From owner-chemistry@ccl.net Thu Mar 16 02:50:00 2006 From: "Sue Lam chsue2004,,yahoo.com" To: CCL Subject: CCL: DFT for pi-pi Interaction Message-Id: <-31210-060316015706-21454-rcnfnP8Q9IyCn7cjmJ7ZKA..server.ccl.net> X-Original-From: Sue Lam Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1012145474-1142492152=:80213" Date: Wed, 15 Mar 2006 22:55:52 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Sue Lam [chsue2004-$-yahoo.com] --0-1012145474-1142492152=:80213 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear all, Thank you very much for your suggested references Sue --------------------------------- Yahoo! Mail Bring photos to life! New PhotoMail makes sharing a breeze. --0-1012145474-1142492152=:80213 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear all,
 
Thank you very much for your suggested references
 
Sue

Yahoo! Mail
Bring photos to life! New PhotoMail makes sharing a breeze. --0-1012145474-1142492152=:80213-- From owner-chemistry@ccl.net Thu Mar 16 04:26:01 2006 From: "Gilles Marcou gilles.marcou[a]pharma.u-strasbg.fr" To: CCL Subject: CCL: How to choose a docking program? Message-Id: <-31211-060316041740-30139-s8GnYuPjs9hoPW+DDRCnkg[A]server.ccl.net> X-Original-From: Gilles Marcou Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-15" Date: Thu, 16 Mar 2006 10:26:17 +0100 MIME-Version: 1.0 Sent to CCL by: Gilles Marcou [gilles.marcou::pharma.u-strasbg.fr] Hi, > I am trying to dock a small DNA (~22nt) to a large protein (~ 770 residues) Your DNA is a big object for most the docking tools. Those are designed for virtual screening of thousands of small molecules. Nonetheless, maybe a program like autodock would be able to manage it. But you cannot stop to this tool. You'll certainly have to do some MD or MC. Beside the approach will be strongly dependent of your question: whether you try to get insight in the binding mode, allosteric effects, the binding free energy, or even more complexe things... Also, I think that the research in protein-protein interactions might give you some ideas, supposing that you already have read the litterature about protein-DNA interactions. Good lucck -- Gilles Marcou Université Louis Pasteur de Strasbourg Faculté de Pharmacie Laboratoire de Pharmacochimie de la Communication Cellulaire, UMR7081 74, Route du Rhin, BP24 67401 Illkirch tel.:(0033)(0)3.90.24.42.21 eMail: marcou:_:pharma.u-strasbg.fr From owner-chemistry@ccl.net Thu Mar 16 06:57:00 2006 From: "Sebastian Rohrer sebastian.rohrer*mail.uni-wuerzburg.de" To: CCL Subject: CCL: OpenEye VIDA 2.1 on different Linux Distros Message-Id: <-31212-060316065308-9669-tcVvgveEkyQWMrPBBYS+vQ-*-server.ccl.net> X-Original-From: Sebastian Rohrer Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 16 Mar 2006 12:53:03 +0100 MIME-Version: 1.0 Sent to CCL by: Sebastian Rohrer [sebastian.rohrer%x%mail.uni-wuerzburg.de] Hi all, I have a strange problem when using OpenEye's VIDA 2.1 to visualize docking results. We have several linux workstations in our lab all running on Mandrake 10.1 (KDE 3.2.3) . Just to give it a try, I recently installed Ubuntu (KDE 3.4.3) on one of them. Now the strange thing is when I use the "Docking View" to visualize docking results, VIDA shows hydrogen bonds between target and ligand on the Mandrake machine but not on the one running Ubuntu. Of course I have enabled "Show hydrogen bonds" in the Docking View preferences on both machines. Does anyone have a clue what is causing this? Maybe some OpenGL configuration of KDE 3.4? Thanks for your help, Sebastian -- Sebastian Rohrer AK Baumann - Molecular Modelling Group Department of Pharmaceutical Chemistry Institute of Pharmacy and Food Chemistry University of Wuerzburg Am Hubland 97074 Wuerzburg Germany From owner-chemistry@ccl.net Thu Mar 16 08:25:00 2006 From: "Ramon Crehuet rcsqtc[a]iiqab.csic.es" To: CCL Subject: CCL:G: Projected frequencies Message-Id: <-31213-060316082430-14547-nBkAMdlhYIDR4+1e5eSIDQ]-[server.ccl.net> X-Original-From: "Ramon Crehuet" Date: Thu, 16 Mar 2006 08:24:27 -0500 Sent to CCL by: "Ramon Crehuet" [rcsqtc()iiqab.csic.es] Dear CCLers, I have a relatively large system where I keep some (external) atoms fixed. After doing an optimisation I want to check that I have a minimum or a TS candidate. So I would like to do a frequency calculation on the free atoms. I think that makes sense from a theoretical point of view. So I do not want to calculate the second derivative with respect to fixed atoms coordinates, although they have to be there for the other derivatives to make sense. Otherwise, I could get the full hessian and project it. I was using gaussian and don't know how to do it with this software. Is is possible? Is is possible with GAMESS-US (which I use regularly)? Is it possible with any other software (that can also do DFT and ONIOM)? And last, but not least... am I asking something very unusual? Thanks in advance, Ramon From owner-chemistry@ccl.net Thu Mar 16 09:00:00 2006 From: "Giulio Vistoli giulio.vistoli- -unimi.it" To: CCL Subject: CCL: How to choose a docking program? Message-Id: <-31214-060316062007-3925-TCDVjqNv/vJGQ0w4TJqoFw^server.ccl.net> X-Original-From: Giulio Vistoli Content-transfer-encoding: 7BIT Content-type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 16 Mar 2006 11:21:47 +0100 MIME-version: 1.0 Sent to CCL by: Giulio Vistoli [giulio.vistoli(0)unimi.it] Dear Jianxi Xiao, In order to dock small DNA to a large protein, I can suggest EscherNG program (www.ddl.unimi.it) which is an enhanced version of the original ESCHER protein-protein automatic docking system developed in 1997 by Gabriele Ausiello, Gianni Cesareni and Manuela Helmer Citterich. EscherNG was reengineered just to dock small DNA to HIV Integrase structure as reported in: L. De Luca, A. Pedretti, G. Vistoli, M.L. Barreca, L. Villa, P. Monforte, A. Chimirri Biochem. Biophys. Res.Comm., Vol. 310/4, 1083-88 (2003) Best regards Giulio Vistoli From owner-chemistry@ccl.net Thu Mar 16 09:35:00 2006 From: "Orlin Blajiev blajiev:+:vub.ac.be" To: CCL Subject: CCL:G: transition moments Message-Id: <-31215-060316085313-2413-l0o1/zYzWwGvVfzY6L4t+Q]^[server.ccl.net> X-Original-From: "Orlin Blajiev" Date: Thu, 16 Mar 2006 08:53:10 -0500 Sent to CCL by: "Orlin Blajiev" [blajiev]*[vub.ac.be] Hi, I will very much appreciate if somebody helps with a question about what is coming out when Gaussian calculates transition moments (dipole derivatives) and how this relates to the vectors which are shown in the Gaussview when "transition moments" box is checked. Specifically, I have the following output but I do not know what is it (directional cosinuses?) and also how it relates to the coordination system of the molecule itself. DipoleDeriv=0.083957,-0.000 0564,0.1143753,0.0000272,-0.1541421,-0.0000432,0.1142125,-0.0000383,-0 .0477401,0.0842112,-0.0002039,-0.1144023,-0.000678,-0.1541442,0.000325 4,-0.1143141,0.0001056,-0.0477902,-0.1137788,-0.0000134,-0.0000544,0.0 000057,-0.1541633,0.0000563,-0.0000658,0.0001889,0.1500937,0.0841015,- 0.0000137,0.1141954,0.0001818,-0.154133,0.0000262,0.1142656,0.0000038, -0.0478301,0.0843152,-0.0003509,-0.1142929,-0.0003297,-0.1541658,0.000 1379,-0.1144373,0.0001815,-0.0478157,-0.1137877,-0.0000207,0.0000262,0 .0000117,-0.1541381,0.0000921,0.0002551,-0.0001181,0.1500536,-0.065117 6,0.0001075,-0.0813605,0.0000539,0.1541509,0.0000802,-0.081324,0.00005 23,0.0288168,-0.0652374,0.0001242,0.0814074,0.0004935,0.1541381,-0.000 2954,0.0813327,-0.0000847,0.028833,0.0757808,0.0000321,0.0000055,0.000 0098,0.1541566,-0.0000744,0.0000171,-0.0001654,-0.1120697,-0.0650622,0 .0001149,-0.0813187,-0.0000217,0.1541518,-0.0000987,-0.0813988,-0.0000 211,0.0287813,-0.0651633,0.0002157,0.0813728,0.0001806,0.1541399,-0.00 00439,0.0814666,-0.0000974,0.0287532,0.0757814,0.0000645,0.0000462,0.0 000653,0.1541494,-0.0001627,-0.0000098,-0.0000071,-0.1120859 Thank you. Orlin From owner-chemistry@ccl.net Thu Mar 16 10:29:00 2006 From: "Satyan Sharma satyan,,sun3.oulu.fi" To: CCL Subject: CCL:G: ONIOM Convergence Message-Id: <-31216-060316102611-31481-wwp8ngrHlYsoWuc4MhYpEw#%#server.ccl.net> X-Original-From: Satyan Sharma Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Thu, 16 Mar 2006 16:48:49 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Satyan Sharma [satyan^-^sun3.oulu.fi] Dear CCLers, I am tryin to do ONIOM B3lyp/6-31G*:AMBER optimization on a big system with 1000 atoms (of which I have ~70 atoms at QM level). I have seen publications with still bigger systems, so hope that its doable with G03RevC.02. But I am struggling with it for quite a long time. Finally i decided to use treat QM atoms at semi-empirical level(PM3). I could not even optimize my system still. Of the two attempts:- This is part of log file for first attempt.. (the second attempt is with opt=gdiis) 917 8 ********************************************* 918 8 ********************************************* 919 8 ********************************************* 920 1 ********************************************* 921 1 ********************************************* 922 1 ********************************************* 923 1 ***************28202.94280287674071.548165837 924 1 37553.86824524112426.31623619431525.186345436 ------------------------------------------------------------------- Cartesian Forces: Max *************** RMS *************** GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. Internal Forces: Max *************** RMS *************** Search for a local minimum. Step number 22 out of a maximum of 450 All quantities printed in internal units (Hartrees-Bohrs-Radians) Update second derivatives using D2CorX and points 21 22 Trust test= 3.93D+01 RLast= 4.03D-01 DXMaxT set to 5.66D-01 Eigenvalues --- ******************** -5.80276 -3.74622 -2.89928 Eigenvalues --- -2.53683 -1.60960 -1.54036 -1.38470 -0.97739 Second attempt's LOG file Then I tried using opt=gdiis. I get this error 3-point extrapolation. It=200 PL= 0.683D-14 DiagD=T ESCF= 1605.332170 Diff=-0.204D-09 RMSDP= 0.112D-04. """""""""""""UNABLE TO ACHIEVE SELF-CONSISTENCE DELTAE= -0.4700E-08 DELTAP= 0.6832E-14 Error termination via Lnk1e in /v/solaris9/appl/chem/gaussian/G03RevC.02/g03/l402.exe at Thu Mar 16 16:22:58 2006. Job cpu time: 0 days 3 hours 37 minutes 18.5 seconds. File lengths (MBytes): RWF= 105 Int= 0 D2E= 0 Chk= 54 Scr= 1 Segmentation Fault real 57:49.44 user 3:30:00.62 sys 7:18.87 --Any help is appreciated. Eagerly waiting! Satyan From owner-chemistry@ccl.net Thu Mar 16 12:25:00 2006 From: "Loan Huynh huynhkl2000**yahoo.ca" To: CCL Subject: CCL: A review of force fields Message-Id: <-31217-060316120748-6658-xeBoO1irt65AmvfxKl0Zog===server.ccl.net> X-Original-From: Loan Huynh Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-370943907-1142525261=:98273" Date: Thu, 16 Mar 2006 11:07:41 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: Loan Huynh [huynhkl2000{:}yahoo.ca] --0-370943907-1142525261=:98273 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi All, I would like to gain knowlegde on force fields that are recently used for the molecular dynamics. Does anyone know if there is a review on the force field that are populated recently? From my understanding, there is force field that is appropriate for macromolecular (i.e polymer), or force filed for protien, or small molecules ... Many thanks for your suggestions. LH. --0-370943907-1142525261=:98273 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hi All,
 
I would like to gain knowlegde on force fields that are recently used for the molecular dynamics.  Does anyone know if there is a review on the force field that are populated recently?  From my understanding, there is force field that is appropriate for macromolecular (i.e polymer), or force filed for protien, or small molecules ...   
Many thanks for your suggestions.
 
LH.

 
--0-370943907-1142525261=:98273-- From owner-chemistry@ccl.net Thu Mar 16 13:08:00 2006 From: "Sengen Sun sengensun()yahoo.com" To: CCL Subject: CCL: ORGLIST: A breakthrough in mechanism of concerted Message-Id: <-31218-060316125809-2007-6Rw5uW0NhbZK4J0M7JDS4g*server.ccl.net> X-Original-From: Sengen Sun Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 16 Mar 2006 09:58:04 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Sengen Sun [sengensun=yahoo.com] --- Sengen Sun wrote: > Date: Thu, 16 Mar 2006 09:40:46 -0800 (PST) > From: Sengen Sun > Subject: Fwd: Re: ORGLIST: A breakthrough in > mechanism of concerted > To: everybody]~[orglist.net > > So far, I have received unexpectedly 23 requests. It > is overwhelming to me. I like it. Please! I will > honor > every request as this article is in a chemistry > journal that is not common for organic chemists. I > will also forward this e-mail to CCL and see any > interest there. > > Thanks, thanks.... > > Regards to all, > > Sengen > > --- George.Caraman]~[unibas.ch wrote: > > > Date: Thu, 16 Mar 2006 10:22:24 +0100 > > From: George.Caraman]~[unibas.ch > > To: Sengen Sun > > Subject: Re: ORGLIST: A breakthrough in mechanism > of > > concerted > > > > Hi Sengen, > > > > > remember, Hoffmann once wrote in a journal an > > article > > > (or maybe a poem) with EXCUSIVELY metaphors > except > > the > > > title on Theoretical Chemistry. If any one is > > > interested in that, I can try to find it and > send > > it > > > to you upon request by e-mail. > > > it would be very nice indeed to see this article. > If > you find it, plese send it > to me as well, I suppose there'll be lots of > people > willing to see it. > > regards, > george > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Thu Mar 16 16:40:00 2006 From: "Ojwang, J.G.O. j.g.o.ojwang-.-tue.nl" To: CCL Subject: CCL: A review of force fields Message-Id: <-31219-060316102611-12345-lgz7wN/Ir5jVnLIpSYDduw]=[server.ccl.net> X-Original-From: "Ojwang, J.G.O." Date: Thu, 16 Mar 2006 20:06:32 +0100 MIME-Version: 1.0 Sent to CCL by: "Ojwang, J.G.O." [j.g.o.ojwang**tue.nl] [the binary winmail.dat attachment removed by CCL admin] Good question! I'm also curious about the same especially in cases where you have ionic or mixed ionic-covalent interactions. Regards to all. Ojwang' JGO Eindhoven University of Technology. -----Original Message----- From: Loan Huynh huynhkl2000**yahoo.ca [mailto:owner-chemistry^^^ccl.net] Sent: Thu 3/16/2006 6:35 PM To: Ojwang, J.G.O. Cc: Subject: CCL: A review of force fields Sent to CCL by: Loan Huynh [huynhkl2000{:}yahoo.ca] Hi All, I would like to gain knowlegde on force fields that are recently used for the molecular dynamics. Does anyone know if there is a review on the force field that are populated recently? From my understanding, there is force field that is appropriate for macromolecular (i.e = polymer), or force filed for protien, or small molecules ... Many thanks for your suggestions.0 LH. From owner-chemistry@ccl.net Thu Mar 16 17:27:00 2006 From: "luis simon luissimonrubio|*|hotmail.com" To: CCL Subject: CCL:G: Projected frequencies Message-Id: <-31220-060316172300-12927-Zic/xRvRePuQ/9d2H0ezFA a server.ccl.net> X-Original-From: "luis simon" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 16 Mar 2006 23:23:19 +0100 MIME-Version: 1.0 Sent to CCL by: "luis simon" [luissimonrubio###hotmail.com] Few days ago I posted a similar question, so maybe it is not such an unusual question (please take a look at March 13th messages). I got some interesting answers. The most promising in gaussian was to include "-1" on frozen atoms when the molecule is specified by the cartesian coordinates. Although it worked, gaussian calculated the full hessian matrix, so it still requires a lot of time. Nevertheless, I guess taht the results would be probably valid, as this hessian is calculated on a real stationary point on the subspace of the not frozen coordinates. I think that you would make a similar work if you write a script to read the hessian matrix (in cartesian coordinates) and then set to 0.0 all those elements concerning derivatives of the position of the frozen atoms, but using the "-1" trick allows you to obtain a .chk file that could be helpful for further thermochemistry and vibrational analysis (you can also write the algorithms to diagonalize the hessian, but there is no need if you can use those implemented in gaussian). Nevertheless, the ideal solution would be that the program really skip the calculation of those derivatives. Maybe it is not possible with gaussian if it uses internal coordinates to build the hessian, but I have observed that even if you specify gaussian to work with numerical derivatives, it calculates second derivatives concerning "-1" tagged atoms. I hope that you receive more useful answer as it will probably be useful to many other people. Regards: Luis ----- Original Message ----- > From: "Ramon Crehuet rcsqtc[a]iiqab.csic.es" To: "Simón, Luis Manuel " Sent: Thursday, March 16, 2006 2:42 PM Subject: CCL:G: Projected frequencies > Sent to CCL by: "Ramon Crehuet" [rcsqtc()iiqab.csic.es] > Dear CCLers, > I have a relatively large system where I keep some (external) atoms fixed. After doing an optimisation I want to check that I have a minimum or a TS candidate. So I would like to do a frequency calculation on the free atoms. I think that makes sense from a theoretical point of view. So I do not want to calculate the second derivative with respect to fixed atoms coordinates, although they have to be there for the other derivatives to make sense. Otherwise, I could get the full hessian and project it. > I was using gaussian and don't know how to do it with this software. Is is possible? Is is possible with GAMESS-US (which I use regularly)? Is it possible with any other software (that can also do DFT and ONIOM)? > And last, but not least... am I asking something very unusual? > Thanks in advance, > Ramon> > > > From owner-chemistry@ccl.net Thu Mar 16 20:49:00 2006 From: "Carlos Nunez carlos_javierna*o*yahoo.com" To: CCL Subject: CCL: A review of force fields Message-Id: <-31221-060316170951-8827-oi5U55ZMI6MpbsYRzXcN3w(~)server.ccl.net> X-Original-From: "Carlos Nunez" Date: Thu, 16 Mar 2006 17:09:50 -0500 Sent to CCL by: "Carlos Nunez" [carlos_javierna{:}yahoo.com] Hi, See this: MacKerell A. D. Jr. 2004. Empirical force fields for biological macromolecules: overview and issues. J. Comput. Chem. 25: 1584-1604. Hasta la proxima vez, Carlos N.