From chemistry-request@server.ccl.net Thu Jun 28 01:34:32 2001 Received: from deakin.edu.au (root@[128.184.136.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5S5YV505977 for ; Thu, 28 Jun 2001 01:34:31 -0400 Received: from [128.184.88.189] (128-184-88-189.bcs.deakin.edu.au [128.184.88.189]) by deakin.edu.au (8.11.4/8.11.4) with ESMTP id f5S5YFT04229 for ; Thu, 28 Jun 2001 15:34:15 +1000 (EST) Mime-Version: 1.0 X-Sender: lim@128.184.136.2 Message-Id: Date: Thu, 28 Jun 2001 15:36:15 +1000 To: chemistry@ccl.net From: "Kieran F Lim (Lim Pak Kwan)" Subject: CCL: help please with ECEPP package Content-Type: text/plain; charset="us-ascii" ; format="flowed" Dear all, I am new to the protein conformation analysis package ECEPP. As test cases, we have run test calculations for (end unit) -- amino acid -- (end unit) where amino acid = Proline, Alanine or Histidine. We'd like to confirm our minimum-energy configurations and compare to experiment to get a better "feel" for the program. Are the experimental configurations (all dihedral angles) published? (We have only those for alanine from Floudas's papers.) For glycine and cystiene, ECEPP refuses to calculate anything saying that these amino acids should have "bridges". How can I get rid of the "bridges"? Thank you Kieran ------------------------------------------------------------ Dr Kieran F Lim Biol. and Chemical Sciences (Lim Pak Kwan) Deakin University ph: + [61] (3) 5227-2146 Geelong VIC 3217 fax: + [61] (3) 5227-1040 AUSTRALIA mailto:lim@deakin.edu.au http://www.deakin.edu.au/~lim From chemistry-request@server.ccl.net Thu Jun 28 05:56:45 2001 Received: from electre.pasteur.fr ([157.99.64.120]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5S9ug515491 for ; Thu, 28 Jun 2001 05:56:43 -0400 Received: from pasteur.fr (xiii.bis.pasteur.fr [157.99.90.14]) by electre.pasteur.fr (8.11.4/8.11.4) with ESMTP id f5S9uK0308321; Thu, 28 Jun 2001 11:56:20 +0200 (CEST) Sender: tru@pasteur.fr Message-ID: <3B3AFF3A.98196348@pasteur.fr> Date: Thu, 28 Jun 2001 11:56:10 +0200 From: Tru Huynh Organization: Institut Pasteur X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.2-SGI_XFS_1.0 i686) X-Accept-Language: en MIME-Version: 1.0 To: "Xiang(Simon) Wang" CC: CHEMISTRY@ccl.net Subject: Re: CCL:SHAKE in Charmm References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit "Xiang(Simon) Wang" wrote: > > 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. > You just need to recompile a bigger CHARMM version. 1)make a XLARGE version or 2)modify line 26 of source/fcm/dimens.fcm > from PARAMETER (LARGE=60120, MEDIUM=25140, SMALL=6120) to PARAMETER (LARGE=100000, MEDIUM=25140, SMALL=6120) ----- extract of dimens.fcm ---- CHARMM Element source/fcm/dimens.fcm 1.1 C C This common file contains all useful dimensioning information. C BRB - 01/12/89 C C----------------------------------------------------------------------- C Standard Size parameters C C XLARGE version - ~240,000 atoms C LARGE version - ~60,000 atoms C MEDIUM version - ~25,000 atoms C SMALL version - ~6,000 atoms C XSMALL version - ~2,000 atoms C REDUCE version - A special version for non-virtual memory machines. C There is an attempt to greatly limit static memory. C C The actual size varies by machine type. C It is listed in the header of the CHARMM output file. C INTEGER LARGE,MEDIUM,SMALL,REDUCE ##IF QUANTA PARAMETER (LARGE=60000, MEDIUM=30000, SMALL=15000) ##ELIF T3D PARAMETER (LARGE=30120, MEDIUM=20160, SMALL=6120) ##ELSE PARAMETER (LARGE=60120, MEDIUM=25140, SMALL=6120) ##ENDIF PARAMETER (REDUCE=15000) INTEGER SIZE ##IF XLARGE PARAMETER (SIZE=LARGE*4) ##ELIF LARGE PARAMETER (SIZE=LARGE) ##ELIF MEDIUM PARAMETER (SIZE=MEDIUM) ##ELIF REDUCE PARAMETER (SIZE=REDUCE) ##ELIF SMALL PARAMETER (SIZE=SMALL) ##ELIF XSMALL PARAMETER (SIZE=SMALL/3) ##ENDIF <...> C----------------------------------------------------------------------- C FROM: shake.fcm C C MAXSHK - The maximum number of SHAKE constraints. C INTEGER MAXSHK ##IF XSMALL PARAMETER (MAXSHK = 20) ##ELIF REDUCE PARAMETER (MAXSHK = 5120) ##ELSE PARAMETER (MAXSHK = SIZE*3/4) ##ENDIF C -- Dr Tru Huynh | Bioinformatique Structurale mailto:tru@pasteur.fr | tel/fax +33 1 45 68 87 37/19 Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France From chemistry-request@server.ccl.net Thu Jun 28 08:05:12 2001 Received: from unlserve.unl.edu ([129.93.1.130]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5SC5C525373 for ; Thu, 28 Jun 2001 08:05:12 -0400 Received: from localhost (rrashid@localhost) by unlserve.unl.edu (8.9.1a/8.9.2) with SMTP id GAA107228 for ; Thu, 28 Jun 2001 06:48:09 -0500 Date: Thu, 28 Jun 2001 06:48:09 -0500 (CDT) From: Ali N Rashid To: chemistry@ccl.net Subject: GamessUS vs GamessUK In-Reply-To: <20010604100303.A87113@eros.iqm.unicamp.br> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I was wandering if someone couldtell me if there is a difference between Gamess-US and Gamess-UK. Are they actually two different programs and if so is one better than the other. I was also wandering if there was some software that can not only help visualise results from Gamess output but also help setup the files. Thanks you in advance. From chemistry-request@server.ccl.net Thu Jun 28 09:55:15 2001 Received: from mail.rpi.edu ([128.113.22.40]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5SDtF527559 for ; Thu, 28 Jun 2001 09:55:15 -0400 Received: from vcmr-19.rcs.rpi.edu (vcmr-19.rcs.rpi.edu [128.113.113.12]) by mail.rpi.edu (8.11.3/8.11.3) with ESMTP id f5SDtFM81282; Thu, 28 Jun 2001 09:55:15 -0400 Received: from localhost (songm@localhost) by vcmr-19.rcs.rpi.edu (8.8.5/8.8.6) with SMTP id JAA38264; Thu, 28 Jun 2001 09:54:58 -0400 X-Authentication-Warning: vcmr-19.rcs.rpi.edu: songm owned process doing -bs Date: Thu, 28 Jun 2001 09:54:58 -0400 (EDT) From: Minghu Song X-Sender: songm@vcmr-19.rcs.rpi.edu To: Andrew Hoofnagle cc: chemistry@ccl.net Subject: Re: CCL:A program to measure solvent accessibility/calculate connolly surface? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I used " Naccess", which can calculate the SASA and %SASA by residues or atoms: http://wolf.bms.umist.ac.uk/naccess/ and Deepview" (http://www.expasy.ch/)(you have to write a script to extract the selected residues) you can also try "whatif", "do_dssp"(http://rugmd0.chem.rug.nl/~gmx/online2.0/do_dssp.html), MSMS"(http://www.scripps.edu/pub/olson-web/people/sanner/html/msms_home.html "ASC" (http://mendel.imp.univie.ac.at/SURFACE/ASC/index.html) cheers, minghu On Wed, 27 Jun 2001, Andrew Hoofnagle wrote: > 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 > > > > -= 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 Thu Jun 28 13:02:50 2001 Received: from dire.bris.ac.uk ([137.222.10.60]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5SH2n532119 for ; Thu, 28 Jun 2001 13:02:49 -0400 Received: from eis.bris.ac.uk by dire.bris.ac.uk with SMTP-PRIV with ESMTP; Thu, 28 Jun 2001 18:02:44 +0100 Received: from localhost (localhost [127.0.0.1]) by eis.bris.ac.uk (8.11.4/8.11.3) with SMTP id f5SH0mv00130 for ; Thu, 28 Jun 2001 18:00:48 +0100 (BST) Date: Thu, 28 Jun 2001 18:00:48 +0100 (BST) From: F Schambach To: chemistry@server.ccl.net Subject: Autodock 3.05 Problems Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I've been trying to get Autodock distribution 3.05 to work on either a Red Hat Linux machine and on a SGI running IRIX 6.3 . The problem I have when I try to dock into my protein structure is that Autodock always docks my small ligand on top of protein residues in positions that are obviously impossible. That occurs on both systems with all kinds of ligands, with the precompiled binaries, with the ones I compiled myself, with standard mkgpf3/mkdpf3 files, who can help ? Should I use an older/newer version ? Thank you very much, Felix Schambach, University of Bristol, Dept of Biochemistry f.schambach@bris.ac.uk From chemistry-request@server.ccl.net Thu Jun 28 11:20:36 2001 Received: from mail04.europe.csc.com ([194.133.99.131]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5SFKZ529303 for ; Thu, 28 Jun 2001 11:20:35 -0400 Received: by mail04.europe.csc.com (8.8.8+Sun/SMI-SVR4) id QAA11835; Thu, 28 Jun 2001 16:28:53 +0100 (BST) Received: from av-int.eu.csc.com (192.168.140.24) by CSCgw. ID xai011788; Thu, 28 Jun 01 16:28:34 +0100 Received: from ukhx48.avecia.com (unverified) by av-is-sweeper.aveciais (Content Technologies SMTPRS 4.1.5) with ESMTP id for ; Thu, 28 Jun 2001 16:20:01 +0100 Received: by UKHX48 with Internet Mail Service (5.5.2653.19) id ; Thu, 28 Jun 2001 16:19:47 +0100 Message-ID: <67DFB9481700D111900E00805F59F861038D96A4@UKHX14> From: Tackley Daniel R To: "'chemistry@ccl.net'" Subject: RE: simulation/calculation of ir/Raman linewidths Date: Thu, 28 Jun 2001 16:19:47 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" I have a Windows program that will read a Gaussian (only tested on Gaussian 98W) output file, extract the vibrational data (frequency, IR and Raman intensities) and apply a lineshape. This lineshape can be pure Gaussian, pure Lorentzian or mixed Gaussian-Lorentzian with a user specified weighting. The linewith for the IR and Raman data can be individually adjusted. The program will then write out two files. One contains just the original frequency/intensity data extracted from the Gaussian file (output of this file is optional). The other will contain the simulated spectral data and the program has options for the data range (e.g.. 200 - 1800 cm-1) and the frequency of points (e.g.. every 0.5 cm-1). If this is of use, let me know. Daniel -- Daniel Tackley Avecia Computational Chemistry Group Email: daniel.tackley@avecia.com Telephone: +44 161 721 2541 -----Original Message----- From: Lars Packschies [mailto:packschies@rrz.Uni-Koeln.de] Sent: 27 June 2001 16:15 To: chemistry@ccl.net Subject: CCL:simulation/calculation of ir/Raman linewidths 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 From chemistry-request@server.ccl.net Wed Jun 27 23:13:07 2001 Received: from hotmail.com ([64.4.17.215]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5S3D6503853 for ; Wed, 27 Jun 2001 23:13:06 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Wed, 27 Jun 2001 20:13:01 -0700 Received: from 161.142.100.86 by lw11fd.law11.hotmail.msn.com with HTTP; Thu, 28 Jun 2001 03:13:01 GMT X-Originating-IP: [161.142.100.86] From: "borhan arifin" To: CHEMISTRY@ccl.net Subject: Dissociation energy -G98 Date: Thu, 28 Jun 2001 03:13:01 -0000 Mime-Version: 1.0 Content-Type: text/html Message-ID: X-OriginalArrivalTime: 28 Jun 2001 03:13:01.0351 (UTC) FILETIME=[3D2B2B70:01C0FF80]

Hello everyone,

I am trying to calculate the dissociation energy of the triplet state of the hydrogen molecule by first optimizing it then calculating the frequencies based on the optimized geometry but the job ends with an error message and the link died. Below is a copy of the job based on an example given in the book written by James B. Foresman. What did I do wrong?

Appreciate if someone can help me. Thank you

Borhan Arifin

%chk=es_h2
#T RCIS/6-31+G(d) Test

H2 Excited States
 
0,1
H
H 1 0.74

--Link1--
%Chk=C:\GaussCalc\es_h2
%NoSave
#T RCIS(Nstates=2,50-50,Read)/6-31+G(d) Opt Freq
   Geom=Check Guess=Read Test 


Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com.

From chemistry-request@server.ccl.net Thu Jun 28 18:55:42 2001 Received: from tucc-exchange.trinity.edu ([131.194.151.15]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5SMtf509011 for ; Thu, 28 Jun 2001 18:55:41 -0400 Received: by tucc15.tucc.trinity.edu with Internet Mail Service (5.5.2653.19) id ; Thu, 28 Jun 2001 17:53:13 -0500 Message-ID: From: "Mills, Nancy S." To: CHEMISTRY@ccl.net Subject: ZINDO/S vs ZINDO-1 Date: Thu, 28 Jun 2001 17:53:12 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" I had asked if there was a difference between ZINDO/S and ZINDO-1 and which was in Gaussian 98, which listed ZINDO-1. Here are the primary responses: yes, there are differences. They are mostly in atomic parameters. ZINDO/S is for spectroscopic simulations (and the method is pretty good at it!). ZINDO/1 is for geometry optimizations (and the method is not so good, unfortunately...). There was a development (see Int. J. Quantum Chemistry, vol.81, 187-201, 2001) by M.C.Zerver group in Florida to fix some problems with ZINDO/1 but I think that the changes have been implemented only in the original ZINDO program, not in Gaussian 98 or HyperChem. Regards, Serge ________________________________________________________________ Sergey I. Gorelsky A bit of history: The "1" in ZINDO-1 (originally called INDO/1) comes from the way the one-center core integrals were obtained from ionization potentials only (as in the original CNDO/1 model) and uses an empirical expression for the two-center coulomb integrals. In Mike's original paper from TCA 1973, they developed the first spectroscopic parameterization for this approach and applied it to benzene, pyrrole and the azines. This method became known as the INDO1/S. Due to the popularity of Mike's ZINDO program, over time the method simply became known as ZINDO/s The INDO/1 (for geometries) approach uses somewhat different parameters and employs analytical two-center coulomb integrals over Slater orbitals. It was fairly useful for geometry optimization for transition metal systems, especially since no other popular semi-empirical approach could treat these systems at the time. However, for general organic systems, INDO/1 (or ZINDO-1) gave poor results. The ZINDO/s method has become more popular with the passing of time. This is remarkable for a semi-empirical method first developed in the early 70's. Mike and I used it to do some of the first calculations of the bacterial photosynthetic reaction center; involving hundreds of quantum-mechanically treated atoms. At the time this calculation required a Cray supercomputer to run. Later, at PNNL, I used ZINDO in a QM/MM polarizable model I developed to re-run the reaction center calculations, this time including the entire reaction center protein in the calculation (as polarizable MM atoms) with very good results (J. Phys. Chem. 1995, vol 99, 6374). This calculation ran on a fast workstation. (now I can routinely rerun these calculations on the pc from which I am typing this message). Over the years, Mike was very interested in getting a single semi-empirical Hamiltonian to work well for both geometries and spectra. In the last 3 years, Mike, Kotker Rosch, and Alexander Voityuk did some interesting work on NDDO-G, which was a new semi-empirical scheme meant to address this issue (J. Phys. Chem A. 1999, vol 103, 4553). There was never any "official" ZINDO/s parameterization that was published with statistical analysis like the AM1 and PM3 methods. For the first row and first transition series the parameters were pretty much stabilized over the years. However, they would often be changed for a particular paper to, for example, improve n->pi* transitions, or to improve triplet spectra. A few years ago, I helped the Gaussian developers with some of the more obscure ZINDO issues when they were implementing their version of ZINDO. To my knowledge, the Gaussian implementation and our ArgusLab implementation of ZINDO should agree pretty well. We are putting in a parameter editor to the next version of ArgusLab to allow for easier modification of ZINDO parameters and to allow new elements to be added. I don't know how HyperChem's results compare with Gaussian and ArgsuLab. Hope this helps a bit. (shameless plug...) You can obtain ArgusLab free of charge at: http://www.planaria-software.com Cheers, Mark Thompson Planaria Software Seattle, WA. > From two readers, including one from Gaussian, confirmation that the version of ZINDO in Gaussian 98 is ZINDO/2, even though the documentation suggests otherwise. Finally, a caution about use: word of advise, be careful with zindo and anions. I am getting very funny results with that. Adrian E. Roitberg [mailto:adrian@qtp.ufl.edu] Thanks to everyone for their help. Nancy Nancy Mills, PhD Phone, (210) 999-7317 Professor Fax, (210) 999-7569 Department of Chemistry nmills@trinity.edu Trinity University 715 Stadium Dr. San Antonio, TX 78212-7200 From chemistry-request@server.ccl.net Thu Jun 28 19:20:46 2001 Received: from exchangefc.gilead.com ([4.20.178.68]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5SNKk509784 for ; Thu, 28 Jun 2001 19:20:46 -0400 Received: by exchangefc.gilead.com with Internet Mail Service (5.5.2653.19) id ; Thu, 28 Jun 2001 16:20:44 -0700 Message-ID: From: Xiaowu Chen To: chemistry@ccl.net Subject: algorithm calculating the volume of a protein pocket ? Date: Thu, 28 Jun 2001 16:20:51 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Hi, I wonder if there are programs that can calcultes the volume of a protein pocket, ideally, such programs should allow users some flexibility in defining pockets. Thanks. Xiaowu Chen From chemistry-request@server.ccl.net Thu Jun 28 20:47:02 2001 Received: from janus.hosting4u.net ([209.15.2.37]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f5T0l2511826 for ; Thu, 28 Jun 2001 20:47:02 -0400 Received: (qmail 21153 invoked from network); 29 Jun 2001 00:47:03 -0000 Received: from zeus.hosting4u.net (HELO proinformatix.com) (209.15.2.56) by mail-gate.hosting4u.net with SMTP; 29 Jun 2001 00:47:03 -0000 Received: from yersina ([198.142.60.14]) by proinformatix.com ; Thu, 28 Jun 2001 19:46:57 -0500 Reply-To: From: "Sergio Manzetti" To: Subject: ISIS, BABEL AND GAUSSIAN 98 Date: Fri, 29 Jun 2001 10:47:16 -0700 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Hello everyone! I am attempting to draw molecules in ISIS Draw (MDL MOL file), and convert them to acceptable GAUSSIAN98 formats, using Babel. Do any of you have an idea of which format is ok to convert to for G98, using BAbel? I have tried many different variants, but the problem is that the structure as drawed in ISIS is far away from energetically favourable, even the bond lengths are 60-70% shorter than what they should be (according to the AMBER5 FF). PDB format was tried too, but G98 doesn't recognize, and "says" "BAD ATOMIC DATA" . Are there any specific preference for PDB import in G98? Best Regards Sergio ____________________________________________________________________________ ___________________________ Sergio Manzetti Research Scholar Centre of Molecular Biotechnology/ Supercomputer Facility Queensland University of Technology 2 George St. BRISBANE 4000 QLD AUSTRALIA email: s.manzetti@student.qut.edu.au Tlf: +61 7 3864 1434 www: http://www.life.sci.qut.edu.au/html/research/cmgenetics.html www2: http://www.its.qut.edu.au/hpc/ From chemistry-request@server.ccl.net Thu Jun 28 23:55:10 2001 Received: from popeye.latrobe.edu.au ([131.172.4.60]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5T3t9514391 for ; Thu, 28 Jun 2001 23:55:09 -0400 Received: from [131.172.148.97] (gln.chem.latrobe.edu.au [131.172.148.97]) by popeye.latrobe.edu.au (8.9.3/8.9.3) with ESMTP id NAA04160; Fri, 29 Jun 2001 13:55:07 +1000 (EST) Mime-Version: 1.0 X-Sender: chemgn@pop.latrobe.edu.au Message-Id: In-Reply-To: <20010627171429.C5696@campfire.rrz.Uni-Koeln.DE> References: <20010627171429.C5696@campfire.rrz.Uni-Koeln.DE> Date: Fri, 29 Jun 2001 13:55:37 +1000 To: chemistry@ccl.net From: "Graeme L. Nyberg" Subject: Re: CCL:simulation/calculation of ir/Raman linewidths Cc: Lars Packschies Content-Type: text/plain; charset="us-ascii" ; format="flowed" If your wavenumber/intensity data are from Gaussian9x, and you are using a Mac,there is a free program called Gaussian Companion that will read a Gaussian output file, extract the vibrational data (frequency, IR and Raman intensities) and apply a lineshape. The lineshape can be either Gaussian or Lorentzian, and the linewiths can be (collectively) adjusted. The spectrum displayed can be either IR or Raman, or all bands. >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...