative speeds, etc. > > VMware (free version) is rather fast as long as you are not doing I/O > (disk access). > > The fastest should be Xen but needs the latest CPU including > vitualization to run an unmodified OS. I never tested Xen up to now. > > Regards > From owner-chemistry@ccl.net Tue Nov 14 11:27:01 2006 From: "Caroline Norris cn29:_:sussex.ac.uk" To: CCL Subject: CCL:G: CC and CI excited states Message-Id: <-33030-061114101742-7153-YLHUwExHGXFx1fJF+K6IbA\a/server.ccl.net> X-Original-From: "Caroline Norris" Date: Tue, 14 Nov 2006 10:17:42 -0500 Sent to CCL by: "Caroline Norris" [cn29 _ sussex.ac.uk] Dear All, What is the best way to calculated excited states using couple cluster or configuration interaction methods (on Gaussian)? I've been using the TD(Root=n) keyword, but I was wondering if there was a better way. Thanks in advance for your help, Caroline NOrrisI was wondering what the best way to From owner-chemistry@ccl.net Tue Nov 14 13:01:00 2006 From: "Jonathan Wynne Essex jwe1-.-soton.ac.uk" To: CCL Subject: CCL: Biomolecular Simulation 2007: faster, bigger, better - Nottingham UK Message-Id: <-33031-061114123820-15046-lNCaeN/Gjrxn1q7of8ZvEw a server.ccl.net> X-Original-From: "Jonathan Wynne Essex" Date: Tue, 14 Nov 2006 12:38:20 -0500 Sent to CCL by: "Jonathan Wynne Essex" [jwe1!A!soton.ac.uk] Registration is still open for the inaugural CCPB annual conference - Biomolecular Simulation 2007: faster, bigger, better. This conference will be held at the University of Nottingham from 3rd-5th January 2007. We have an exciting list of invited speakers: Tamar Schlick (New York); Steve Homans (Leeds); Modesto Orozco (Barcelona); Martin Zacharias (Bremen); Holger Gohlke (Frankfurt); and an afternoon devoted to 'showcase' talks from institutions and small companies who have facilities or software which you may find useful in your research. Because of our BBSRC funding we are able to offer substantial discounts to our members from UK academia, with registration being totally free for all UK CCPB student members and only 50 for UK CCPB academic members. The registration fee for anyone else wishing to attend will be 150. The registration deadline is Friday 24th November 2006. Further information can be found on our website www.ccpb.ac.uk/meetings/conference/ Jonathan Essex, jwe1\a/soton.ac.uk From owner-chemistry@ccl.net Tue Nov 14 23:54:01 2006 From: "Nehru viji amini nehru_viji ~~ yahoo.co.in" To: CCL Subject: CCL: SMILE to Internal coordinates Message-Id: <-33032-061114231738-10868-2aeQb10ZPiTJxXKXmUXz1g/./server.ccl.net> X-Original-From: "Nehru viji amini" Date: Tue, 14 Nov 2006 23:17:38 -0500 Sent to CCL by: "Nehru viji amini" [nehru_viji::yahoo.co.in] Dear sir, I'm a student of University of Madras,my part of work is to generate the 3D coordinates from the SMILE strings, but now i have written a code that would convert the internalcoordinates into 3D cartesian coordinates. The first part is to convert the SMILE strings into internal coordinates(bond length,bond angle,dihedral angle),and then internal to cartesian. For the first part i need the methods of parsing the SMILE strings,so i request for your help. I saw the following link which was very useful for me. http://www.wag.caltech.edu/cgi-bin/peter/cgiParseSmiles.pl If you can kindly provide me with the source code of converting smile string into connection table,it will be of most helpful to me. Thanks in advance, Nehru Viji.