From owner-chemistry@ccl.net Wed Apr 29 01:59:00 2009 From: "vadicherla tati reddy tatireddy.vadicherla ~~ gmail.com" To: CCL Subject: CCL: Any Freely avaliable NaturalProduct Database for Download Message-Id: <-39193-090429012843-29945-NjblqZL+k7zjQU36+ZF/sA%x%server.ccl.net> X-Original-From: vadicherla tati reddy Content-Type: multipart/alternative; boundary=001636283b0a636c990468aad9dc Date: Wed, 29 Apr 2009 10:58:27 +0530 MIME-Version: 1.0 Sent to CCL by: vadicherla tati reddy [tatireddy.vadicherla**gmail.com] --001636283b0a636c990468aad9dc Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Thanks a lot.............. On Tue, Apr 28, 2009 at 11:07 PM, Abdul Hameed, MohamedDiwanMo mabdu3*_* email.uky.edu wrote: > Hi, > > > > Check in ZINC database subsets: > > > > http://zinc.docking.org/vendor0/ > > > > =91ZINC natural product=92 is the name of the subset. > > > > Cheers, > > Mohamed Diwan > > College of Pharmacy > > University of Kentucky. > ------------------------------ > > *From:* owner-chemistry+mabdu3=3D=3Demail.uky.edu#,#ccl.net[mailto: > owner-chemistry+mabdu3 =3D=3Demail.uky.edu#,#cc= l.net] > *On Behalf Of *vadicherla tati reddy tatireddy.vadicherla^-^gmail.com > *Sent:* Tuesday, April 28, 2009 5:29 AM > *To:* Abdul Hameed, MohamedDiwanMo > *Subject:* CCL: Any Freely avaliable NaturalProduct Database for Download > > > > Hi All, > > > > Is there any Freely avaliable Natural Product database in ( sdf,mol,smi > )format for download... if yes can u plz mail me the link.... > > > > > > > > > > Thanks > > TatiReddy > --001636283b0a636c990468aad9dc Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Thanks a lot..............

On Tue, Apr 28, 2009 at 11:07 PM, Abdul Hameed, = MohamedDiwanMo mabdu3*_*email.uky.edu = <owner-chem= istry:_:ccl.net> wrote:

Hi,

=A0

Check in ZINC databas= e subsets:

=A0

http://zinc.docking.org/vendor0/<= /a>

=A0

=91ZINC natural produ= ct=92 is the name of the subset.

=A0

Cheers,=

Mohamed Diwan<= /font>

College of Pharmacy

University of Kentuck= y.

From:<= font face=3D"Tahoma" size=3D"2"> owner-chemistry+mabdu3=3D=3Demail.uky.edu#,#ccl.net [mai= lto:owner-che= mistry+mabdu3=3D=3Demail.uky.edu#,#ccl.net] On Behalf Of vadicherla tati reddy tatireddy.vadicherla^-^gmail.com
Sent: Tuesday, April 28, 20= 09 5:29 AM
To: Abdul Ham= eed, MohamedDiwanMo
Subject:= CCL: Any Freely avaliable NaturalProduct Database for Download<= /font>

=A0

Hi All,

=A0

Is there any=A0Freely avaliable Natural Product database i= n ( sdf,mol,smi )format for download... if yes can u plz=A0mail me the link= ....

=A0

=A0

=A0

=A0

Thanks

TatiReddy=A0


--001636283b0a636c990468aad9dc-- From owner-chemistry@ccl.net Wed Apr 29 03:45:01 2009 From: "Uwe Huniar uwe.huniar- -cosmologic.de" To: CCL Subject: CCL: Kindly solve my Turbomol problem Message-Id: <-39194-090428163227-29922-995VNH2IwKtpkFCtZ9G9Zw_._server.ccl.net> X-Original-From: Uwe Huniar Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 28 Apr 2009 21:37:16 +0200 MIME-Version: 1.0 Sent to CCL by: Uwe Huniar [uwe.huniar^^^cosmologic.de] Hello, first of all, such technical problems should be addressed directly to the Turbomole support. Most problems with larger calculations come from user limits, namely too low stack size (check ulimit -a if you run bash/sh/ksh or limit for csh/tcsh). Getting no error message from the Turbomole program itself also is an indication that the job has been killed by the system, so you could check /var/log/messages if there have been any problems with the memory. See also FAQs http://www.turbo-forum.com/index.php?topic=23.0 or http://www.cosmologic.de/index.php?cosId=3026&crId=3#a4 By the way, we nowadays recommend to use the ricc2 module of Turbomole to do RI-MP2 calculations (standard or spin-scaled). It is the direct successor of rimp2, faster, much more functionality and parallelized. Regards, Uwe Narayan Chandra Bera ncbera05%a%gmail.com schrieb: > Dear Sir, I am a turbomol user, I am doing single point energy > calculation of a molecule having 43 atoms, its charge is -1 and multiplicity > is 1 at RI-MP2/aug-cc-pVTZ level . To perform this ri-mp2 calculation i did > dscf calculation and all the necessary input through define comment, the > dscf calculation has been performed successfully but problem arises in rimp2 > calculation during calculation, after calculating some steps it stopped > automatically without giving any error massage (please see below, i'm giving > the last few lines). I cant understand whats the problem. Kindly help me. > Waiting for your reply. > > With best regards, > Narayan > > > echeck from tr(Qit) > mp2 energy difference between galoop and gamder=-0.1243449787580D-13 > > ----------------------------------------------------- > prepare right hand side of z-vector equations > ----------------------------------------------------- > > total memory allocated for eval. of r.h.s. of z-vector equation : 51 > MByte > > disc space (kbyte) allocation for 1 2e-integral file(s) : > -------------------------------------------------------- > twoint 0 > -------------------------------------------------------- > > maximum number of buffers which may be written onto 2e-file(s) = 0 > > > 0 2 e - integrals written in 0 blocks requiring 0 > k-byte > > total zprep cpu-time : 4 hours 44 minutes and 58 seconds > total zprep wall-time : 4 hours 45 minutes and 18 seconds > additional memory allocated for solution of z-vector equation : 17 MByte > > ------------------------------------------------- > -CPHF- contribution to MP2-Gradient via Z-vector > ------------------------------------------------- > > Requested convergence is 0.1000000000E-10 RMS > and a residual norm of 0.1000000000E-02 > > Iteration RMS |R| > > 1 0.6245080095E-06 0.2526108240E+00 > 2 0.5572694041E-07 0.7545978248E-01 > 3 0.1043855378E-07 0.3265901752E-01 > 4 0.1252709341E-08 0.1131378984E-01 > 5 0.1215664530E-09 0.3524437567E-02 > 6 0.1871648610E-10 0.1382913790E-02 > rimp2.out lines 777-821/821 (END) > > > > > > -- ------------------------------------------------------------------------------ Dr. Uwe Huniar COSMOlogic GmbH&Co.KG Burscheider Str. 515 D-51381 Leverkusen Germany Tel. +49 - 2171 - 36 36 65 Fax +49 - 2171 - 73 16 89 EMail: uwe.huniar|,|cosmologic.de turbomole|,|cosmologic.de info|,|turbomole.com From owner-chemistry@ccl.net Wed Apr 29 05:19:00 2009 From: "Shuping Huang huangshp]^[fjirsm.ac.cn" To: CCL Subject: CCL: Mp2 calculations on triplet system Message-Id: <-39195-090429050757-25911-3Bgv28Vz/0h018aNY8dyaA*_*server.ccl.net> X-Original-From: "Shuping Huang" Date: Wed, 29 Apr 2009 05:07:54 -0400 Sent to CCL by: "Shuping Huang" [huangshp[A]fjirsm.ac.cn] Dear all, I use MP2 to do single point energy calculations. I find that there is a PMP2-0 energy in the calcultaion of triplet system. The PMP2-0 energy is lower than the MP2 energy. Which one should I adopt? In additon,the results on spin contamination is "S2=2.06155\S2-1 =2.023285\S2A=2.001057". What are the differnces among S2,S2-1,and S2A. Any suggestion or related material would be highly apriciated. From owner-chemistry@ccl.net Wed Apr 29 06:22:00 2009 From: "Truong BaTai truong.batai^chem.kuleuven.be" To: CCL Subject: CCL: European Matster inTheoretical Chemistry and Compt Modelling Message-Id: <-39196-090429061646-5343-SPXJaZBVzN1XrLttnsi47w*_*server.ccl.net> X-Original-From: "Truong BaTai" Date: Wed, 29 Apr 2009 06:16:42 -0400 Sent to CCL by: "Truong BaTai" [truong.batai[]chem.kuleuven.be] Dear CCL I would like to inform all you a summer school in Theoretical Chemistry and Compt Modelling will jointly be organized by University Groningen, The Netherlands and Katholike Universitet Leuven, Belgium from 24 August 2009 to 16 September 2009. If you are interested in this course, please visit website to more detailed information: http://www.chem.kuleuven.be/tccm2009/ From owner-chemistry@ccl.net Wed Apr 29 06:58:00 2009 From: "Sharan sara180681,,gmail.com" To: CCL Subject: CCL: Organic Synthesis and Green chemistry community........ Message-Id: <-39197-090429065614-24731-o8CW68VLV4InJgBD5nYXWg{=}server.ccl.net> X-Original-From: Sharan Content-Type: multipart/alternative; boundary=0016362835a6e16d240468af6c07 Date: Wed, 29 Apr 2009 16:26:02 +0530 MIME-Version: 1.0 Sent to CCL by: Sharan [sara180681[#]gmail.com] --0016362835a6e16d240468af6c07 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear all I would like to share about a community, which is group of expert chemist and biologist with special interest towards organic synthesis and Green Chemistry. Please make use of the community for your benefits. http://elabtool.ning.com/ welcome to see you guys there....... -- SARAVANAN.I Jr. Scientist Chemoinformatics --0016362835a6e16d240468af6c07 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear all=A0

I would like to share about a community, whi= ch is group of expert chemist and biologist with special interest towards o= rganic synthesis and Green Chemistry. Please make use of the community for = your=A0benefits.


welcome to see you guys there...= ....


--
SARAVANAN.I
Jr. Scientist Chem= oinformatics



--0016362835a6e16d240468af6c07-- From owner-chemistry@ccl.net Wed Apr 29 08:02:01 2009 From: "miguel k escobedo kmiguelescobedo/a\yahoo.com" To: CCL Subject: CCL:G: critical points and Density Message-Id: <-39198-090429080034-30763-0VWsJTv4lzsK8bcFsMsvJA- -server.ccl.net> X-Original-From: "miguel k escobedo" Date: Wed, 29 Apr 2009 08:00:30 -0400 Sent to CCL by: "miguel k escobedo" [kmiguelescobedo*|*yahoo.com] Hey CCLers, I need to calculate the density and critical points, can someone give me an example of how to calculate these properties in gaussian. Thank you in advance, Miguel Escobedo From owner-chemistry@ccl.net Wed Apr 29 09:11:00 2009 From: "Sofie Van Damme sofvdamm%a%gmail.com" To: CCL Subject: CCL:G: G03 cubegen density Message-Id: <-39199-090429031000-29118-Vv8/lDI8lg6si7vU9T00wg,+,server.ccl.net> X-Original-From: "Sofie Van Damme" Date: Wed, 29 Apr 2009 03:09:56 -0400 Sent to CCL by: "Sofie Van Damme" [sofvdamm{}gmail.com] Dear CCL-members, Can anybody give me some information about the way the electron density is calculated with the Gaussian03 cubegen density=SCF keyword, especially near the core positions? I tried to calculate the electron density at each of the points given by cubegen, but near the core positions, my electron density is nearly 25 times as big as the electron density given by cubegen. Kind Regards, Sofie Van Damme From owner-chemistry@ccl.net Wed Apr 29 09:47:00 2009 From: "Andreas Klamt klamt*cosmologic.de" To: CCL Subject: CCL:G: critical points and Density Message-Id: <-39200-090429090850-30814-i9RZM/+66KUIOqYenAwodQ{}server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Wed, 29 Apr 2009 15:08:40 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt%cosmologic.de] Dear Miguel, density and critical point data are fluid phase thermodynamics properties, which depend on the electron distribution of the molecule and the statistical termodynamics of the interactions of the molecules in the pure liquid phase of the compound. Gaussian does not have any liquid phase thermodynamics capability. COSMO-RS is the only quantum chemically based method to do fluid phase thermodynamics. Indeead out COSMotherm program (our implementation of COSMO-RS) includes a prediction of the density. There is no prediction of critical properties, yet, but these should be easily achievable from a QSAR based on COSMO-RS descriptors. Indeed, we plan to have these in the next release of COSMOtherm. Unfortunately the link between COSMOtherm and Gaussian has been removed by Gaussian. Hence you need other programs, e.g. TURBOMOLE, to do these calculations. In addition you need our COSMOtherm, which is available for academics at a low price. Best regards Andreas miguel k escobedo kmiguelescobedo/ayahoo.com schrieb: > Sent to CCL by: "miguel k escobedo" [kmiguelescobedo*|*yahoo.com] > Hey CCLers, > > I need to calculate the density and critical points, can someone give me an example of how to calculate these properties in gaussian. > > > > Thank you in advance, > > > > Miguel Escobedo> > > > > -- -------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt|,|cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------- From owner-chemistry@ccl.net Wed Apr 29 10:21:00 2009 From: "Herbert Fruchtl herbert.fruchtl__st-andrews.ac.uk" To: CCL Subject: CCL:G: G03 cubegen density Message-Id: <-39201-090429095331-22037-l++JlVY7kVoIYkNElc2Zww ~~ server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 29 Apr 2009 14:52:47 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl..st-andrews.ac.uk] By default you get the frozen-core density (i.e. only the valence electrons). Use fdensity instead of density to get the full density. HTH, Herbert Sofie Van Damme sofvdamm%a%gmail.com wrote: > Sent to CCL by: "Sofie Van Damme" [sofvdamm{}gmail.com] > Dear CCL-members, > > Can anybody give me some information about the way the electron density is calculated with the Gaussian03 cubegen density=SCF keyword, especially near the core positions? I tried to calculate the electron density at each of the points given by cubegen, but near the core positions, my electron density is nearly 25 times as big as the electron density given by cubegen. > > Kind Regards, > Sofie Van Damme> > -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Wed Apr 29 10:56:00 2009 From: "Nicolas Ferr nicolas.ferre%up.univ-mrs.fr" To: CCL Subject: CCL:G: critical points and Density Message-Id: <-39202-090429102758-15639-OrvLLQS/lI8RGDw/I2r21w[#]server.ccl.net> X-Original-From: "Nicolas Ferr " Date: Wed, 29 Apr 2009 10:27:54 -0400 Sent to CCL by: "Nicolas Ferr " [nicolas.ferre ~ up.univ-mrs.fr] Well, this is one (rather long ... advertisement-based) interpretation of the question. But it could also be understood as a question relative to the use of AIM in gaussian, which is no more available if i remember well. NF Andreas Klamt klamt*cosmologic.de a crit : > > Sent to CCL by: Andreas Klamt [klamt%cosmologic.de] > Dear Miguel, > > density and critical point data are fluid phase thermodynamics properties, which depend on the electron distribution of the molecule and the statistical termodynamics of the interactions of the molecules in the pure liquid phase of the compound. Gaussian does not have any liquid phase thermodynamics capability. > > COSMO-RS is the only quantum chemically based method to do fluid phase thermodynamics. Indeead out COSMotherm program (our implementation of COSMO-RS) includes a prediction of the density. There is no prediction of critical properties, yet, but these should be easily achievable from a QSAR based on COSMO-RS descriptors. Indeed, we plan to have these in the next release of COSMOtherm. > > Unfortunately the link between COSMOtherm and Gaussian has been removed by Gaussian. Hence you need other programs, e.g. TURBOMOLE, to do these calculations. In addition you need our COSMOtherm, which is available for academics at a low price. > > Best regards > > Andreas > > > > > miguel k escobedo kmiguelescobedo/ayahoo.com schrieb: >> Sent to CCL by: "miguel k escobedo" [kmiguelescobedo*|*yahoo.com] >> Hey CCLers, >> >> I need to calculate the density and critical points, can someone give me an example of how to calculate these properties in gaussian. >> >> Thank you in advance, >> >> Miguel Escobedo> >> >> >> >> From owner-chemistry@ccl.net Wed Apr 29 11:31:01 2009 From: "Rzepa, Henry h.rzepa]^[imperial.ac.uk" To: CCL Subject: CCL:G: critical points and Density Message-Id: <-39203-090429101928-9894-8jz0uwivPcI6bYvMDI+YOw/a\server.ccl.net> X-Original-From: "Rzepa, Henry" Content-Type: text/plain; charset="us-ascii" Date: Wed, 29 Apr 2009 15:19:08 +0100 Mime-Version: 1.0 Sent to CCL by: "Rzepa, Henry" [h.rzepa*|*imperial.ac.uk] >Sent to CCL by: "miguel k escobedo" [kmiguelescobedo*|*yahoo.com] >Hey CCLers, > >I need to calculate the density and critical points, can someone give me an example of how to calculate these properties in gaussian. > The Gaussian code is old, and not maintained (this may still be the case in Gaussian 09). Instead, use eg http://aim.tkgristmill.com/ (AIMALL) or the commercial http://www.aim2000.de/ The former is largely text only, the latter more GUI/Visual. They mostly give the same results (but not always, for reasons too complex to note here). Miroslav Kohout has also written a program called DGrid, now at V 4.4 which also does ELF as well as rho(r) density analysis (again command line, not GUI driven). Finally, Paul Popelier has written Morphy; http://morphy.mib.man.ac.uk/ for which a small charge is levied and Bernard Silvi offers Topmod (http://www.lct.jussieu.fr/pagesperso/silvi/clark.html) although this has to be compiled first (i.e. no binaries). These programs take either a .wfn file (Gaussian keyword output=wfn) or the fchk file. One issue with all these programs (I have not tried Morphy in this context) is that none run in parallel mode, and for larger systems (say > 300 basis functions) they can be VERY slow (> 24 hours). From my point of view, a parallelized version running on eg 8-core systems would be a real breakthrough, enabling larger molecules to be analyzed. -- Henry Rzepa. +44 (020) 7594 5774 (Voice); http://www.ch.ic.ac.uk/rzepa/rzepa.xrdf (FOAF) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax). From owner-chemistry@ccl.net Wed Apr 29 12:06:01 2009 From: "Johannes Hachmann jh388++cornell.edu" To: CCL Subject: CCL:G: G03 cubegen density Message-Id: <-39204-090429113909-7783-xt2b6gGambsU7Ol4u7hnwQ**server.ccl.net> X-Original-From: "Johannes Hachmann" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 29 Apr 2009 09:46:18 -0400 MIME-Version: 1.0 Sent to CCL by: "Johannes Hachmann" [jh388|*|cornell.edu] Hi Sofie, if you only use the 'density' keyword, your core electrons are frozen and not considered in the density, so no surprise that your value close to the nucleus is off ;-). Use 'fdensity' instead - but make sure that your grid is sufficiently dense. Best Johannes --------------------------------------------------------------- Johannes Hachmann Chan Research Group 140D Baker Laboratory Department of Chemistry and Chemical Biology Cornell University Ithaca, NY 14853-1301 USA --------------------------------------------------------------- > -----Original Message----- > From: owner-chemistry+jh388==cornell.edu a ccl.net > [mailto:owner-chemistry+jh388==cornell.edu a ccl.net] On Behalf > Of Sofie Van Damme sofvdamm%a%gmail.com > Sent: Wednesday, April 29, 2009 3:10 AM > To: Hachmann, Johannes > Subject: CCL:G: G03 cubegen density > > > Sent to CCL by: "Sofie Van Damme" [sofvdamm{}gmail.com] Dear > CCL-members, > > Can anybody give me some information about the way the > electron density is calculated with the Gaussian03 cubegen > density=SCF keyword, especially near the core positions? I > tried to calculate the electron density at each of the points > given by cubegen, but near the core positions, my electron > density is nearly 25 times as big as the electron density > given by cubegen. > > Kind Regards, > Sofie Van Damme > > > > -= This is automatically added to each message by the mailing > script =- To recover the email address of the author of the > message, please change the strange characters on the top line > to the a sign. You can also look up the X-Original-From: line > in the mail header.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/> > From owner-chemistry@ccl.net Wed Apr 29 12:44:01 2009 From: "Andreas Klamt klamt=cosmologic.de" To: CCL Subject: CCL:G: critical points and Density Message-Id: <-39205-090429120713-28156-uHjd5/Nn9dRkWcbCu1BemQ!=!server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 29 Apr 2009 18:07:02 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt|,|cosmologic.de] Ooops, I am afraid that we have to clarify what Miguel meant by density and critical points! Henry, you talk about the electron density and the critical points of the isosurface, right? I was talking about the density of the liquid and the critical points of the liquids. Most likely I misunderstood the question! Sorry Andreas Rzepa, Henry h.rzepa]^[imperial.ac.uk schrieb: > Sent to CCL by: "Rzepa, Henry" [h.rzepa*|*imperial.ac.uk] > >> Sent to CCL by: "miguel k escobedo" [kmiguelescobedo*|*yahoo.com] >> Hey CCLers, >> >> I need to calculate the density and critical points, can someone give me an example of how to calculate these properties in gaussian. >> >> > > > The Gaussian code is old, and not maintained (this may still be the case in Gaussian 09). Instead, use eg http://aim.tkgristmill.com/ (AIMALL) or the commercial http://www.aim2000.de/ > > The former is largely text only, the latter more GUI/Visual. They mostly give the same results (but not always, for reasons too complex to note here). > > Miroslav Kohout has also written a program called DGrid, now at V 4.4 which also does ELF as well as rho(r) density analysis (again command line, not GUI driven). > > Finally, Paul Popelier has written Morphy; http://morphy.mib.man.ac.uk/ for which a small charge is levied and Bernard Silvi offers Topmod (http://www.lct.jussieu.fr/pagesperso/silvi/clark.html) although this has to be compiled first (i.e. no binaries). > > These programs take either a .wfn file (Gaussian keyword output=wfn) or the fchk file. One issue with all these programs (I have not tried Morphy in this context) is that none run in parallel mode, and for larger systems (say > 300 basis functions) they can be VERY slow (> 24 hours). From my point of view, a parallelized version running on eg 8-core systems would be a real breakthrough, enabling larger molecules to be analyzed. > -- -------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt(~)cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------- From owner-chemistry@ccl.net Wed Apr 29 13:41:00 2009 From: "Soaring Bear soaringbear[A]yahoo.com" To: CCL Subject: CCL: Any Freely avaliable NaturalProduct Database for Download Message-Id: <-39206-090428214309-5757-GdiyXr9pQp5pkqF7kkQOjg-$-server.ccl.net> X-Original-From: Soaring Bear Content-Type: text/plain; charset=us-ascii Date: Tue, 28 Apr 2009 17:42:51 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Soaring Bear [soaringbear{:}yahoo.com] zinc is good http://zinc.docking.org/vendor0/index_meta.shtml check out other possibilities at http://soaringbear.com/biomed/chem.html Soaring Bear Ph.D. Pharmacology http://soaringbear.com/nature/WeedsforNeeds.html http://www.nlm.nih.gov/mesh/presentations/bear_2005_aug/index.htm author of http://HerbMed.org --- On Tue, 4/28/09, vadicherla tati reddy tatireddy.vadicherla^-^gmail.com wrote: > Is there any Freely avaliable Natural Product database in ( > sdf,mol,smi > )format for download... if yes can u plz mail me the link.... > > Thanks > TatiReddy From owner-chemistry@ccl.net Wed Apr 29 15:50:01 2009 From: "N. Sukumar nagams|,|rpi.edu" To: CCL Subject: CCL:G: critical points and Density Message-Id: <-39207-090429150823-30323-6sXkud2z1eAQSu4OJYRHSQ+/-server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Wed, 29 Apr 2009 13:57:08 -0400 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams]=[rpi.edu] No, not the critical points of the isosurface, AIM codes determine the critical points of the total electron density in 3D. Dr. N. Sukumar http://www.rpi.edu/research/biotech/researchers/sukumar.html ==============Original message text=============== On Wed, 29 Apr 2009 12:07:02 EDT "Andreas Klamt klamt=cosmologic.de" wrote: Sent to CCL by: Andreas Klamt [klamt|,|cosmologic.de] Ooops, I am afraid that we have to clarify what Miguel meant by density and critical points! Henry, you talk about the electron density and the critical points of the isosurface, right? I was talking about the density of the liquid and the critical points of the liquids. Most likely I misunderstood the question! Sorry Andreas Rzepa, Henry h.rzepa]^[imperial.ac.uk schrieb: > Sent to CCL by: "Rzepa, Henry" [h.rzepa*|*imperial.ac.uk] > >> Sent to CCL by: "miguel k escobedo" [kmiguelescobedo*|*yahoo.com] >> Hey CCLers, >> >> I need to calculate the density and critical points, can someone give me an example of how to calculate these properties in gaussian. >> >> > > > The Gaussian code is old, and not maintained (this may still be the case in Gaussian 09). Instead, use eg http://aim.tkgristmill.com/ (AIMALL) or the commercial http://www.aim2000.de/> > The former is largely text only, the latter more GUI/Visual. They mostly give the same results (but not always, for reasons too complex to note here). > > Miroslav Kohout has also written a program called DGrid, now at V 4.4 which also does ELF as well as rho(r) density analysis (again command line, not GUI driven). > > Finally, Paul Popelier has written Morphy; http://morphy.mib.man.ac.uk/ for which a small charge is levied and Bernard Silvi offers Topmod (http://www.lct.jussieu.fr/pagesperso/silvi/clark.html) although this has to be compiled first (i.e. no binaries).> > These programs take either a .wfn file (Gaussian keyword output=wfn) or the fchk file. One issue with all these programs (I have not tried Morphy in this context) is that none run in parallel mode, and for larger systems (say > 300 basis functions) they can be VERY slow (> 24 hours). From my point of view, a parallelized version running on eg 8-core systems would be a real breakthrough, enabling larger molecules to be analyzed. > -- -------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt[-]cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics --------------------------------------------------------------------------http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text=========== From owner-chemistry@ccl.net Wed Apr 29 16:25:01 2009 From: "Jerome Kieffer Jerome.Kieffer*terre-adelie.org" To: CCL Subject: CCL:G: G03: NMR Spin coupling and readatoms Message-Id: <-39208-090429160339-7666-wkALTZx1620obpeaWUDH8Q/./server.ccl.net> X-Original-From: Jerome Kieffer Content-Type: multipart/alternative; boundary="b1_686f43b0277587a1cdd80e50a071c261" Date: Wed, 29 Apr 2009 22:03:42 +0200 MIME-Version: 1.0 Sent to CCL by: Jerome Kieffer [Jerome.Kieffer#,#terre-adelie.org] --b1_686f43b0277587a1cdd80e50a071c261 Content-Type: text/plain; charset = "utf-8" Content-Transfer-Encoding: quoted-printable Dear CCLers, I encountered a problem trying to calculate the spin-spin NMR coupling for = a limited set of atoms using the "readatoms" option of the NMR keywork in Gaussian'03 (rev E01).=20 Many problems have been reported on this mailing list regarding this option/keyword but no answer seemed to have been posted.=20 Is the IOp(10/48=3D10) equivalent to the readatoms ? Thanks for your help. With my best regards, Jerome Kieffer -- J=C3=A9r=C3=B4me Kieffer http://www.terre-adelie.org --b1_686f43b0277587a1cdd80e50a071c261 Content-Type: text/html; charset = "utf-8" Content-Transfer-Encoding: quoted-printable Dear CCLers,

I encountered a problem trying to calculate the spin-spin NMR coupling for = a limited set of atoms using the "readatoms" option of the NMR = keywork in Gaussian'03 (rev E01).
Many problems have been reported on this mailing list regarding this = option/keyword but no answer seemed to have been posted.
Is the IOp(10/48=3D10) equivalent to the readatoms ?
Thanks for your help.

With my best regards,

Jerome Kieffer
Jérôme Kieffer
http://www.terre-adelie.org --b1_686f43b0277587a1cdd80e50a071c261--