From owner-chemistry@ccl.net Sun Mar 19 12:50:01 2006 From: "Eric M. Bennett benne278 a umn.edu" To: CCL Subject: CCL: A review of force fields Message-Id: <-31240-060318125705-7722-+E5jFbzA4LMyUDcLYZQmjg(_)server.ccl.net> X-Original-From: "Eric M. Bennett" Content-Type: text/plain; charset="us-ascii" ; format="flowed" Date: Sat, 18 Mar 2006 11:07:51 -0600 Mime-Version: 1.0 Sent to CCL by: "Eric M. Bennett" [benne278=umn.edu] Jeffrey L. Nauss wrote: > >I find these references useful for small molecule comparisons. > >Gundertofte et al. J. Comp. Chem. 1996, 17:429-49 >Pettersson & Liljefors Rev. Comp. Chem. 1996, 9:167-90 >Nicklaus, J. Comp. Chem. 1997, 18:1056-60 >Halgren, J. Comp. Chem. 1999, 20:730-748 > >For proteins there is also this reference: > >Price DJ, Brooks CL, III. 2002. Modern protein force fields behave >comparably in molecular dynamics simulations. J Comp Chem 23: 1045 Another good paper is Beachy et al, JACS 1997, 119, 5908-5920 -- Eric Bennett Center for Drug Design, University of Minnesota http://www.cdd.umn.edu From owner-chemistry@ccl.net Sun Mar 19 18:24:00 2006 From: "Christian Pilger christian.pilger===gmx.net" To: CCL Subject: CCL: alignment of dipole moments Message-Id: <-31241-060319094819-9224-QMI+zUiA/P/SfMUQD4Z+tw+*+server.ccl.net> X-Original-From: "Christian Pilger" Date: Sun, 19 Mar 2006 09:48:15 -0500 Sent to CCL by: "Christian Pilger" [christian.pilger\a/gmx.net] Dear CCLers, > from QM calculations (Turbomole/DFT) on a set of heterocyclic compounds I obtained the dipole moment for each molecule. In order to be able to easily compare the structures, I wish to orientate all molecules according to their dipole moments. For a small set I displayed the dipole moments within my modelling software together with the structures. "By hand" I then aligned dipole moments with the x-axis of a cartesian coordinate system by rotating and translating the individual molecules and stored the new coordinates. However, this procedure is impracticable for the complete set of compunds (several hundreds). Hence I need a procedure to do this automatically. I ask for your input: has anybody come across this problem ? Is there (commercial) software available for this purpose ? Or can you provide me with a recipe how to do this in a semi-automatic way ? I have access to SYBYL, Insight, Cerius etc. Best regards, Christian