From owner-chemistry@ccl.net Thu Oct 1 04:26:01 2009 From: "Georg Lefkidis lefkidis-.-physik.uni-kl.de" To: CCL Subject: CCL:G: SAC-CI: density matrix Message-Id: <-40386-091001041059-28789-38Pe7fmOgiRS0g/8Q3xFcw#server.ccl.net> X-Original-From: "Georg Lefkidis" Content-Language: de Content-Type: multipart/alternative; boundary="----=_NextPart_000_000A_01CA427B.24281E20" Date: Thu, 1 Oct 2009 09:39:58 +0200 MIME-Version: 1.0 Sent to CCL by: "Georg Lefkidis" [lefkidis : physik.uni-kl.de] This is a multi-part message in MIME format. ------=_NextPart_000_000A_01CA427B.24281E20 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hello everyone, I have been wondering whether it is possible to extract the density matrix out of the SAC-CI states. The keyword e.g. SINGLE=(NSTATES=(2,2,2,2),DENSITY) in Gaussian combined with ALLPROPERTIES does Mulliken analysis and does not print the density matrix D, but the population matrix instead P. Does anyone know of a method to extract the density matrix? Best regards George ------------------------------------------------------------------- Dr. Georg Lefkidis Dept. of Physics University of Kaiserslautern PO Box 3049 67653 Kaiserslautern e-mail: lefkidis(at)physik(dot)uni(dash)kl(dot)de Tel.: +49 631 205 3207 ------------------------------------------------------------------- ------=_NextPart_000_000A_01CA427B.24281E20 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hello everyone,

I have been wondering whether it = is possible to extract the density matrix out of the SAC-CI states. The keyword e.g. = SINGLE=3D(NSTATES=3D(2,2,2,2),DENSITY) in Gaussian combined with ALLPROPERTIES does Mulliken analysis and does = not print the density matrix D, but the population matrix instead P. =

Does anyone know of a method to = extract the density matrix?

Best = regards

George

------------------------------------------------------------= -------

Dr. Georg = Lefkidis

Dept. of = Physics

University of = Kaiserslautern

PO Box = 3049

67653 Kaiserslautern

e-mail: = lefkidis(at)physik(dot)uni(dash)kl(dot)de

Tel.: +49 631 205 3207

-------------------------------------------------------= ------------

------=_NextPart_000_000A_01CA427B.24281E20-- From owner-chemistry@ccl.net Thu Oct 1 05:00:01 2009 From: "Carsten Detering detering=biosolveit.de" To: CCL Subject: CCL: Drug design book Message-Id: <-40387-091001045758-11828-kBcj5DeJaf8KcqDlvBZjuQ+*+server.ccl.net> X-Original-From: "Carsten Detering" Date: Thu, 1 Oct 2009 04:57:54 -0400 Sent to CCL by: "Carsten Detering" [detering:_:biosolveit.de] Hi Werner, if you have command of the German language, I highly recommend the new edition of "Wirkstoffdesign" by G. Klebe et al. (2nd Edition) To me, this is clearly the best introduction to the field of drug discovery, with excellent references for further reading, and actually quite entertaining. Unfortunately, there is no english translation (yet). Hope this helps. Cheers Carsten __________________________________________________________________ Dr. Carsten Detering; Appl. Scientist detering###biosolveit.com Phone EU: +49-2241-2525-0 / Fax: -525 www.biosolveit.com Phone US: +1-617-297-2770 BioSolveIT GmbH - An der Ziegelei 79 - 53757 St.Augustin - Germany Geschftsfhrer Dr. Christian Lemmen Amtsgericht Siegburg HRB 6261 > Sent to CCL by: "Werner K" [werner.schroedinger_._googlemail.com] > Hi, > > I am looking for a good reference book or web source of information for Drug Design. With this I mean, once I use software for virtual screening, how to be able to understand the interactions betweem the ligand and the protein, and how to determine or undersatnd what would be the modifications that would lead to drugs or better ligands. > > Thanks > > From owner-chemistry@ccl.net Thu Oct 1 05:39:00 2009 From: "Chris Swain swain(-)mac.com" To: CCL Subject: CCL: Drug design book Message-Id: <-40388-091001051942-15619-Q/fVjLAIDRh+8aASj8CpcQ]![server.ccl.net> X-Original-From: Chris Swain Content-transfer-encoding: 7BIT Content-type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Thu, 01 Oct 2009 10:19:27 +0100 MIME-version: 1.0 Sent to CCL by: Chris Swain [swain:mac.com] Hi, Forgive the self publicity, I'm a tutor at the RSC biannual Medicinal Chemistry School and we have thought about creating a book based on the course but it is not a high priority. In the meantime I've started to put the information on my website http://homepage.mac.com/swain/CMC/DDResources/DDR.html It is very much a work in progress and I'd certainly appreciate suggestions/comments, in the longer term I can't help but feel the area of science is changing such that a book only represents a snapshot in time and that a website might be easier to keep up to date? Cheers, Chris On 30 Sep 2009, at 22:40, Soaring Bear soaringbear[-]yahoo.com wrote: > > Sent to CCL by: Soaring Bear [soaringbear,,yahoo.com] > Richard Silverman > The Organic Chemistry of Drug Design and Drug Action > > > Soaring Bear Ph.D. Pharmacology soaringbear at yahoo.com > http://soaringbear.com/nature/WeedsforNeeds.html > http://www.nlm.nih.gov/mesh/presentations/bear_2005_aug/index.htm > author of http://HerbMed.org & http://HerbInsight.com > > > --- On Wed, 9/30/09, Werner K werner.schroedinger(~)googlemail.com > wrote: > >> I am looking for a good reference book or web source of >> information for Drug Design. With this I mean, once I use >> software for virtual screening, how to be able to understand >> the interactions betweem the ligand and the protein, and how >> to determine or undersatnd what would be the modifications >> that would lead to drugs or better ligands. > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/> > From owner-chemistry@ccl.net Thu Oct 1 11:37:00 2009 From: "Jens Spanget-Larsen spanget^ruc.dk" To: CCL Subject: CCL:G: SelectAnharmonicModes Message-Id: <-40389-091001113548-28742-jbak9LPGpz8SBICWNxwoyQ=server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Thu, 01 Oct 2009 17:35:32 +0200 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget++ruc.dk] Dear CCL! Anybody tried to use the option "SelectAnharmonicModes" in a frequency calculation with Gaussian09? I have run several trial calculations on a water molecule with specification of the mode to treat in the anharmonic calculation, but I cannot make it work. No matter how I specify the mode, I allways get all three modes. Any hints? Yours, Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget|*|ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ From owner-chemistry@ccl.net Thu Oct 1 14:27:01 2009 From: "Rahim Ghadari r_ghadari_k ~ yahoo.com" To: CCL Subject: CCL: IRC calculations can not converge???? Message-Id: <-40390-091001125639-30708-/5skQuMtzqQRhsvn7AvhcQ**server.ccl.net> X-Original-From: "Rahim Ghadari" Date: Thu, 1 Oct 2009 12:56:36 -0400 Sent to CCL by: "Rahim Ghadari" [r_ghadari_k-x-yahoo.com] Hi I'm trying to use IRC calculation.But after 15 steps it can not converge. I used the maxcycle=1000, but it didn't help me. May using "tight" or "stepsize" keywords help me or no??? Thank you in advance for your help Rahim Ghadari r_ghadari_k|-|yahoo.com From owner-chemistry@ccl.net Thu Oct 1 15:02:01 2009 From: "Ciaran Murray ciaran.a.murray%nuim.ie" To: CCL Subject: CCL:G: Adding extra diffuse functions to Pople basis sets Message-Id: <-40391-091001121625-16236-IzrrMKdTDfXTv5SN35uc8A-x-server.ccl.net> X-Original-From: "Ciaran Murray" Date: Thu, 1 Oct 2009 12:16:21 -0400 Sent to CCL by: "Ciaran Murray" [ciaran.a.murray]~[nuim.ie] Hi all, I'm trying to improve some excited state calculations using Gaussian 03 and was hoping add more diffuse coefficients to the standard 6-311++G(d,p) basis set (i.e. 6-311(2+,+)G(d,p), 6-311(2+,2+)G(d,p) etc) for C, N and H. Unfortunately I can't get access to the papers I think these functions are described in- M.J. Frisch, J.A. Pople, and J.S. Binkley, J. Chem. Phys. 80, 3265 1984 and T. Clark, J. Chandrasekhar, and P.V.R. Schleyer, J. Comput. Chem. 4, 294 1983. Does anyone know anywhere else where I can get the relevant coefficients or full basis sets? Or has anyone seen another more recent paper describing these basis sets? Yours Sincerely, Ciarn A. Murray Department of Chemistry, NUI Maynooth, Maynooth, Co. Kildare, Rep. Of Ireland. E-mail: ciaran.a.murray(-at-)nuim.ie