From chemistry-request@server.ccl.net Wed Apr 24 05:41:57 2002 Received: from mserv.itpa.lt ([193.219.53.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3O9ftA21766 for ; Wed, 24 Apr 2002 05:41:56 -0400 Received: from localhost (tamulis@localhost) by mserv.itpa.lt (8.11.6/8.11.0) with ESMTP id g3O9fkw20087 for ; Wed, 24 Apr 2002 11:41:50 +0200 (EET) (envelope-from tamulis@itpa.lt) Date: Wed, 24 Apr 2002 11:41:46 +0200 (EET) From: Arvydas Tamulis To: Subject: Atomic charges and potentials in ABINIT v3.3.2 (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Colleagues, We are starting calculations using program ABINIT version 3.3.2 Do it is possible to calculate atomic charges in different excited states using DFT-TD of ABINIT version 3.3.2 ? As you know that in Gaussian 98 DFT-TD atomic charges in excited states are calculating using one-particle electron densities and atomic charges in the ground state are calculating using HF electron density. Therefore it is difficult to compare these two in principle different values obtained by G98. How are calculating atomic charges in excited and ground states using ABINIT version 3.3.2 ? I have two questions concerning DFT potentials in this ABINIT version 3.3.2 program: 1) Do ABINIT using GGA's functionals possess some density inhomogeneity as it is in the case of PerdewWang91 ? I am asking because we are interesting in charge transfer calculations in excited non-symmetrical large supermolecules. 2) Do it is possible to use well known potentials B3LYP, B3PW91 in ABINIT version 3.3.2 ? Thanking your in advance. With best regards, Arvydas Tamulis ******************************************************************* Arvydas Tamulis Doctor of Natural Sciences, senior research fellow Institute of Theoretical Physics and Astronomy, Vilnius University, Theoretical Molecular Electronics Research Group, A. Gostauto 12, Vilnius 2600, Lithuania e-mail: TAMULIS@ITPA.lt; WEBsite: http://www.itpa.lt/~tamulis/ fax: +(370-2)-225361 or +(370-2)-224694 Phone: +(370-2)-620861 Home address: Didlaukio 27-40, Vilnius 2057, Lithuania Mobile phone: +370-9919397 ******************************************************************* Date: Thu, 21 Mar 2002 09:21:45 +0100 From: Xavier Gonze To: abinit@pcpm.ucl.ac.be Subject: (ABINIT) v3.3.2 Dear ABINITioners, ABINIT version 3.3.2 is available ... You will find it on the Web site, as usual. The complete sources and tests are available, as well as the sequential and MPI-parallel executable versions for Compaq/DEC_EV56_Linux, Compaq/DEC_EV67_OSF, IBM 44P , CRAY T3E, and the sequential version on PCLinux with the PGI compiler. The list of modifications of v3.3.2 is written below, and can be found also in the file ~ABINIT/changes.3.3.x . In particular, with contrast to v3.3.1, ABINITv3.3.2 works ..... *************** From chemistry-request@server.ccl.net Wed Apr 24 09:45:13 2002 Received: from mserv.itpa.lt ([193.219.53.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3ODjAA25360 for ; Wed, 24 Apr 2002 09:45:11 -0400 Received: from localhost (tamulis@localhost) by mserv.itpa.lt (8.11.6/8.11.0) with ESMTP id g3ODium22086; Wed, 24 Apr 2002 15:44:56 +0200 (EET) (envelope-from tamulis@itpa.lt) Date: Wed, 24 Apr 2002 15:44:56 +0200 (EET) From: Arvydas Tamulis To: cc: Subject: Re: CCL:Atomic charges ... In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Professor Spanget-Larsen, Thank you for your comment on my mistake that arrive from my text concerning HF-TD calculation analysis. In any case, I wanted to say that in G98 DFT-TD the absolute values of atomic charge change have not any physical meaning and can not be interpreted as electron density amount transfer during excitation. The main question of my former letter was: what it is the algorithm of charge transfer in ABINIT DFT-TD ? I have just received response from Professor Gonze, who is one of authors of ABINIT: No analysis of static charges is yet available in ABINIT. The reason is simple: we use a plane-wave basis set, for which there is no such concept as a Mulliken population analysis. We are now implementing Hirshfeld analysis, then Bader analysis, but it will take some time. Best regards, Arvydas Tamulis ********************** On Wed, 24 Apr 2002, Jens Spanget-Larsen wrote: > Arvydas Tamulis: > > > .. As you know that in > > Gaussian 98 DFT-TD atomic charges in excited states are calculating > > using one-particle electron densities and atomic charges in the > > ground state are calculating using HF electron density. > > Dear Arvydas, > just one comment: It is not true that the ground state atomic charges > obtained by a G98 TD-DFT calculation are derived from a Hartree-Fock > (HF) electron density. The printed ground state charges are the > results of a Mulliken population analysis performed with the DFT > Kohn-Sham molecular orbitals. > > Yours, Jens >--< > > NB! Please note new mail address: > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > JENS SPANGET-LARSEN Office: +45 4674 2710 > Department of Chemistry Fax: +45 4674 3011 > Roskilde University (RUC) Mobile: +45 2320 6246 > P.O.Box 260 E-Mail: spanget@ruc.dk > DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > From chemistry-request@server.ccl.net Wed Apr 24 11:02:27 2002 Received: from smtp9.jaring.my ([61.6.32.59]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3OF2QA26965 for ; Wed, 24 Apr 2002 11:02:26 -0400 Received: from vplaces.net (j125.crc20.jaring.my [61.6.157.139]) by smtp9.jaring.my (8.11.4/8.11.4) with ESMTP id g3OF2Ed25696 for ; Wed, 24 Apr 2002 23:02:15 +0800 (MYT) Message-ID: <3CC6C9FC.484B2B39@vplaces.net> Date: Wed, 24 Apr 2002 23:06:36 +0800 From: Rowyna X-Mailer: Mozilla 4.75 [en] (Win98; U) X-Accept-Language: en,pdf MIME-Version: 1.0 To: CCL Subject: change upon binding Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I have a question regarding Autodock. I had a crystalised protein-ligand complex, in which I took out the ligand and docked it with Autodock. THe results have been consistent with the crystal structure. But when I used a different ligand for docking, the results are not quite as expected. I believe that the conformation of the binding site has been shifted favourable to the original ligand and so therefore, as autodock treats the protein rigid, the prediction of the interactions with a different ligand is not a good. Has anybody been through this sort of problem? I'd love to hear some opinions on it. Actually, I'd like to find out how the binding of the another ligand affects the conformation of the binding site, and I can't quite do it with autodock. So, I am giving molecular dynamics a try. If there's somebody who encountered something like this before, would be glad to hear your input. I've learned a lot from the mailing list so I thank all of you for your help. Rowyna K. From chemistry-request@server.ccl.net Wed Apr 24 06:45:29 2002 Received: from relay.unizar.es ([155.210.3.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3OAjSA22530 for ; Wed, 24 Apr 2002 06:45:28 -0400 Received: from posta.unizar.es (root@posta.unizar.es [155.210.11.16]) by relay.unizar.es (8.11.1/8.11.1) with ESMTP id g3OAjFp22841 for ; Wed, 24 Apr 2002 12:45:15 +0200 (MET DST) Received: from QOTTFP4 ([155.210.90.178]) by posta.unizar.es (8.11.1/8.11.1) with SMTP id g3OAgE829684 for ; Wed, 24 Apr 2002 12:42:14 +0200 (MET DST) Message-ID: <001201c1eb7d$1b13db10$b25ad29b@QOTTFP4> From: =?iso-8859-1?Q?Jes=FAs_Orduna?= To: "CCL" Subject: Two photon absorption cross section units Date: Wed, 24 Apr 2002 12:45:09 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000F_01C1EB8D.DE551AC0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-Virus-Scanned: TAMIZ + Sophos en unizar.es This is a multi-part message in MIME format. ------=_NextPart_000_000F_01C1EB8D.DE551AC0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable dear CCLers, I am becoming interested in Two Photon Absortion (TPA) processes and the = use of quantum chemical calculations to predict TPA cross sections. > From a three level aproach, the TPA cross section is expresed as: (mu(0,1))^2 (mu(1,2))^2/(delta E)^2 So it should have the dimensions of "dipole moment^4/Energy^2" but the TPA cross section is usually expresed in "cm^4 s/molecule" units = which at least at first sight have a completely different dimension. Could somebody clarify the relationship between these ways to express = the TPA cross sections? How can I convert calculated croos sections in atomic units to cm^4 = s/molecule? Thanks =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Jes=FAs Orduna Instituto de Ciencia de Materiales de Aragon Unidad de Nuevos Materiales Org=E1nicos Facultad de Ciencias CSIC-Universidad de Zaragoza E-50009 Zaragoza (Spain) Phone/FAX: +34 976 761194 e-mail: jorduna@posta.unizar.es =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D ------=_NextPart_000_000F_01C1EB8D.DE551AC0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
dear CCLers,
 
I am becoming interested in Two Photon = Absortion=20 (TPA) processes and the use of quantum chemical calculations to predict = TPA=20 cross sections.
 
From a three level aproach, the TPA = cross section=20 is expresed as:
 
 (mu(0,1))^2 (mu(1,2))^2/(delta=20 E)^2
 
So it should have the dimensions = of  "dipole=20 moment^4/Energy^2"
 
but the TPA cross section is usually = expresed in=20 "cm^4 s/molecule" units which at least at first sight have a completely=20 different dimension.
 
Could somebody clarify the relationship = between=20 these ways to express the TPA cross sections?
 
How can I convert calculated croos = sections in=20 atomic units to cm^4 s/molecule?
 
 
Thanks
 
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Jes= =FAs Orduna
Instituto=20 de Ciencia de Materiales de Aragon
Unidad de Nuevos Materiales=20 Org=E1nicos
Facultad de Ciencias
CSIC-Universidad de = Zaragoza
E-50009=20 Zaragoza (Spain)
Phone/FAX: +34 976 761194
e-mail: jorduna@posta.unizar.es
=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
------=_NextPart_000_000F_01C1EB8D.DE551AC0-- From chemistry-request@server.ccl.net Wed Apr 24 11:06:05 2002 Received: from f04n01.cac.psu.edu ([128.118.141.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3OF65A27093 for ; Wed, 24 Apr 2002 11:06:05 -0400 Received: from ra.chem.psu.edu (ra.chem.psu.edu [128.118.199.40]) by f04n01.cac.psu.edu (8.9.3/8.9.3) with ESMTP id LAA36596 for ; Wed, 24 Apr 2002 11:05:59 -0400 Content-Type: text/plain; charset="us-ascii" From: Rajarshi Guha Reply-To: rajarshi@presidency.com To: Subject: compiling Mopac 7.01-4 Date: Wed, 24 Apr 2002 11:05:24 -0400 X-Mailer: KMail [version 1.4] MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Message-Id: <200204241105.30946.rajarshi@presidency.com> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, I'm trying to compile Mopac 7.01-4 on Linux (kernel 2.4.7-10) with g77 -I've tried both 2.96 and 3.0 and I get the same results: matou1.f: In subroutine `matou1': matou1.f:5: PARAMETER (MAXDIM=MAX(MAXORB,3*NUMATM)) ^ Invalid declaration of or reference to symbol `max' at (^) [initially seen at (^)] And a series of other errors. I'm sure somebody must have compiled it on Linux but I cant seem to find anything relevant to the problem in the archives. I also looked at the makefile and there does'nt seem to be any reference to f2c but all the docs say that I need f2c. I'm a little confused and ny pointers would be appreciated. TIA, - -- - ------------------------------------------------------------------- Rajarshi Guha | email: rajarshi@presidency.com 417 Davey Laboratory | web : http:// www.jijo.cjb.net Dept. Of Chemistry | ICQ : 123242928 Pennsylvania State University | AIM : LoverOfPanda - ------------------------------------------------------------------- GPG Fingerprint: DCCB 4D1A 5A8B 2F5A B5F6 1F9E CDC4 5574 9017 AF2A Public Key : http://pgp.mit.edu/ - ------------------------------------------------------------------- Gravity brings me down. -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.6 (GNU/Linux) Comment: For info see http://www.gnupg.org iD8DBQE8xsm6zcRVdJAXryoRAiogAJ9ddVzJq7ez4zJkAPHc5xJjPC3SDwCfYl8v PSvfX6v+Z0zqJuTVVnqwNDY= =DPDE -----END PGP SIGNATURE----- From chemistry-request@server.ccl.net Tue Apr 23 17:05:20 2002 Received: from f04n07.cac.psu.edu ([128.118.141.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3NL5KA13622 for ; Tue, 23 Apr 2002 17:05:20 -0400 Received: from ra.chem.psu.edu (ra.chem.psu.edu [128.118.199.40]) by f04n07.cac.psu.edu (8.9.3/8.9.3) with ESMTP id RAA392826 for ; Tue, 23 Apr 2002 17:05:10 -0400 Content-Type: text/plain; charset="us-ascii" From: Rajarshi Guha Reply-To: rajarshi@presidency.com To: chemistry@ccl.net Subject: physical properties for c60 Date: Tue, 23 Apr 2002 17:04:43 -0400 X-Mailer: KMail [version 1.4] MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Message-Id: <200204231704.43273.rajarshi@presidency.com> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, could somebody point me to papers or online sources regarding the physical properties C60 - I'm looking for specific heat capaciy and entropy. TIA, - -- - ------------------------------------------------------------------- Rajarshi Guha | email: rajarshi@presidency.com 417 Davey Laboratory | web : http:// www.jijo.cjb.net Dept. Of Chemistry | ICQ : 123242928 Pennsylvania State University | AIM : LoverOfPanda - ------------------------------------------------------------------- GPG Fingerprint: DCCB 4D1A 5A8B 2F5A B5F6 1F9E CDC4 5574 9017 AF2A Public Key : http://pgp.mit.edu/ - ------------------------------------------------------------------- "355/113 -- Not the famous irrational number PI, but an incredible simulation!" -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.6 (GNU/Linux) Comment: For info see http://www.gnupg.org iD8DBQE8xcxrzcRVdJAXryoRAsiOAJ9C0H4EsAtCYVHYlxayGhScTBLL1wCffxvL GmG7xxkQNxZaRtXshaa8A7g= =B7ko -----END PGP SIGNATURE----- From chemistry-request@server.ccl.net Wed Apr 24 13:10:02 2002 Received: from thor.chem.sdu.dk ([130.225.142.15]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3OHA2A29343 for ; Wed, 24 Apr 2002 13:10:02 -0400 Received: from localhost (tetz@localhost) by thor.chem.sdu.dk (SGI-8.9.3/8.9.3) with ESMTP id TAA66906; Wed, 24 Apr 2002 19:12:08 +0200 (MDT) Date: Wed, 24 Apr 2002 19:12:07 +0200 From: Per Tetzschner Olsen To: Rajarshi Guha cc: chemistry@ccl.net Subject: Re: CCL:physical properties for c60 In-Reply-To: <200204231704.43273.rajarshi@presidency.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi TIA I am not sure if it is a help but try Professor Lawrence T. Scott. He works with C60 at Boston College Per On Tue, 23 Apr 2002, Rajarshi Guha wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Hi, > could somebody point me to papers or online sources regarding the physical > properties C60 - I'm looking for specific heat capaciy and entropy. > > TIA, > > - -- > - ------------------------------------------------------------------- > Rajarshi Guha | email: rajarshi@presidency.com > 417 Davey Laboratory | web : http:// www.jijo.cjb.net > Dept. Of Chemistry | ICQ : 123242928 > Pennsylvania State University | AIM : LoverOfPanda > - ------------------------------------------------------------------- > GPG Fingerprint: DCCB 4D1A 5A8B 2F5A B5F6 1F9E CDC4 5574 9017 AF2A > Public Key : http://pgp.mit.edu/ > - ------------------------------------------------------------------- > "355/113 -- Not the famous irrational number PI, but an incredible > simulation!" > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.0.6 (GNU/Linux) > Comment: For info see http://www.gnupg.org > > iD8DBQE8xcxrzcRVdJAXryoRAsiOAJ9C0H4EsAtCYVHYlxayGhScTBLL1wCffxvL > GmG7xxkQNxZaRtXshaa8A7g= > =B7ko > -----END PGP SIGNATURE----- > > > > -= 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 Apr 24 13:30:24 2002 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3OHUOA29655 for ; Wed, 24 Apr 2002 13:30:24 -0400 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id NAA60688; Wed, 24 Apr 2002 13:23:15 -0400 (EDT) Date: Wed, 24 Apr 2002 13:23:14 -0400 From: Rick Venable To: Rajarshi Guha cc: CHEMISTRY@ccl.net Subject: Re: CCL:compiling Mopac 7.01-4 In-Reply-To: <200204241105.30946.rajarshi@presidency.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 24 Apr 2002, Rajarshi Guha wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Hi, > I'm trying to compile Mopac 7.01-4 on Linux (kernel 2.4.7-10) with g77 -I've > tried both 2.96 and 3.0 and I get the same results: > > matou1.f: In subroutine `matou1': > matou1.f:5: > PARAMETER (MAXDIM=MAX(MAXORB,3*NUMATM)) > ^ > Invalid declaration of or reference to symbol `max' at (^) [initially seen at > (^)] > > And a series of other errors. I'm sure somebody must have compiled it on Linux > but I cant seem to find anything relevant to the problem in the archives. I > also looked at the makefile and there does'nt seem to be any reference to f2c > but all the docs say that I need f2c. I'm a little confused and ny pointers > would be appreciated. For f2c, Fortran front-end is often a cover script named 'fort77'; look for that in the Makefile. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@server.ccl.net Wed Apr 24 13:48:37 2002 Received: from qtp.ufl.edu ([128.227.89.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3OHmbA29923 for ; Wed, 24 Apr 2002 13:48:37 -0400 Received: from pc1 (pc1 [128.227.192.187]) by qtp.ufl.edu (8.9.1a/8.9.1/deumens) with SMTP id NAA00656; Wed, 24 Apr 2002 13:48:33 -0400 (EDT) Message-ID: <0f4501c1ebb9$2f606c50$bbc0e380@qtp.ufl.edu> From: "Stefan Fau" To: "Yubo Fan" Cc: "CCL - all" References: <3CC625CD.68BBC46B@mail.chem.tamu.edu> Subject: Re: CCL:NLMO - Highest occupied NBOs are not at the beginning of the NBO list Date: Wed, 24 Apr 2002 13:55:08 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Hi Yubo, it is a problem most often encountered with transition metals: the program finds low occupancy NBOs where it expects high occupancy NBOs. Sometimes it helps to reorganize the sequence of atoms in the input: put the offending atom last in the geometry specification. A convenient way of doing that is to cut the LAST "standard orientation" out of the optimization output and convert it into xyz-coordinates. Shuffle the lines and use it in the new input. Stefan ______________________________________________________________________ Dr. Stefan Fau | fau@qtp.ufl.edu University of Florida | (352) 392-6714 Quantum Theory Project 2341 NPB #92, P.O.Box 117200 Gainesville, FL 32611-7200 From chemistry-request@server.ccl.net Wed Apr 24 14:04:14 2002 Received: from gate.ggr.co.uk ([193.128.25.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3OI4DA30122 for ; Wed, 24 Apr 2002 14:04:13 -0400 Received: (uucp@localhost) by gate.ggr.co.uk; Wed, 24 Apr 2002 19:05:43 +0100 (BST) Received: from uk-stv-mhub1.ggr.co.uk(147.184.212.132) by gb-stv-fw2.ggr.co.uk via smap (V5.5) id xma004139; Wed, 24 Apr 02 19:04:53 +0100 Received: from ukz590.ggr.co.uk (ukz590.ggr.co.uk [147.184.226.247]) by mailhub.ggr.co.uk; Wed, 24 Apr 2002 19:03:17 +0100 (BST) Received: from ukz792.ggr.co.uk (unverified) by ukz590.ggr.co.uk (Content Technologies SMTPRS 2.0.15) with ESMTP id for ; Wed, 24 Apr 2002 19:03:11 +0100 Received: by ukz792.ggr.co.uk with Internet Mail Service (5.5.2654.89) id ; Wed, 24 Apr 2002 19:03:13 +0100 Message-Id: From: "Mclay, Iain" To: "'chemistry@ccl.net'" Subject: RE: UK QSAR and ChemoInformatics Discussion Group Date: Wed, 24 Apr 2002 19:03:08 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2654.89) Content-Type: text/plain > Please find details of the next UK QSAR and ChemoInformatics Group > Meeting > > UK QSAR and ChemoInformatics Group will be holding their next > meeting at > > Accelrys' new UK Centre, Cambridge, > > on the 11th June 2002 > > The programme will include a session on analysis of HTS data and a > session > of QSAR related topics. The main speakers will be: > > John Topliss, (U. Michigan) > > Jon Mason (Pfizer UK), > > Rob Brown (Accelrys), > > Eric Jamois(Accelrys), > > Darren Flower (Jenner Institute) > > Dick Cramer (Tripos Inc) > > ***The closing date for registration is Friday 31st May.*** > > If you would like to register for the meeting, or find out more, > then > please go to the meeting website at > > http://www.accelrys.com/events/qsar/ > > or > > visit the group web site at > > http://www.ukqsar.co.uk > or > http://www.iainm.demon.co.uk/ > > > > From chemistry-request@server.ccl.net Wed Apr 24 14:33:13 2002 Received: from kineo.bowdoin.edu ([139.140.14.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3OIXDA30630 for ; Wed, 24 Apr 2002 14:33:13 -0400 Received: from dhcp-135-123.bowdoin.edu ([139.140.135.123]) by kineo.bowdoin.edu (Netscape Messaging Server 4.15) with ESMTP id GV34V700.I2Q; Wed, 24 Apr 2002 14:33:07 -0400 Date: Wed, 24 Apr 2002 14:33:07 -0400 Subject: Re: CCL:physical properties for c60 Content-Type: text/plain; charset=US-ASCII; format=flowed Mime-Version: 1.0 (Apple Message framework v481) Cc: Rajarshi Guha , chemistry@ccl.net To: Per Tetzschner Olsen From: "Ha-Yeon Cheong" In-Reply-To: Message-Id: Content-Transfer-Encoding: 7bit X-Mailer: Apple Mail (2.481) Dear TIA, You should also try Professor Yves Rubin in UCLA. His e-mail is rubin@chem.ucla.edu. He works with C60 as well. Yours, Ha-Yeon Cheong Bowdoin College On Wednesday, April 24, 2002, at 01:12 PM, Per Tetzschner Olsen wrote: > > Hi TIA > > I am not sure if it is a help but try Professor Lawrence T. Scott. > He works with C60 at Boston College > > Per > > On Tue, 23 Apr 2002, Rajarshi Guha wrote: > >> -----BEGIN PGP SIGNED MESSAGE----- >> Hash: SHA1 >> >> Hi, >> could somebody point me to papers or online sources regarding the >> physical >> properties C60 - I'm looking for specific heat capaciy and entropy. >> >> TIA, >> >> - -- >> - ------------------------------------------------------------------- >> Rajarshi Guha | email: rajarshi@presidency.com >> 417 Davey Laboratory | web : http:// www.jijo.cjb.net >> Dept. Of Chemistry | ICQ : 123242928 >> Pennsylvania State University | AIM : LoverOfPanda >> - ------------------------------------------------------------------- >> GPG Fingerprint: DCCB 4D1A 5A8B 2F5A B5F6 1F9E CDC4 5574 9017 AF2A >> Public Key : http://pgp.mit.edu/ >> - ------------------------------------------------------------------- >> "355/113 -- Not the famous irrational number PI, but an incredible >> simulation!" >> -----BEGIN PGP SIGNATURE----- >> Version: GnuPG v1.0.6 (GNU/Linux) >> Comment: For info see http://www.gnupg.org >> >> iD8DBQE8xcxrzcRVdJAXryoRAsiOAJ9C0H4EsAtCYVHYlxayGhScTBLL1wCffxvL >> GmG7xxkQNxZaRtXshaa8A7g= >> =B7ko >> -----END PGP SIGNATURE----- >> >> >> >> >> >> >> >> >> > > > -= 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 Apr 24 14:58:29 2002 Received: from argyle.richmond.edu ([141.166.188.18]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3OIwTA31224 for ; Wed, 24 Apr 2002 14:58:29 -0400 Received: from sabrash.richmond.edu (lfa221037.richmond.edu [141.166.221.37]) by argyle.richmond.edu (8.11.6/8.11.6) with ESMTP id g3OIsIV17128; Wed, 24 Apr 2002 14:54:18 -0400 Message-Id: <5.1.0.14.0.20020424145400.02efa330@facstaff.richmond.edu> X-Sender: sabrash@facstaff.richmond.edu X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Wed, 24 Apr 2002 14:56:25 -0400 To: "Ha-Yeon Cheong" , Per Tetzschner Olsen From: "Samuel A. Abrash" Subject: Re: CCL:physical properties for c60 Cc: Rajarshi Guha , chemistry@ccl.net In-Reply-To: References: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed You should look at the NIST Webbook, http://webbook.nist.gov/ The heat capacity information is there. Best regards, Sam Abrash At 02:33 PM 04/24/2002 -0400, Ha-Yeon Cheong wrote: >Dear TIA, > >You should also try Professor Yves Rubin in UCLA. His e-mail is >rubin@chem.ucla.edu. He works with C60 as well. > >Yours, >Ha-Yeon Cheong >Bowdoin College > >On Wednesday, April 24, 2002, at 01:12 PM, Per Tetzschner Olsen wrote: > >> >>Hi TIA >> >>I am not sure if it is a help but try Professor Lawrence T. Scott. >>He works with C60 at Boston College >> >>Per >> >>On Tue, 23 Apr 2002, Rajarshi Guha wrote: >> >>>-----BEGIN PGP SIGNED MESSAGE----- >>>Hash: SHA1 >>> >>>Hi, >>> could somebody point me to papers or online sources regarding the >>> physical >>>properties C60 - I'm looking for specific heat capaciy and entropy. >>> >>>TIA, >>> >>>- -- >>>- ------------------------------------------------------------------- >>>Rajarshi Guha | email: rajarshi@presidency.com >>>417 Davey Laboratory | web : http:// www.jijo.cjb.net >>>Dept. Of Chemistry | ICQ : 123242928 >>>Pennsylvania State University | AIM : LoverOfPanda >>>- ------------------------------------------------------------------- >>>GPG Fingerprint: DCCB 4D1A 5A8B 2F5A B5F6 1F9E CDC4 5574 9017 AF2A >>>Public Key : http://pgp.mit.edu/ >>>- ------------------------------------------------------------------- >>>"355/113 -- Not the famous irrational number PI, but an incredible >>>simulation!" >>>-----BEGIN PGP SIGNATURE----- >>>Version: GnuPG v1.0.6 (GNU/Linux) >>>Comment: For info see http://www.gnupg.org >>> >>>iD8DBQE8xcxrzcRVdJAXryoRAsiOAJ9C0H4EsAtCYVHYlxayGhScTBLL1wCffxvL >>>GmG7xxkQNxZaRtXshaa8A7g= >>>=B7ko >>>-----END PGP SIGNATURE----- >>> >>> >>> >>> >>> >>> >>> >>> >> >> >>CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >>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 >> >> >> >> > > >-= 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 > > > Samuel A. Abrash Associate Professor Department of Chemistry University of Richmond Richmond, VA 23173 Phone: (804) 289-8248 Fax: (804) 287-1897 E-mail: sabrash@richmond.edu http://www.richmond.edu/~sabrash "Research is to teaching as sin is to confession - if you don't participate in one you don't have anything to say at the other." From chemistry-request@server.ccl.net Wed Apr 24 15:56:16 2002 Received: from mxout3.cac.washington.edu ([140.142.32.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3OJuGA32109 for ; Wed, 24 Apr 2002 15:56:16 -0400 Received: from mailscan-out2.cac.washington.edu (mailscan-out2.cac.washington.edu [140.142.33.17]) by mxout3.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW02.01) with SMTP id g3OJuA8J013745 for ; Wed, 24 Apr 2002 12:56:10 -0700 Received: FROM dante19.u.washington.edu BY mailscan-out2.cac.washington.edu ; Wed Apr 24 12:56:10 2002 -0700 Received: from localhost (jzheng73@localhost) by dante19.u.washington.edu (8.12.1+UW01.12/8.12.1+UW02.01) with ESMTP id g3OJu9lD075616 for ; Wed, 24 Apr 2002 12:56:09 -0700 Date: Wed, 24 Apr 2002 12:56:09 -0700 (PDT) From: "J. Zheng" cc: chemistry@ccl.net Subject: ask for workshop of charmm or linux cluster. In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII hi, my question is a little bit out of subject of this forum. Now, I am working on how to write a script by using CHARMM software package. It really takes me lots of time to learn how to use it. I am wondering that if there is any workshop for teaching how to use CHARMM. I think it would be much better for me in order to save the time and learn more stuff from CHARMM. I am also looking for the workshop, "how to build a bewolf cluster". if anybody has this information, please tell me. I will appreciate for your informing. thanks in advance. jie From chemistry-request@server.ccl.net Wed Apr 24 14:52:33 2002 Received: from umbi3.umbi.umd.edu ([136.160.7.51]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3OIqXA31156 for ; Wed, 24 Apr 2002 14:52:33 -0400 Received: from umbi.umd.edu ([129.6.113.76]) by umbi3.umbi.umd.edu (Netscape Messaging Server 4.15) with ESMTP id GV35SU00.3Z6 for ; Wed, 24 Apr 2002 14:53:18 -0400 Message-ID: <3CC6FF48.E0C70024@umbi.umd.edu> Date: Wed, 24 Apr 2002 14:54:00 -0400 From: "Michael K. Gilson" X-Mailer: Mozilla 4.78 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: cyclic urea data set at BindingDB Content-Type: multipart/alternative; boundary="------------6C195188F33452E5D948EEE6" --------------6C195188F33452E5D948EEE6 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit In response to several requests, we have made an sdf file of the cyclic urea data available on the front page of www.bindingdb.org. Look for the blue "sdf" link partway down the page. Let me know if you have any problems with it. If you use these or other data from Binding DB, we ask that you cite Chen,X., Lin,Y., Liu,M. and Gilson,M.K. The Binding Database: Data Management and Interface Design. Bioinformatics 18:130-139,2002. Please contact me if you have useful data collections -- preferably in electronic format -- that can be shared via BindingDB. Happy modeling, Mike Gilson --------------6C195188F33452E5D948EEE6 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit In response to several requests, we have made an sdf file of the cyclic urea data available on the front page of www.bindingdb.org. Look for the blue "sdf" link partway down the page. Let me know if you have any problems with it.

If you use these or other data from Binding DB, we ask that you cite Chen,X., Lin,Y., Liu,M. and Gilson,M.K. The Binding Database: Data Management and Interface Design. Bioinformatics 18:130-139,2002.

Please contact me if you have useful data collections -- preferably in electronic format -- that can be shared via BindingDB.

Happy modeling,
Mike Gilson --------------6C195188F33452E5D948EEE6--