From owner-chemistry@ccl.net Thu Sep 7 02:39:00 2006 From: "David A. Case case-$-scripps.edu" To: CCL Subject: CCL: umbrella sampling using amber 8/9 Message-Id: <-32499-060906121412-4986-vOf0L9Gpg7jf8YS+wOtYYw%server.ccl.net> X-Original-From: "David A. Case" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 6 Sep 2006 08:38:00 -0700 Mime-Version: 1.0 Sent to CCL by: "David A. Case" [case]*[scripps.edu] On Tue, Sep 05, 2006, Yubo Fan wrote: > > I am trying to analyze the reaction coordinate using umbrella sampling. > What I want to do is to get the free energy along the reaction coordiate > for ammonia transfer in a protein. This method is not very well > documented in Amber's manual. Is there any similar example available? Or > any advice. Thanks in advance. You might get a better reply if you post to the amber mailing list; see http://amber.scripps.edu for information on how to subscribe. (We do ask users to send plain text e-mail.) Have you looked at the example in $AMBERHOME/test/umbrella? This is a short test-case/example that illustrates umbrella sampling. ...good luck....dac From owner-chemistry@ccl.net Thu Sep 7 05:03:01 2006 From: "fuji fuji yamafuji6*yahoo.com" To: CCL Subject: CCL:G: counterpoise and SCRF in g03 Message-Id: <-32500-060907050124-30685-FdeTEabSUI0c6gme4nr9KQ()server.ccl.net> X-Original-From: "fuji fuji" Date: Thu, 7 Sep 2006 05:01:23 -0400 Sent to CCL by: "fuji fuji" [yamafuji6+/-yahoo.com] Dear members, My counterpoise calculation was error terminated with the error message given below : ------------------------------------------------------------------------ Warning! SCF SP cutoffs with diffuse functions may be unreliable. Consider SCF=Tight No SCRF with Counterpoise. Error termination via Lnk1e in /usr/ap/g03/l1.exe at Thu Sep 7 17:06:50 2006. Job cpu time: 0 days 0 hours 0 minutes 3.2 seconds. File lengths (MBytes): RWF= 8 Int= 0 D2E= 0 Chk= 1 Scr= 1 "gag-cp.log" 95L, 4354C ------------------------------------------------------------------------- 1) can you please comment on the SCF SP cutoffs with diffuse functions? 2) SCRF is not possible with the Counterpoise calculations? Is there no effect of solvent on BSSE? I think sovent doesn't have any effect on the basis function (it all depends on the number of atoms and the basis set which we use) and perhapbs on BSSE, rite? Please give me ur comments and suggest me useful readings.. thanks in advance Best Regards.. From owner-chemistry@ccl.net Thu Sep 7 08:32:00 2006 From: "John McKelvey jmmckel::attglobal.net" To: CCL Subject: CCL:G: DFT Symposium next week: " DFTB: An Approximate DFT Method" Message-Id: <-32501-060907082605-11095-FghTnz87uRThZEpb/aHNEA[#]server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 07 Sep 2006 08:22:38 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel . attglobal.net] Folks, Next Monday-Wednesday there will be 38 talks and 4 posters in a COMP Divisioon Symposium on Density Functional Tight Binding, an approximate DFT method that has computational speed comparable to most popular semiempirical methods and many computed properties that are in good/reasonable agreement with those from "full blown" DFT methods. DFTB has the capability to significantly enhance QM/MM results and has been installed in CHARMM and work is in progress for AMBER. It has also been installed in G03. Release dates for G03 are unknown at this time. This Symposium is sponsored by Elsevier Publishing, Gaussian, Inc, Schrodinger, SemiChem, Proctor and Gamble, and of course the COMP Division of ACS. See you there! Organizers John McKelvey Thomas Frauenheim Marcus Elstner From owner-chemistry@ccl.net Thu Sep 7 10:00:00 2006 From: "Tom Sundius Tom.Sundius{=}helsinki.fi" To: CCL Subject: CCL: Fermi resonance & Vib spectroscopy Message-Id: <-32502-060907094846-14789-BXf4oXJGMLJqud5nvITAFA,server.ccl.net> X-Original-From: Tom Sundius Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 07 Sep 2006 16:48:38 +0300 MIME-Version: 1.0 Sent to CCL by: Tom Sundius [Tom.Sundius~~helsinki.fi] RICHARD JILL WOOD wrote: > As a person with a background (master's degree and 2 more years) in > vibrational absorption and circular dichroism spectroscopy, I can say > that what you say isn't entirely true. There are NO books that "teach" > one how to assign IR bands, to my knowledge. One can look up tables in > books, and get approximate ranges of bands, but to actually USE a book > to do assignments, no. When I was a grad student, I would ask my > advisor (I was working with tetrasubstituted biphenyls) about band > assignments, and he'd look at me like I was a nut expecting him to know > how to assign them. I needed to know band assignments because I was > calculating band strengths (R and D) using a DCO model. > > Richard > Richard Wood is quite right: you cannot learn everything about vibrational assignment from a book (although to start with, it can be good). Nowadays frequency assignments are often checked by ab initio or DFT calculations. As is well known, B3LYP frequencies (although harmonic) are (often) rather close to experimental frequencies, so it is not always necessary to perform scaling (although a proper force field scaling can give much better agreement). The calculated band intensities are also helpful in the assignment, although Raman activities are much less accurate than infrared intensities. The quantum chemical frequency calculations should also be complemented by PED calculations, since the normal modes are often mixtures of simple internal modes. Assignment is not easy! -- Tom Sundius University of Helsinki, Dept of Physical Sciences phone +358-9-191 50672 P.O.Box 64, FIN-00014 Helsinki, Finland fax +358-9-191 50610 +++ for we know in part, and we prophesy in part +++ From owner-chemistry@ccl.net Thu Sep 7 10:47:01 2006 From: "Tamas Gunda tgunda2005(!)puma.unideb.hu" To: CCL Subject: CCL: Sterimol software Message-Id: <-32503-060906034144-2550-kQuAVBhHjzPHAN4rNpgCoQ::server.ccl.net> X-Original-From: "Tamas Gunda" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Wed, 6 Sep 2006 08:40:37 +0200 MIME-Version: 1.0 Sent to CCL by: "Tamas Gunda" [tgunda2005]-[puma.unideb.hu] Sterimol can be used even today with some cautions for characterizing the shape of a molecule or substituent (mainly in the case of rigid substituents). Sterimol is implemented to and available in the program Mol2mol : http://web.interware.hu/frenzy/mol2mol/index.html Prof. Tamas E. Gunda University of Debrecen Department of Pharmaceutical Chemistry H-4010 Debrecen, POB 36, Hungary tgunda2005 [at] puma.unideb.hu ----- Original Message ----- > From: "Rick Venable rvenable]=[pollux.cber.nih.gov" To: "Gunda, Tamas E " Sent: Tuesday, September 05, 2006 22:54 PM Subject: CCL: Sterimol software > Sent to CCL by: Rick Venable [rvenable__pollux.cber.nih.gov] > On Tue, 5 Sep 2006, Catherine Hayes catherine.hayes=-=nuigalway.ie wrote: >> Sorry for this probably basic question, but I've read an oldish paper >> (1986) which mentions using the STERIMOL software. Is this still >> available, or is there an alternative that people could possibly >> suggest using? > > STERIMOL appears to be a group of shape based QSAR descriptors > introduced by Verloop which a number of programs can compute, such as > ChemDraw, as well as a QCPE offering. > > ------------------------------------- > Rick Venable 29/500 > Membrane Biophysics Section > NIH/NHLBI Lab. of Comp. Biology > Bethesda, MD 20892-8014 U.S.A. > (301) 496-1905 Rick_Venable AT nih*gov > ALT email: rvenable AT speakeasy*org > -------------------------------------> > > From owner-chemistry@ccl.net Thu Sep 7 11:21:01 2006 From: "rajesh c rajesh_chinagandham%rediffmail.com" To: CCL Subject: CCL: challenging problems in comp. chem Message-Id: <-32504-060907105545-27159-HGhDA9FU0WDpUE+4hnELzg__server.ccl.net> X-Original-From: "rajesh c" Date: Thu, 7 Sep 2006 10:55:44 -0400 Sent to CCL by: "rajesh c" [rajesh_chinagandham,+,rediffmail.com] hi people.. Is there any place where open computational research problems r posted .. for example : search for stable neutral planar tetra co-ordinate carbon systems is hot .. so something like these ... well.. journals r always there .. but still some problems which r eluding the mortals if posted (like open problems in mathematics) should be of help for younger peole to take up intersting and challenging problems... thanx in advance... rajesh From owner-chemistry@ccl.net Thu Sep 7 16:52:00 2006 From: "Rachel Crespo Otero rachel]=[fq.uh.cu" To: CCL Subject: CCL: molecular units in NBO Message-Id: <-32505-060907164723-17151-1UidyRA/sBPQoQmJHSzGeA/a\server.ccl.net> X-Original-From: Rachel Crespo Otero Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Thu, 7 Sep 2006 16:41:10 -0400 (CDT) MIME-Version: 1.0 Sent to CCL by: Rachel Crespo Otero [rachel * fq.uh.cu] Dear CCL members I had calculated a simple molecule and NBO detects that the system has 3 molecular units. Which is the criteria that NBO uses for detect different molecular units? Best regards Rachel From owner-chemistry@ccl.net Thu Sep 7 20:02:01 2006 From: "Guosheng Wu wu_guosheng2002===yahoo.com" To: CCL Subject: CCL: sp2 or sp3 for the single-bonded ester oxygen atom Message-Id: <-32506-060907193514-7494-guIQ21pWCzveboQljYID1A a server.ccl.net> X-Original-From: Guosheng Wu Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 7 Sep 2006 15:35:08 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Guosheng Wu [wu_guosheng2002]^[yahoo.com] Hi there, For the first O atom in ester like CH3OC(=O)CH3, what kind of hybrid state we should assign? Certainly it's within the context of molecular mechanics, although I tried a little QM study with electrostatic potential and electron density calculation, and did not get a clue. (Any QM expert can help me on it ?) I looked up the literature or the web(google), but all I can find out for this problem is that it has been called sp3 at many occasions. One paper (Kresimir Molcanov et al, Acta Crys. B, 2004, B60, 424) and some force fields (CVFF, AMBER,...) explicitly call/type it as sp3. However, that conflicts my chemistry intuition, since 2 electrons of that O should form so-called p-pi conjugation with C=O, so it should be in sp2 hybrid state. That also explains the coplanar structure of ester or simple organic acids. Like the paper mentioned above, I did some CSD search for that O as H-bond acceptor, there are only ~200 hits (dependent on parameter such as resolution, bond length etc), so it's certainly not much statistically meaningful, but still what I found out is that most of the O..H-X (X=O or N) H-bonds are more or less in the same plane of the ester. So shall we call it sp2 oxygen in the future when we talk about molecular mechanics, and apply this concept in any related study? I find this an interesting study, and hope to receive your insights, especially those who work in QM areas. Thanks for your attention, -Guosheng __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com