From chemistry-request@server.ccl.net Wed Jun 27 02:14:21 2001 Received: from statchem.snu.ac.kr ([147.46.41.143]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5R6EH503954 for ; Wed, 27 Jun 2001 02:14:20 -0400 Received: from ercc ([147.46.41.198]) by statchem.snu.ac.kr (8.9.3/8.9.3) with SMTP id PAA21065 for ; Wed, 27 Jun 2001 15:21:24 -0900 (ROT) Message-ID: <000f01c0fed0$1ccb1da0$c6292e93@snu.ac.kr> From: "JinhyukLee" To: "ccl ccl" Subject: Program for checking secondary structure of protein Date: Wed, 27 Jun 2001 15:12:04 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="ks_c_5601-1987" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id f5R6EL503955 Hello CCLers, Who know the program checking secondary structure of protein? I know DSSP and PROCHECK. Let me recommend good and simple program that can calculate secodnary structure as function of time. Thx in advance for your help. Bye. ============================================================ Jinhyuk Lee Email: mack@statchem.snu.ac.kr School of Chemistry Tel: 82-2-879-2721 Seoul National University Seoul, Korea ============================================================ From chemistry-request@server.ccl.net Wed Jun 27 11:14:43 2001 Received: from mail1.rrz.Uni-Koeln.DE ([134.95.100.208]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5RFEg524154 for ; Wed, 27 Jun 2001 11:14:42 -0400 Received: from campfire.rrz.Uni-Koeln.DE (IDENT:39358@campfire.rrz.Uni-Koeln.DE [134.95.19.27]) by mail1.rrz.Uni-Koeln.DE (8.9.3/8.9.3) with ESMTP id RAA16701 for ; Wed, 27 Jun 2001 17:14:41 +0200 (MET DST) Received: (from a0580@localhost) by campfire.rrz.Uni-Koeln.DE (8.9.1a/8.9.1) id RAA24675 for chemistry@ccl.net; Wed, 27 Jun 2001 17:14:30 +0200 (MET DST) Date: Wed, 27 Jun 2001 17:14:30 +0200 From: Lars Packschies To: chemistry@ccl.net Subject: simulation/calculation of ir/Raman linewidths Message-ID: <20010627171429.C5696@campfire.rrz.Uni-Koeln.DE> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.3.19i Hi All, I'm looking for a program (free software if possiple) that is able to "simulate" ir/raman spectra from wavenumber/intensity data. Lineshape calculation (Lorentz ?) etc... Answers will be summarized, of course. Thanks in advance, Lars -- ,H + Dr. Lars Packschies ZAIK/RRZK, Robert-Koch-Str.10 + H H O | Chemistry Dpt. Support D-50931 Cologne | `O-H. | ,' `H | Comp.Dpt., Univ. of Cologne Phn (+49)221-478-7022 | `O-H + Packschies@rrz.uni-koeln.de Fax (+49)221-478-5568 + From chemistry-request@server.ccl.net Wed Jun 27 12:10:03 2001 Received: from correo.us.es ([150.214.186.112]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5RGA2525221 for ; Wed, 27 Jun 2001 12:10:02 -0400 Received: from simulux.us.es (IDENT:root@simulux.us.es [150.214.145.66]) by correo.us.es (8.11.0/8.11.1) with ESMTP id f5RG28k20043; Wed, 27 Jun 2001 18:02:08 +0200 Received: from localhost (rafapa@localhost) by simulux.us.es (8.9.3/8.9.3) with ESMTP id UAA20444; Wed, 27 Jun 2001 20:09:35 +0200 Date: Wed, 27 Jun 2001 20:09:35 +0200 (CEST) From: "Rafael R. Pappalardo" To: Lars Packschies cc: Subject: Re: CCL:simulation/calculation of ir/Raman linewidths In-Reply-To: <20010627171429.C5696@campfire.rrz.Uni-Koeln.DE> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 27 Jun 2001, Lars Packschies wrote: > Hi All, > > I'm looking for a program (free software if possiple) that is able to > "simulate" ir/raman spectra from wavenumber/intensity data. Lineshape > calculation (Lorentz ?) etc... > > Answers will be summarized, of course. > > Thanks in advance, > > Lars > > I believe that there is such program in the CCL archives. It's called spectrum or something similar. Let me know if you cannot find it and I will try to find it myself. Regards, Rafael -- Dr. Rafael R. Pappalardo Dept. Quimica Fisica, Fac. de Quimica, Univ. de Sevilla. 41012-Sevilla (Spain) e-mail: rafapa@simulux.us.es From chemistry-request@server.ccl.net Wed Jun 27 14:15:02 2001 Received: from ivory.trentu.ca ([192.75.12.103]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5RIF1528364 for ; Wed, 27 Jun 2001 14:15:01 -0400 Received: from trentu.ca ([204.225.13.50]) by trentu.ca (PMDF V5.2-32 #37862) with ESMTP id <01K59IYHJKOU000UZH@trentu.ca> for chemistry@ccl.net; Wed, 27 Jun 2001 14:14:04 EDT Date: Wed, 27 Jun 2001 14:20:08 -0400 From: elewars Subject: Re: CCL:simulation/calculation of ir/Raman linewidths To: Lars Packschies Cc: chemistry@ccl.net Message-id: <3B3A23D8.40CDD882@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en References: <20010627171429.C5696@campfire.rrz.Uni-Koeln.DE> Hello, I don't know if this will help with a free program, but papers in which IR spectra are simulated with regard to lineshape are; H. Lampert, W. Mikemda, and A. Karpfen, J Phys Chem A, 1997, 101, 2254. P. J. Stephens et al., J Phys Chem, 1994, 98, 11623. E. Lewars ===== Lars Packschies wrote: > Hi All, > > I'm looking for a program (free software if possiple) that is able to > "simulate" ir/raman spectra from wavenumber/intensity data. Lineshape > calculation (Lorentz ?) etc... > > Answers will be summarized, of course. > > Thanks in advance, > > Lars > > -- > ,H + Dr. Lars Packschies ZAIK/RRZK, Robert-Koch-Str.10 + > H H O | Chemistry Dpt. Support D-50931 Cologne | > `O-H. | ,' `H | Comp.Dpt., Univ. of Cologne Phn (+49)221-478-7022 | > `O-H + Packschies@rrz.uni-koeln.de Fax (+49)221-478-5568 + > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Wed Jun 27 15:08:25 2001 Received: from chem.ufl.edu ([128.227.16.141]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5RJ8P529601 for ; Wed, 27 Jun 2001 15:08:25 -0400 Received: from chem.ufl.edu (chem.ufl.edu [128.227.76.141]) by chem.ufl.edu (8.9.1/8.9.1/map) with ESMTP id PAA08434 for ; Wed, 27 Jun 2001 15:08:24 -0400 (EDT) Date: Wed, 27 Jun 2001 15:08:24 -0400 (EDT) From: "Xiang(Simon) Wang" To: CHEMISTRY@ccl.net Subject: SHAKE in Charmm Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers: I met the following ERROR message when running SHAKE BONH within a TIP3 droplet model: CHARMM> SHAKE BONH SHKSET: *** ERROR *** NO. OF CONSTRAINTS 45091 IS LARGER THAN MAXSHK 45090 *** LEVEL -2 WARNING *** BOMLEV IS -2 My version of Charmm is c25b2, compiled w/ large and FULL. Please give me your valuable advices or suggestions. Thanks a lot. Xiang(Simon) WANG From chemistry-request@server.ccl.net Wed Jun 27 16:15:25 2001 Received: from postal.sdsc.edu (IDENT:5d1LdQiynOhMoPIRdaa/UC2ChAQdJYDK@[132.249.20.114]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5RKFP530759 for ; Wed, 27 Jun 2001 16:15:25 -0400 Received: from yerkes.sdsc.edu (IDENT:QbmuaGelmlE61jgUTO7SZ/H933zPW65W@yerkes.sdsc.edu [132.249.40.94]) by postal.sdsc.edu (8.9.3/8.9.3/SDSCserver-17) with ESMTP id NAA03428 for ; Wed, 27 Jun 2001 13:15:23 -0700 (PDT) Received: from localhost by yerkes.sdsc.edu (SGI-8.9.3/1.11-IRIXclient) with ESMTP id NAA92321; Wed, 27 Jun 2001 13:15:23 -0700 (PDT) Date: Wed, 27 Jun 2001 13:15:22 -0700 From: Andrew Hoofnagle To: Subject: A program to measure solvent accessibility/calculate connolly surface? In-Reply-To: <3B3A23D8.40CDD882@trentu.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Greetings- Does anyone know of freeware or code to calculate a connolly surface for a macromolecule? I am also interested in calculating the solvent accessibility of residues and atoms in the molecule, if anyone has any information regarding this as well. Thank for any help, Andy Hoofnagle From chemistry-request@server.ccl.net Wed Jun 27 22:17:29 2001 Received: from sungod.ccs.yorku.ca ([130.63.236.104]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5S2HS503142 for ; Wed, 27 Jun 2001 22:17:29 -0400 Received: from curl.gkcl.yorku.ca (curl.gkcl.yorku.ca [130.63.232.224]) by sungod.ccs.yorku.ca (8.9.3/8.9.3) with ESMTP id WAA00460 for ; Wed, 27 Jun 2001 22:17:28 -0400 (EDT) Received: (from chan@localhost) by curl.gkcl.yorku.ca (8.10.0/8.10.0) id f5S2HSX05318 for chemistry@ccl.net; Wed, 27 Jun 2001 22:17:28 -0400 (EDT) From: Wai-To Chan Message-Id: <200106280217.f5S2HSX05318@curl.gkcl.yorku.ca> Subject: CCL: CASSCF and degenerate state To: chemistry@ccl.net Date: Wed, 27 Jun 2001 22:17:27 -0400 (EDT) X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit <<<<<<<<<<<<<<<<< Dear CCL! I have problems performing a CASSCF calculation on an open shell pi-system with a doubly degenerate ground state (using Gaussian98). Any help? Thanks, Jens >--< >>>>>>>>>>>>>>>>> Appended to this message is a g98 multi-step input file for a CASSCF calculation of the open-shell singlet of molecular oxygen. It gives an optimized bond distance of 1.2072 angstrom in close agreement with the value quoted in a previous g98-casscf study from IJQC, vol 65, pg 787-801 (1997). Note that the second part of this job is just to show you the natural orbitals used in the subsequent CASSCF step. Hope this is pertinent to your study. Wai-To Chan ************************************* %chk=o2oss-cas %mem=64MB # uhf/6-311G* guess=mix O2 biradical singlet symmetry-broken UHF solution 0 1 O O 1 roo roo 1.20 --Link1-- %chk=o2oss-cas # uhf/6-311G* geom=check guess=read symm=noscf pop=(regular,no) O2 biradical singlet natural orbitals 0 1 --Link1-- %chk=o2oss-cas %mem=64MB # cas(2,4,qc)/6-311G* geom=check guess=read nosymm opt O2 biradical singlet CASSCF. 2 SOMO electrons 4 Active MOs 0 1 ******************************************* From chemistry-request@server.ccl.net Wed Jun 27 22:29:38 2001 Received: from sungod.ccs.yorku.ca ([130.63.236.104]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5S2Tc503330 for ; Wed, 27 Jun 2001 22:29:38 -0400 Received: from curl.gkcl.yorku.ca (curl.gkcl.yorku.ca [130.63.232.224]) by sungod.ccs.yorku.ca (8.9.3/8.9.3) with ESMTP id WAA01243 for ; Wed, 27 Jun 2001 22:29:37 -0400 (EDT) Received: (from chan@localhost) by curl.gkcl.yorku.ca (8.10.0/8.10.0) id f5S2Tck05350 for chemistry@ccl.net; Wed, 27 Jun 2001 22:29:38 -0400 (EDT) From: Wai-To Chan Message-Id: <200106280229.f5S2Tck05350@curl.gkcl.yorku.ca> Subject: CCL: CASSCF and degenerate states To: chemistry@ccl.net Date: Wed, 27 Jun 2001 22:29:37 -0400 (EDT) X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I just noticed that the command card from the CASSCF step in my g98 input file: # cas(2,4,qc)/6-311G* geom=check guess=read nosymm opt miss the 'uno' option. So I am not sure if the UHF-natural orbitals > from the previous step was used in the calculation. I must point out that I am not really familar with running casscf using g98. The g98 input file was actually prepared to duplicate a UNO-MCSCF calculaion performed with GAMESS by trial and error. Wai-To Chan From chemistry-request@server.ccl.net Wed Jun 27 14:52:53 2001 Received: from sas.asc.hpc.mil ([129.48.244.126]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5RIqN529365 for ; Wed, 27 Jun 2001 14:52:53 -0400 Received: from asc.hpc.mil (wk32.asc.hpc.mil [129.48.245.32]) by sas.asc.hpc.mil (8.11.4/8.11.4) with ESMTP id f5RIq6x1051588; Wed, 27 Jun 2001 14:52:06 -0400 (EDT) Sender: duanx@asc.hpc.mil Message-ID: <3B3A2B48.D72350AF@asc.hpc.mil> Date: Wed, 27 Jun 2001 14:51:53 -0400 From: XIAOFENG FRANK DUAN Organization: CSC X-Mailer: Mozilla 4.76 [en] (X11; U; IRIX 6.5 IP22) X-Accept-Language: en MIME-Version: 1.0 To: Lars Packschies CC: chemistry@ccl.net Subject: Re: CCL:simulation/calculation of ir/Raman linewidths References: Content-Type: multipart/alternative; boundary="------------C0D905ADC9ADBB9E6A10C606" --------------C0D905ADC9ADBB9E6A10C606 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, If your wavenumber/intensity data are from Gaussian9x or GAMESS calculations, I have a C program that can read the data from the output files and convert (Lorentz or Gauss fitting) them to spectrum data files which are ready to be plotted by graphing programs such as KaleidaGraph. Frank "Rafael R. Pappalardo" wrote: > On Wed, 27 Jun 2001, Lars Packschies wrote: > > > Hi All, > > > > I'm looking for a program (free software if possiple) that is able to > > "simulate" ir/raman spectra from wavenumber/intensity data. Lineshape > > calculation (Lorentz ?) etc... > > > > Answers will be summarized, of course. > > > > Thanks in advance, > > > > Lars > > > > > > I believe that there is such program in the CCL archives. It's called > spectrum or something similar. Let me know if you cannot find it and > I will try to find it myself. > > Regards, > Rafael > > -- > Dr. Rafael R. Pappalardo > Dept. Quimica Fisica, Fac. de Quimica, Univ. de Sevilla. 41012-Sevilla (Spain) > e-mail: rafapa@simulux.us.es > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- Xiaofeng Frank Duan, Ph.D | Phone: 937-904-8307 ASC MSRC | Email: duanx@asc.hpc.mil 2435 5th St., ASC/HP Bldg. 676 | URL: http://www.asc.hpc.mil Wright-Patterson AFB, OH 45433 | --------------C0D905ADC9ADBB9E6A10C606 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi,

If your wavenumber/intensity data are from Gaussian9x or GAMESS calculations, I have a C program that can read the data from the output files and convert (Lorentz or Gauss fitting) them to spectrum data files which are ready to be plotted by graphing programs such as KaleidaGraph.

Frank

"Rafael R. Pappalardo" wrote:

On Wed, 27 Jun 2001, Lars Packschies wrote:

> Hi All,
>
> I'm looking for a program (free software if possiple) that is able to
> "simulate" ir/raman spectra from wavenumber/intensity data. Lineshape
> calculation (Lorentz ?) etc...
>
> Answers will be summarized, of course.
>
> Thanks in advance,
>
> Lars
>
>

I believe that there is such program in the CCL archives. It's called
spectrum or something similar. Let me know if you cannot find it and
I will try to find it myself.

Regards,
        Rafael

--
Dr. Rafael R. Pappalardo
Dept. Quimica Fisica, Fac. de Quimica, Univ. de Sevilla. 41012-Sevilla (Spain)
e-mail: rafapa@simulux.us.es

-= This is automatically added to each message by mailing script =-
CHEMISTRY@ccl.net -- To Everybody  | CHEMISTRY-REQUEST@ccl.net -- To Admins
MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH
CHEMISTRY-SEARCH@ccl.net -- archive search    |    Gopher: gopher.ccl.net 70
Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | Jan: jkl@ccl.net

-- 
 Xiaofeng Frank Duan, Ph.D         |  Phone: 937-904-8307
 ASC MSRC                          |  Email: duanx@asc.hpc.mil   
 2435 5th St., ASC/HP Bldg. 676    |  URL:   http://www.asc.hpc.mil
 Wright-Patterson AFB, OH 45433    |
  --------------C0D905ADC9ADBB9E6A10C606-- From chemistry-request@server.ccl.net Wed Jun 27 06:59:12 2001 Received: from web14101.mail.yahoo.com ([216.136.172.131]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f5RAxC520174 for ; Wed, 27 Jun 2001 06:59:12 -0400 Message-ID: <20010627105912.13211.qmail@web14101.mail.yahoo.com> Received: from [164.164.130.13] by web14101.mail.yahoo.com; Wed, 27 Jun 2001 03:59:12 PDT Date: Wed, 27 Jun 2001 03:59:12 -0700 (PDT) From: saradha ramamurthy Subject: MM2 force field parameters To: CHEMISTRY@server.ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCL users, It would be kind enough if anyone could tell me the references for getting the MM2 and MM3 force field parameters. Thanks in advance, Saradha. __________________________________________________ Do You Yahoo!? Get personalized email addresses from Yahoo! Mail http://personal.mail.yahoo.com/ From chemistry-request@server.ccl.net Tue Jun 26 23:14:49 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5R3En502466 for ; Tue, 26 Jun 2001 23:14:49 -0400 Received: from eyou.com ([61.136.62.73]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with SMTP id XAA14696 for ; Tue, 26 Jun 2001 23:14:41 -0400 (EDT) Received: (qmail 64527 invoked from network); 27 Jun 2001 11:14:36 +0800 Received: from unknown (HELO eyou.com) (172.16.2.1) by 172.16.1.1 with SMTP; 27 Jun 2001 11:14:36 +0800 Received: (qmail 88586 invoked by uid 65534); 27 Jun 2001 11:14:37 +0800 Date: 27 Jun 2001 11:14:37 +0800 Message-ID: <20010627111437.88585.qmail@eyou.com> From: "王明韬" To: CHEMISTRY@ccl.net Reply-To: "王明韬" Subject: hi Dear all: How can I calculate the binding energy when the ligand and the protein have a covalent interaction? Thanks! --http://www.eyou.com --稳定可靠的免费电子信箱 语音邮件 移动书签 日历服务 网络存储...亿邮未尽