From owner-chemistry@ccl.net Wed Sep 21 01:38:35 2005 From: "CCL" To: CCL Subject: CCL: Problem runing job in G03 Message-Id: <-29247-050920180241-23906-6n6wftz2z9QioLgBgjAIWw|"|server.ccl.net> X-Original-From: Laurence Cuffe Content-disposition: inline Content-language: en Content-transfer-encoding: 7BIT Content-type: text/plain; charset=us-ascii Date: Tue, 20 Sep 2005 23:02:34 +0100 MIME-version: 1.0 Sent to CCL by: Laurence Cuffe [Laurence.Cuffe|"|ucd.ie] --Replace strange characters with the "at" sign to recover email address--. ----- Original Message ----- > From: CCL Date: Tuesday, September 20, 2005 2:14 pm Subject: CCL: Problem runing job in G03 > Dear CCLers, > When I run job in Guaussian 03, the job filed to run with the > following error message: > > Returned from execl,istat=-1,errno=2! > Returned from execl! > Command exited with non-zero status 1 > 9.09user 1.77system 5:25.68elapsed 3%CPU (0avgtext+0avgdata > 0maxresident)k0inputs+0outputs (23295major+278624minor)pagefaults > 0swaps > I used B3LYP/6-311G** . I would be grateful if anyone help me to > identify the problem and suggest me how to solve it. This looks more like an operating system problem than a Gaussian problem. A couple of questions, the answers to which would give a clearer picture of whats going on; 1) Have you sucesfuly run any job on this system? 2) was a log file created? 3) what does your input file look like? 4) do you get this sort of eror with all gausian jobs or just some? finaly were you running as root or as a member of the gaussian users group, I know G03 had some isues with jobs being run by acounts with root permisions. My gut feeling on this is that its an error relating to either the group membership isue or acces rights to either scratch or program directories. All the best Dr Laurence Cuffe > > Thank you. > Sincerely yours, > Delwar Hossain > > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > From owner-chemistry@ccl.net Wed Sep 21 09:52:11 2005 From: "CCL" To: CCL Subject: CCL: W:CINF-IO Informatics Scholarship for Scientific Excellence Message-Id: <-29248-050921095041-26062-LDunhSfTTEZ+CigbSnRioQ###server.ccl.net> X-Original-From: "Wendy A Warr" Sent to CCL by: "Wendy A Warr" [wendy###warr.com] --Replace strange characters with the "at" sign to recover email address--. Posted on behalf of Guenter Grethe CINF-IO Informatics Scholarship for Scientific Excellence The scholarship program of the Division of Chemical Information (CINF) of the American Chemical Society (ACS) funded by IO Informatics is designed to reward graduate students in chemical information and related sciences for scientific excellence and to foster their involvement in CINF. Five scholarships valued at 1,000 each will be given out at both the Spring and Fall ACS National Meetings in a given year for a total of 10,000/year. Additionally, the winners will receive an annual license, free-of-charge, of IO Informatics software Sentinent for their academic institution. The grants have been awarded for the first time at the 230th National Meeting of ACS in Washington, DC. Applicants must be enrolled at a certified college or university. They have to present a poster at the respective National Meeting. Abstracts for the poster have to be submitted according to ACS rules on or before the deadline for electronic submission using OASYS (http://oasys.acs.org/oasys.htm). Point to the division (CINF) and select Poster session. Applications are accepted for the 2006 Spring ACS Meeting in Atlanta (March 26 30, 2006). The deadline for submission of an abstract is November 23, 2005. Additionally, a 2,000-word long abstract describing the work to be presented has to be sent in electronic form before February 1st, 2006, to the chair of the selection committee at ggrethe###comcast.net. Any questions related to applying for one of the scholarships should be directed to the same e-mail address. Winners will be chosen based on content, presentation and relevance of the poster and will be announced at the meeting. The content shall reflect upon the students work and describe research in the field of chemoinformatics and related sciences. Winning posters will be marked Winner of the CINF-IO Informatics Scholarship for Scientific Excellence at the poster session. Guenter Grethe Dr. Guenter Grethe 352 Channing Way Alameda, CA 94502-7409 Tel/Fax: 510-865-5152 Mobile: 510-333-7526 e-mail: ggrethe###comcast.net From owner-chemistry@ccl.net Wed Sep 21 13:11:35 2005 From: "CCL" To: CCL Subject: CCL: High Raman intensities Message-Id: <-29249-050921024640-5192-5yEiJFSpWRD6xA5X8eka8w*|*server.ccl.net> X-Original-From: "Roma Oakes" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 21 Sep 2005 07:46:15 +0100 MIME-Version: 1.0 Sent to CCL by: "Roma Oakes" [r.e.oakes*|*btconnect.com] --Replace strange characters with the "at" sign to recover email address--. Dear Laurent I'm not sure what you mean by 'high' Raman intensities? Do you mean intensities at high wavenumber, or calculated intensities that are higher than experimental? Perhaps these papers will help you Zuzana Benkova, A. J. Sadlej, R.E. Oakes and S.E.J. Bell, "Reduced Size Polarized Basis Sets for Calculations of Molecular Electric Properties. I. The Basis Set Generation." Journal of Computational Chemistry, 2005, Vol 26, p 145-153. Roma E. Oakes, S.E.J. Bell, Z. Benkova and A. J. Sadlej, "Reduced Size Polarized Basis Sets for Calculations of Molecular Electric Properties. II. Simulation of the Raman Spectra." Journal of Computational Chemistry, 2005, Vol 26, p 154-159. Zuzana Benkova, Andrzej J. Sadlej, Roma E. Oakes and Steven E. J. Bell. "Reduced-size polarized basis sets for calculations of molecular electric properties. III. Second-row atoms." Theoretical Chemistry Accounts, 2005, Vol 4, p 238-247. Roma E. Oakes, J.R. Beattie, B.W. Moss, S.E.J. Bell, "Conformations, Vibrational Frequencies and Raman Intensities of Short-Chain Fatty Acid Methyl Esters using DFT with 6-31G(d) and Sadlej pVTZ Basis Sets", Journal of Molecular Structure - Theochem, 2002, Vol 586, Issue 1-3, p 91-110. Best regards, Roma Dr Roma E Oakes Visiting Research Fellow Innovative Molecular Materials Group School of Chemistry and Chemical Engineering Queen's University Belfast. BT9 5NW Visit my Website at; http://home.btconnect.com/reoakes/ -----Original Message----- > From: owner-chemistry*|*ccl.net [mailto:owner-chemistry*|*ccl.net] Sent: 20 September 2005 23:49 To: Oakes, roma Subject: CCL: High Raman intensities Sent to CCL by: laurent favaro [laurent.favaro * lpces.u-psud.fr] --Replace strange characters with the "at" sign to recover email address--. Hi I am searching for informations on high Raman intensities. Does anyone heard about theoretical investigation ? Thank you very much. Best regards, L. Favaro From owner-chemistry@ccl.net Wed Sep 21 14:40:20 2005 From: "CCL" To: CCL Subject: CCL: multi-reference CI Message-Id: <-29250-050921143659-21449-GK4I6qI88Tzaqh6Caabf/A|-|server.ccl.net> X-Original-From: jz7|-|duke.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 21 Sep 2005 14:36:37 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: jz7|-|duke.edu --Replace strange characters with the "at" sign to recover email address--. Dear all, Which program can do the multi-reference CI calculation? I checked the most popular Gaussian program. The manual only mentions the direct CI. What other programs should I check? Thanks a lot! Jeny From owner-chemistry@ccl.net Wed Sep 21 15:21:14 2005 From: "CCL" To: CCL Subject: CCL: overalying samll molecules Message-Id: <-29251-050921115021-20406-i6N9sMv1ARhkn/GUUfESZQ!=!server.ccl.net> X-Original-From: Pedro Antonio Reche Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Date: Wed, 21 Sep 2005 10:50:13 -0400 Mime-Version: 1.0 (Apple Message framework v622) Sent to CCL by: Pedro Antonio Reche [reche!=!research.dfci.harvard.edu] --Replace strange characters with the "at" sign to recover email address--. Hi, I am trying to overlaying the 3D structures of two small molecules one which is not peptide. Is there any free software I can do this? Thanks in advance for any help. Regards, pedro From owner-chemistry@ccl.net Wed Sep 21 15:21:15 2005 From: "CCL" To: CCL Subject: CCL: PCM error termination Gaussian03 Message-Id: <-29252-050921085724-22425-Oa3FgK2BgJramveFTF6Efw]![server.ccl.net> X-Original-From: Sofia Godinho Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 21 Sep 2005 14:03:20 +0200 MIME-Version: 1.0 Sent to CCL by: Sofia Godinho [godinho.sofia]![gmail.com] --Replace strange characters with the "at" sign to recover email address--. Dear CCL member, some time ago I posted this question and obtained one answer. This answer solved my problem so I would like to share it with you. Thank you Dr. Hess. "This is a problem that sometimes occurs when Gaussian is using a very large number of added spheres to built the cavity. In most cases, specifying "scrf=read" and supplying the PCM options "OFAC=0.8 RMIN=0.5" will resolve the issue. These options decrease the number of added spheres." Cheers, Sofia Godinho godinho.sofia at gmail.com > > Sent to CCL by: Sofia Godinho > Dear CCL member, > while running a PCM calculation with Gaussian03 I got an error > message. This happens both when I try to optimise with IEFPCM or to > run just a PCM SinglePoint. And not just with one conformation. I > tried two different for the same molecule. > > The last part of one the output files is as follows: > ---------------------------------------------------------------------- > ----------------------------------------------------- > Polarizable Continuum Model (PCM) > ================================= > Model : PCM. > Atomic radii : UAHF (United Atom Topological Model). > Polarization charges : Total charges. > Charge compensation : None. > Solution method : Matrix inversion. > Cavity : GePol (RMin=0.200 OFac=0.890). > Default sphere list used, NSphG= 13. > Tesserae with average area of 0.200 Ang**2. > Solvent : Water, Eps = 78.390000 > Eps(inf)= 1.776000 > RSolv = 1.385000 Ang. > > ---------------------------------------------------------------------- > -------- > AdVTs1: ISph= 648 is engulfed by JSph= 649 but Ae( 648) is not > yet zero! > Error termination via Lnk1e in /usr/local/chem/g03.C02/g03/l301.exe > at Sat Jul 16 17:39:50 2005. > ---------------------------------------------------------------------- > ------------------------------------------------------------- > > What does this means?...How to get around it? > > Could you kindly help me to solve the problem? > Many thanks! > > Sofia Godinho > godinho.sofia at gmail.com From owner-chemistry@ccl.net Wed Sep 21 15:21:15 2005 From: "CCL" To: CCL Subject: CCL: input structure creation/editing Message-Id: <-29253-050921131443-32165-eQDf/0HnEqikT/Cap9txwA;;server.ccl.net> X-Original-From: Konstantin Ivanov Content-Type: multipart/alternative; boundary="----=_Part_1008_6582340.1127319145409" Date: Wed, 21 Sep 2005 12:12:25 -0400 MIME-Version: 1.0 Sent to CCL by: Konstantin Ivanov [konsantin.iv;;gmail.com] --Replace strange characters with the "at" sign to recover email address--. ------=_Part_1008_6582340.1127319145409 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear CCLers, which program running under GNU/Linux would you recommend for the creation and editing of the input structures for the quantum-chemical calculations? Molden is good for inputs using Z-matrices, but is very inconvenient for the free-hand "fine-tuning" of the guess structures, say for the transition states. Ghemical is not bad but it= s development seem to be stopped. Something as simple as the editor built-in in WebMO would be good... Thank you. Best regards, Konstantin Ivanov ------=_Part_1008_6582340.1127319145409 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
Dear CCLers,
 
which program running under GNU/Linux would you recommend for the= creation and editing of the input structures
for the quantum-chemical calculations? Molden is good for inputs using= Z-matrices, but is very inconvenient for the free-hand "fine-tun= ing" of the guess structures, say for the transition states. Ghemical = is not bad but its development seem to be stopped.=20
Something as simple as the editor built-in in WebMO would be good...
 
Thank you.
 
 
Best regards,
   Konstantin Ivanov
------=_Part_1008_6582340.1127319145409-- From owner-chemistry@ccl.net Wed Sep 21 16:03:57 2005 From: "CCL" To: CCL Subject: CCL: multi-reference CI Message-Id: <-29254-050921160021-12938-Y3QEVQEVoowf8wwUTYbDkQ_+_server.ccl.net> X-Original-From: Mikael Johansson Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 21 Sep 2005 23:00:14 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson_+_helsinki.fi] --Replace strange characters with the "at" sign to recover email address--. Hello Jeny and All! On Wed, 21 Sep 2005, CCL wrote: > Which program can do the multi-reference CI calculation? I checked the > most popular Gaussian program. The manual only mentions the direct CI. > What other programs should I check? At least Molcas (http://www.teokem.lu.se/molcas/) and Molpro (http://www.molpro.net/) have MR-CI capability. Have a nice day, Mikael J. http://www.helsinki.fi/~mpjohans/ From owner-chemistry@ccl.net Wed Sep 21 16:28:44 2005 From: "CCL" To: CCL Subject: CCL: multi-reference CI Message-Id: <-29256-050921162717-26221-Nf7/pSDarmhUDSuEnDy/OQ__server.ccl.net> X-Original-From: "Abrash, Samuel" content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Date: Wed, 21 Sep 2005 15:51:06 -0400 MIME-Version: 1.0 Sent to CCL by: "Abrash, Samuel" [sabrash__richmond.edu] --Replace strange characters with the "at" sign to recover email address--. MolPro is one program capable of doing MRD-CI. For applications that don't require the precision of MRD-CI (which is a difficult method for non-experts), TD-DFT can give decent answers. Gaussian 03 does support TD-DFT. Best, Sam Samuel A. Abrash Department of Chemistry University of Richmond Richmond, VA 23173 Phone: 804-289-8248 Fax: 804-297-1897 E-mail: sabrash__richmond.edu Web-page: http://oncampus.richmond.edu/~sabrash "Rabbi Yitzhak said: At the time God created the world and desired to reveal the depth of His being from out of the hidden, the light came > from the darkness and they were joined together. Because of this, out of darkness came the light and out of the hidden came the revealed and out of the good came evil and out of mercy came severe judgement, and everything is intertwined with everything else...the good inclination and the evil inclination, the right and the left." - The Zohar -----Original Message----- > From: owner-chemistry__ccl.net [mailto:owner-chemistry__ccl.net] Sent: Wednesday, September 21, 2005 2:37 PM To: Abrash, Samuel Subject: CCL: multi-reference CI Sent to CCL by: jz7|-|duke.edu --Replace strange characters with the "at" sign to recover email address--. Dear all, Which program can do the multi-reference CI calculation? I checked the most popular Gaussian program. The manual only mentions the direct CI. What other programs should I check? Thanks a lot! Jeny From owner-chemistry@ccl.net Wed Sep 21 16:27:41 2005 From: "CCL" To: CCL Subject: CCL: multi-reference CI Message-Id: <-29255-050921162356-11610-J8MDJQxufTAXxR/YK0P7Aw^-^server.ccl.net> X-Original-From: Alex Brown Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Date: Wed, 21 Sep 2005 13:41:15 -0600 Mime-Version: 1.0 (Apple Message framework v622) Sent to CCL by: Alex Brown [alex.brown^-^ualberta.ca] --Replace strange characters with the "at" sign to recover email address--. Dear Jeny, > Which program can do the multi-reference CI calculation? I checked the > most popular Gaussian program. The manual only mentions the direct CI. > What other programs should I check? Two programs that can be used to perform multi-reference CI calculations are MOLPRO (http://www.molpro.net) and COLUMBUS (http://www.univie.ac.at/columbus/) Regards, Alex Alex Brown Assistant Professor Department of Chemistry University of Alberta Edmonton, AB T6G 2G2 http://www.chem.ualberta.ca/~abrown/ From owner-chemistry@ccl.net Wed Sep 21 18:20:00 2005 From: "CCL" To: CCL Subject: CCL: overlaying small molecules Message-Id: <-29257-050921180310-26557-d13bc3mUg8HuskBwXZnnXQ^_^server.ccl.net> X-Original-From: Pedro Antonio Reche Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Wed, 21 Sep 2005 18:03:03 -0400 Mime-Version: 1.0 (Apple Message framework v622) Sent to CCL by: Pedro Antonio Reche [reche^_^research.dfci.harvard.edu] --Replace strange characters with the "at" sign to recover email address--. Dear Rajan, Thanks for the email. The 3D structures I want overlay correspond to a peptide ( 9 residues) and that of a compound that it is supposed simulate the structure of the peptide. The structures are in PDB format. Any help welcome! pedro On Sep 21, 2005, at 5:56 PM, Rajan Vatassery wrote: > Dear Pedro, > I think this would depend on the type of input file you are using. if > it is something as simple as a GAMESS input, or some other electronic > structure calc where bonds aren't explicitly marked, then simply > combining the two coordinates should work. > however, i have a feeling that your problem is a bit more complex than > my interpretation of it from your email. i'd be glad to help you if you > clarify your problem and maybe some of your background (so i don't > speak > beneath your level). otherwise, good luck > raj > > > > On Wed, 2005-09-21 at 09:50, CCL wrote: >> Sent to CCL by: Pedro Antonio Reche >> [reche!=!research.dfci.harvard.edu] >> >> --Replace strange characters with the "at" sign to recover email >> address--. >> >> Hi, >> I am trying to overlaying the 3D structures of two small molecules one >> which is not peptide. Is there any free software I can do this? >> Thanks in advance for any help. >> Regards, >> >> pedro >> >> >> >> -= This is automatically added to each message by the mailing script >> =- >> To send e-mail to subscribers of CCL put the string CCL: on your >> Subject: line>> >> Send your subscription/unsubscription requests to: >> CHEMISTRY-REQUEST^_^ccl.net>> >> If your is mail bouncing from ccl.net domain due to spam filters, >> please>> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- >> +-+ >> >> >> > From owner-chemistry@ccl.net Wed Sep 21 22:33:01 2005 From: "CCL" To: CCL Subject: CCL: multi-reference CI Message-Id: <-29260-050921175808-26218-QO7nW/TN2E2pZaIukKysoQ+*+server.ccl.net> X-Original-From: "Shobe, David" content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 21 Sep 2005 17:55:35 -0400 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe+*+sud-chemieinc.com] --Replace strange characters with the "at" sign to recover email address--. GAMESS [both US and UK flavors] does multi-reference CI. --David Shobe, Ph.D., M.L.S. Süd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- > From: owner-chemistry+*+ccl.net [mailto:owner-chemistry+*+ccl.net] Sent: Wednesday, September 21, 2005 2:37 PM To: Shobe, David Subject: CCL: multi-reference CI Sent to CCL by: jz7|-|duke.edu --Replace strange characters with the "at" sign to recover email address--. Dear all, Which program can do the multi-reference CI calculation? I checked the most popular Gaussian program. The manual only mentions the direct CI. What other programs should I check? Thanks a lot! Jeny From owner-chemistry@ccl.net Wed Sep 21 22:33:01 2005 From: "CCL" To: CCL Subject: CCL: Summary) spin contamination and S**2 Message-Id: <-29262-050921162414-14473-fgmcqWsJBX3C35vqwQRwUA[]server.ccl.net> X-Original-From: "Telkuni Tsuru" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-2022-jp" Date: Thu, 22 Sep 2005 05:16:56 +0900 MIME-Version: 1.0 Sent to CCL by: "Telkuni Tsuru" [telkuni[]venus.dti.ne.jp] --Replace strange characters with the "at" sign to recover email address--. Hello, CCLers. A few days ago I've sent the following question: ----- Original Question ----- Sent: Monday, September 19, 2005 5:28 AM Subject: CCL: spin contamination and S**2 > I like to ask the relationship between the spin contamination and > S**2 value. > > As mentioned before, S**2 shows the spin state, singlet(=0 [+/- 10%]), > doublet (=0.75 [+/- 10%]), triplet (=2.0 [+/- 10%]), etc. When one > molecule's multiplicity is singlet and its S**2 is 0.5, can I say that > the molecule has spin contamination ? > And the same manner, the multiplicity is doublet and its S**2 is 1.2, > can I say that the molecule has spin contamination too ? > > (What should I call "S**2"? Is it "S star 2"?) > > All responses, I will appreciate. > I will summarize them and send to CCL. I've received useful replies. To say simply, when S**2 is grater than S(S+1), the system has spin contamination. Thank you very much. ///////////////// Summary ////////////////// --- 1) from dr. Marcel Swart --- Hello Telkuni, yes, "S squared" of 0.5 for a singlet, and 1.2 for a doublet are spin contaminated. There are some correction schemes available to "project out" the pure state; we've recently reported some results for iron porphyrins in: J. Phys. Chem. A 2005, 109, 3411 --- 2) from Pr. Xavier Assfeld --- Hi, for S**2 pronounce "S squared" (S multiplied by S). It is the expectation value of the total spin operator. If for a wavefunction of a singlet you get a S**2 value greater than 0 then it is spin contaminated. Spin contamination can only arises with states of higher multiplicity and of the same parity (odd or even) than the desired state. Hope this helps. ...Xav --- 3) from Wang, Dongqi --- Dear Telkuni, according to my understanding, you can compare the S**2 (S Square) value with the scheme of S(S+1). if they are not equal, generally it's safe for you to say your calculation has spin contamination. according to this scheme, S**2 is 0 for singlet and 0.75 for doublet. i remember there is topic in Young's webpage. you can find the link from CCL homepage. good luck. wang ////////////////////////////////// Sincerely yours, ---------------------------------------------------- Telkuni Tsuru telkuni[]venus.dti.ne.jp From owner-chemistry@ccl.net Wed Sep 21 22:33:01 2005 From: "CCL" To: CCL Subject: CCL: multi-reference CI Message-Id: <-29259-050921172919-10859-FDAHXLtQDd1FvdKyLJQ18A]_[server.ccl.net> X-Original-From: Mario Barbatti Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 21 Sep 2005 22:23:52 +0200 MIME-Version: 1.0 Sent to CCL by: Mario Barbatti [mario.barbatti]_[univie.ac.at] --Replace strange characters with the "at" sign to recover email address--. Dear Jeny, A very good program to perform MRCI calculations is the COLUMBUS. http://www.univie.ac.at/columbus/ Best regards, Mario CCL wrote: >Sent to CCL by: jz7|-|duke.edu > >--Replace strange characters with the "at" sign to recover email address--. > >Dear all, > >Which program can do the multi-reference CI calculation? I checked the >most popular Gaussian program. The manual only mentions the direct CI. >What other programs should I check? > >Thanks a lot! >Jeny> > > > > From owner-chemistry@ccl.net Wed Sep 21 22:33:01 2005 From: "CCL" To: CCL Subject: CCL: overalying samll molecules Message-Id: <-29261-050921192051-14297-6FvkVR/wHLqeXOdVEXnL3w-#-server.ccl.net> X-Original-From: "Niels Johan Christensen" Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Thu, 22 Sep 2005 00:20:36 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: "Niels Johan Christensen" [s991418-#-student.dtu.dk] --Replace strange characters with the "at" sign to recover email address--. Hi, You can accomplish this with VMD. Check out the section "Aligning Two Molecules" in the tutorial http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node3.html You will have to tweak this example to match your demands, but it should be managable. Regards, Niels On Wed, 21 Sep 2005, CCL wrote: > > Sent to CCL by: Pedro Antonio Reche [reche!=!research.dfci.harvard.edu] > > --Replace strange characters with the "at" sign to recover email address--. > > Hi, > I am trying to overlaying the 3D structures of two small molecules one > which is not peptide. Is there any free software I can do this? > Thanks in advance for any help. > Regards, > > pedro> > > > From owner-chemistry@ccl.net Wed Sep 21 22:33:01 2005 From: "CCL" To: CCL Subject: CCL: High Raman intensities Message-Id: <-29258-050921175612-26082-O2AbIsL4llDsU18CaH+hRA[A]server.ccl.net> X-Original-From: "Shobe, David" content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 21 Sep 2005 17:54:04 -0400 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe[A]sud-chemieinc.com] --Replace strange characters with the "at" sign to recover email address--. Dr Roma E Oakes wrote: > I'm not sure what you mean by 'high' Raman intensities? Do you mean > intensities at high wavenumber, or calculated intensities that are > higher than experimental? I just assumed Laurent meant that the *intensities* were high, i.e. higher than for a typical (organic?) compound. ...and Laurent, Do you have particular compounds in mind and wish to know how to calculate the raman intensities? Or do you not have any particular compounds in mind and wish to know what chemical structures are likely to cause high raman activity? --David Shobe, Ph.D., M.L.S. Süd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- > From: owner-chemistry[A]ccl.net [mailto:owner-chemistry[A]ccl.net] Sent: Wednesday, September 21, 2005 2:46 AM To: Shobe, David Subject: CCL: High Raman intensities Sent to CCL by: "Roma Oakes" [r.e.oakes*|*btconnect.com] --Replace strange characters with the "at" sign to recover email address--. Dear Laurent I'm not sure what you mean by 'high' Raman intensities? Do you mean intensities at high wavenumber, or calculated intensities that are higher than experimental? Perhaps these papers will help you Zuzana Benkova, A. J. Sadlej, R.E. Oakes and S.E.J. Bell, "Reduced Size Polarized Basis Sets for Calculations of Molecular Electric Properties. I. The Basis Set Generation." Journal of Computational Chemistry, 2005, Vol 26, p 145-153. Roma E. Oakes, S.E.J. Bell, Z. Benkova and A. J. Sadlej, "Reduced Size Polarized Basis Sets for Calculations of Molecular Electric Properties. II. Simulation of the Raman Spectra." Journal of Computational Chemistry, 2005, Vol 26, p 154-159. Zuzana Benkova, Andrzej J. Sadlej, Roma E. Oakes and Steven E. J. Bell. "Reduced-size polarized basis sets for calculations of molecular electric properties. III. Second-row atoms." Theoretical Chemistry Accounts, 2005, Vol 4, p 238-247. Roma E. Oakes, J.R. Beattie, B.W. Moss, S.E.J. Bell, "Conformations, Vibrational Frequencies and Raman Intensities of Short-Chain Fatty Acid Methyl Esters using DFT with 6-31G(d) and Sadlej pVTZ Basis Sets", Journal of Molecular Structure - Theochem, 2002, Vol 586, Issue 1-3, p 91-110. Best regards, Roma Dr Roma E Oakes Visiting Research Fellow Innovative Molecular Materials Group School of Chemistry and Chemical Engineering Queen's University Belfast. BT9 5NW Visit my Website at; http://home.btconnect.com/reoakes/ -----Original Message----- > From: owner-chemistry[A]ccl.net [mailto:owner-chemistry[A]ccl.net] Sent: 20 September 2005 23:49 To: Oakes, roma Subject: CCL: High Raman intensities Sent to CCL by: laurent favaro [laurent.favaro * lpces.u-psud.fr] --Replace strange characters with the "at" sign to recover email address--. Hi I am searching for informations on high Raman intensities. Does anyone heard about theoretical investigation ? Thank you very much. Best regards, L. Favaro