From owner-chemistry@ccl.net Mon Apr 11 04:21:01 2011 From: "Toomas Tamm tt-ccl2,+,yki.ttu.ee" To: CCL Subject: CCL:G: Conformational analysis Message-Id: <-44342-110411040328-1125-9sxhNOOSFntxXFkx8o6SaA(0)server.ccl.net> X-Original-From: Toomas Tamm Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Mon, 11 Apr 2011 11:03:18 +0300 Mime-Version: 1.0 Sent to CCL by: Toomas Tamm [tt-ccl2,yki.ttu.ee] On Sun, 2011-04-10 at 22:24 +0200, Arne Dieckmann adieckma]*[googlemail.com wrote: > Sent to CCL by: Arne Dieckmann [adieckma!^!googlemail.com] > Dear Gary, > > thanks a lot for your answer, but I do not think this is going to help here. I am looking for a program that is able to generate the desired structures to help me set up an automatized work flow. Is there no free/open tool out there that is able to perform a conformational analysis on small molecule hydrogen-bonded complexes? > If the molecules are not too large, you can also build a Z-matrix by hand, and vary one or several variables, such as dihedral angles, to generate the conformers. The Gaussian software will do the stepping automatically; but it may be wiser in the long run to use some scripting language (we have used /bin/sh + sed) to generate the necessary inputs in a loop, then submit these to computation individually. -- Toomas Tamm e-mail: tt-ccl2 (at) kky . ttu . ee Chair of Inorganic Chemistry voice: INT+372-620-2810 Tallinn University of Technology fax: INT+372-620-2828 Ehitajate tee 5, EE-19086 Tallinn, Estonia http://www.kk.ttu.ee/toomas/ From owner-chemistry@ccl.net Mon Apr 11 05:07:01 2011 From: "Arne Dieckmann adieckma(a)googlemail.com" To: CCL Subject: CCL:G: Conformational analysis Message-Id: <-44343-110411050553-11641-fMM5ZM31vH7bY/eL2tW0qA ~ server.ccl.net> X-Original-From: Arne Dieckmann Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Mon, 11 Apr 2011 11:05:11 +0200 MIME-Version: 1.0 Sent to CCL by: Arne Dieckmann [adieckma(-)googlemail.com] Thanks, that would be an option. However, I was just wondering if there is something like obconf/confab/dg-ammos/frog2/... that would handle hydrogen bonds properly. ----------------------- Dr. Arne Dieckmann Bioorganic Chemistry (Room: NC 2/125) Ruhr-University Bochum Universitätsstraße 150 44780 Bochum, Germany phone: +49 234 3224216 email: adieckma##googlemail.com http://www.ruhr-uni-bochum.de/oc1/mitarbeiter/Arne-Dieckmann.html On Monday, April 11, 2011 at 10:03 AM, Toomas Tamm tt-ccl2,+,yki.ttu.ee wrote: > > Sent to CCL by: Toomas Tamm [tt-ccl2,yki.ttu.ee] > On Sun, 2011-04-10 at 22:24 +0200, Arne Dieckmann > adieckma]*[googlemail.com wrote: > > Sent to CCL by: Arne Dieckmann [adieckma!^!googlemail.com] > > Dear Gary, > > > > thanks a lot for your answer, but I do not think this is going to help here. I am looking for a program that is able to generate the desired structures to help me set up an automatized work flow. Is there no free/open tool out there that is able to perform a conformational analysis on small molecule hydrogen-bonded complexes? > > If the molecules are not too large, you can also build a Z-matrix by > hand, and vary one or several variables, such as dihedral angles, to > generate the conformers. The Gaussian software will do the stepping > automatically; but it may be wiser in the long run to use some scripting > language (we have used /bin/sh + sed) to generate the necessary inputs > in a loop, then submit these to computation individually. > > -- > Toomas Tamm e-mail: tt-ccl2 (at) kky . ttu . ee > Chair of Inorganic Chemistry voice: INT+372-620-2810 > Tallinn University of Technology fax: INT+372-620-2828 > Ehitajate tee 5, EE-19086 Tallinn, Estonia http://www.kk.ttu.ee/toomas/> From owner-chemistry@ccl.net Mon Apr 11 08:52:01 2011 From: "angeline vedha anna.vedha/./gmail.com" To: CCL Subject: CCL: Computational Chemistry Message-Id: <-44344-110411015933-20320-9sxhNOOSFntxXFkx8o6SaA^_^server.ccl.net> X-Original-From: "angeline vedha" Date: Mon, 11 Apr 2011 01:59:31 -0400 Sent to CCL by: "angeline vedha" [anna.vedha-*-gmail.com] Iam a beginner in AIM2000.While i know to get the Molecular graph and other things using it , icouldnt get the Virial graph. Do any one know this ? pl. help me. From owner-chemistry@ccl.net Mon Apr 11 10:45:00 2011 From: "Geoffrey Hutchison geoffh- -pitt.edu" To: CCL Subject: CCL: Conformational analysis Message-Id: <-44345-110411100650-8929-XxWg+v3RceloXUtyP6Yk3g(~)server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=us-ascii Date: Mon, 11 Apr 2011 10:06:21 -0400 MIME-version: 1.0 (Apple Message framework v1084) Sent to CCL by: Geoffrey Hutchison [geoffh{:}pitt.edu] > Thanks, that would be an option. However, I was just wondering if there is something like obconf/confab/dg-ammos/frog2/... that would handle hydrogen bonds properly. Remember that most open source chemistry packages are developed to solve particular problems for their developers. Most of these are to solve the internal molecular conformation problem, so they identify molecular dihedrals and subtract out symmetric and inter-ring degrees of freedom. Your problem is a bit different, since it requires the program to: a) recognize a hydrogen-bonding motif b) determine appropriate rotations / transformations of the fragments c) generate the resulting complexes Obviously, you can code this, but in terms of "getting things done," I'd write a short little Python or other script which generates appropriate z-matrices. Steps (a) and (c) are certainly already solved in tools like obconf/confab, but not step (b). Best regards, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh .. pitt.edu web: http://hutchison.chem.pitt.edu/ From owner-chemistry@ccl.net Mon Apr 11 13:39:01 2011 From: "Sergio Emanuel Galembeck segalemb(a)usp.br" To: CCL Subject: CCL: Conformational analysis Message-Id: <-44346-110411132704-18129-EyKEL0Uy92B9fDZaKfwoew%server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Mon, 11 Apr 2011 14:26:53 -0300 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb*_*usp.br] Dear Anne, Two free softwares that do conformational analysis are: Tinker (http://dasher.wustl.edu/tinker/) and balloon (http://users.abo.fi/mivainio/balloon/). Hope this help you, Sergio Emanuel Galembeck Citando "Arne Dieckmann adieckma]*[googlemail.com" : > > Sent to CCL by: Arne Dieckmann [adieckma!^!googlemail.com] > Dear Gary, > > thanks a lot for your answer, but I do not think this is going to > help here. I am looking for a program that is able to generate the > desired structures to help me set up an automatized work flow. Is > there no free/open tool out there that is able to perform a > conformational analysis on small molecule hydrogen-bonded complexes? > > > Cheers, > Arne > > ----------------------- > Dr. Arne Dieckmann > > Bioorganic Chemistry > (Room: NC 2/125) > Ruhr-University Bochum > Universitätsstraße 150 > 44780 Bochum, Germany > > phone: +49 234 3224216 > email: adieckma * googlemail.com > http://www.ruhr-uni-bochum.de/oc1/mitarbeiter/Arne-Dieckmann.html > On Friday, April 8, 2011 at 3:36 PM, Gary M Battle > battle^^^ccdc.cam.ac.uk wrote: >> >> Sent to CCL by: "Gary M Battle" [battle^_^ccdc.cam.ac.uk] >> Dear Arne, >> >> You can implicitly account for hydrogen bonding by performing >> conformational analyses against experimentally determined small >> molecule structures in the Cambridge Structural Database (CSD). >> >> Containing >540,000 structures the CSD is used routinely to analyse >> conformations and check computationally derived geometries against >> experimentally observed low-energy conformations. >> >> For an excellent paper on use of the CSD System tools for these >> purposes, see: >> K. A. Brameld, B. Kuhn, D.C. Reuter, M. Stahl, J. Chem. Inf. >> Model., 48, 124, 2008. >> >> Regards, >> Gary. >> >> -- >> Gary M Battle >> Cambridge Crystallographic Data Centre >> 12 Union Rd, Cambridge, CB2 1EZ >> Web: http://www.ccdc.cam.ac.uk >> >> >> >> >> >> > "Arne Dieckmann adieckma*|*googlemail.com" wrote: >> > >> > Sent to CCL by: Arne Dieckmann [adieckma]|[googlemail.com] >> > Dear all, >> > >> > I would like to perform a conformational analysis for a number of >> small molecule complexes (bound by hydrogen bonding). However, >> standard tools do not seem to take hydrogen bonding into account >> properly and I am not able to generate any conformers at all. Can >> you recommend a good tool for that? >> > >> > >> > Cheers, >> > Arne >> > >> > >> > ----------------------- >> > Dr. Arne Dieckmann >> > >> > Bioorganic Chemistry >> > (Room: NC 2/125) >> > Ruhr-University Bochum >> > Universittsstrae 150 >> > 44780 Bochum, Germany >> > >> > phone: +49 234 3224216 >> > email: adieckma(-)googlemail.com >> > http://www.ruhr-uni-bochum.de/oc1/mitarbeiter/Arne-Dieckmann.html> > > From owner-chemistry@ccl.net Mon Apr 11 15:33:00 2011 From: "Dr. Xiaofeng (Frank) Duan duanx.ctr**afrl.hpc.mil" To: CCL Subject: CCL: FW: smearing with NWChem Message-Id: <-44347-110411152410-7670-mKI274xTM/GlE+JF9f3mZA!=!server.ccl.net> X-Original-From: "Dr. Xiaofeng (Frank) Duan" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 11 Apr 2011 15:23:52 -0400 MIME-Version: 1.0 Sent to CCL by: "Dr. Xiaofeng (Frank) Duan" [duanx.ctr:afrl.hpc.mil] Dear Phil, I really appreciate your explanations. It will save me a lot of calculations. I learnt much from the discussions of the topic. Thanks, Frank On 04/10/11 16:45, Phil Hasnip phil.hasnip=york.ac.uk wrote: > > Sent to CCL by: Phil Hasnip [phil.hasnip ~ york.ac.uk] > Dear Frank, > >>> all you need are E and E-TS and you can correct it yourself >> As Huub noticed too, the T*S term is zero in all my cases with NWChem. >> Looks like I have to re-run all the calculations. > > No, not at all. If the TS term is zero, then that means that the > smearing you used didn't actually do anything. Why would that be? Well, > imagine you set a smearing of 0.2eV, but the band-gap (or HOMO-LUMO gap > if you prefer) is 3eV. In this case the smearing isn't enough to cause > occupation of the conduction band (LUMO) so you don't actually have any > partial occupancies and the entropy is zero. This in turn means there is > no need for a correction to recover the zero-smearing energy -- the > smearing made no difference so you've already calculated it! It won't > have affected any of the other properties either. > > Yours, > > Phil Hasnip > > ------------------------------------------------------- > Dr Phil Hasnip Email: pjh503*york.ac.uk > Dept of Physics University of York Tel: +44 (0)1904 434624 > York YO10 5DDhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/>