From owner-chemistry@ccl.net Mon Oct 20 03:14:01 2008
From: "Jens Spanget-Larsen spanget+/-ruc.dk" <owner-chemistry::server.ccl.net>
To: CCL
Subject: CCL:G: A problem about the CI expansion coefficients
Message-Id: <-37951-081020030730-19481-l0o1/zYzWwGvVfzY6L4t+Q::server.ccl.net>
X-Original-From: Jens Spanget-Larsen <spanget() ruc.dk>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Mon, 20 Oct 2008 09:07:10 +0200
MIME-Version: 1.0


Sent to CCL by: Jens Spanget-Larsen [spanget#ruc.dk]

Dear Youzhao Lan,

coefficients larger than unity are quite normal with TD-UDFT
calculations, at least in the Gaussian version (see, e.g., Radsziszewski
et al., J. Chem. Phys. 115 (2001) 9733). This probably originates in the
circumstance that the TD-UDFT results are biorthonormal and Gaussian
does not give normalized coefficients in this case.

Jens >--<

  ------------------------------------------------------
  JENS SPANGET-LARSEN         Office:      +45 4674 2710
  Dept. of Science (18.1)     Fax:         +45 4674 3011
  Roskilde University         Mobile:      +45 2320 6246
  P.O.Box 260                 E-Mail:     spanget%a%ruc.dk
  DK-4000 Roskilde, Denmark   http://www.ruc.dk/~spanget
  ------------------------------------------------------



Youzhao Lan lyzhao%zjnu.cn wrote:
> Sent to CCL by: "Youzhao  Lan" [lyzhao() zjnu.cn]
> I calculated the first excited state of a doublet molecule using TDDFT under Gaussian03 and got the result:
>
> Excited State   1:   ?Spin  -BG     0.2962 eV 4185.32 nm  f=0.0000
>      98B -> 99B        1.03006
>  This state for optimization and/or second-order correction.
>  Total Energy, E(RPA) =  -5114.25187004    
>  Copying the excited state density for this state as the 1-particle RhoCI density.
> Excited State   2:   ?Spin  -BU     1.0708 eV 1157.87 nm  f=0.0040
>      98A ->101A        0.11472
>      98A ->102A        0.24101
>      99A ->100A        0.35207
>      97B -> 99B        0.96071
>      98B ->100B        0.22098
>
> Could anyone tell me whether it is available that the CI expansion coefficient 1.03006 is larger than 1? I have investigated the excitation properties of many systems and hardly gotten such CI expansion coefficient.
>
> Great thanks for any help!! 
> Welcome any references.>
>
>


From owner-chemistry@ccl.net Mon Oct 20 04:11:00 2008
From: "Brandt, Wolfgang wbrandt]^[ipb-halle.de" <owner-chemistry ~~ server.ccl.net>
To: CCL
Subject: CCL: AW: Problems in protein modeling
Message-Id: <-37952-081020034351-9444-8/aziBNl+XbJm8WTCvuJ0Q ~~ server.ccl.net>
X-Original-From: "Brandt, Wolfgang" <wbrandt_._ipb-halle.de>
content-class: urn:content-classes:message
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain;
	charset="iso-8859-1"
Date: Mon, 20 Oct 2008 09:05:47 +0200
MIME-Version: 1.0


Sent to CCL by: "Brandt, Wolfgang" [wbrandt _ ipb-halle.de]
Did you try the ab initio server?:

http://www.bioinfo.rpi.edu/~bystrc/hmmstr/server.php
or phyre ?
http://www.sbg.bio.ic.ac.uk/~3dpssm/

Theae are the only chance to ge more ideas.
Best Wolfgang Brandt

-----Urspr=FCngliche Nachricht-----
Von: owner-chemistry _ ccl.net [mailto:owner-chemistry _ ccl.net]
Gesendet: Sonntag, 19. Oktober 2008 04:28
An: Brandt, Wolfgang
Betreff: CCL: Problems in protein modeling



Sent to CCL by: "Bruno  Andrade" [bandradefsa^^yahoo.com.br]
Hi people!

I have been working with protein homology modeling, but now I a have a=20
protein sequence wich have a very low identity with other proteins =
deposited=20
in the PDB and other database (very high e-value, and low score, too). =
When=20
I submit my protein to an homology modeling process, the result is very=20
bad... the program returns to a small part of this molecule modeled. So, =
I=20
thougth someone can help in another kind of molecular modeling, such ab=20
initio, and as I can solve me protein structure.

If you know something about any free program or tool on the internet, it =

will be very helpfull to my work.

Thank you very much.

Bruno Andrade.



-=3D This is automatically added to each message by the mailing script =
=3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20Search Messages: http://www.ccl.net/htdig  (login: ccl, Password: =
search)http://www.ccl.net/spammers.txt

From owner-chemistry@ccl.net Mon Oct 20 10:07:00 2008
From: "Pierre Archirel pierre.archirel.=-=.lcp.u-psud.fr" <owner-chemistry=-=server.ccl.net>
To: CCL
Subject: CCL: Answer to : PMF with implicit Solvent
Message-Id: <-37953-081020100448-17165-MI9vGdXs0w8o4d06iKnMdA=-=server.ccl.net>
X-Original-From: Pierre Archirel <pierre.archirel()lcp.u-psud.fr>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Mon, 20 Oct 2008 16:03:45 +0200
MIME-Version: 1.0


Sent to CCL by: Pierre Archirel [pierre.archirel*o*lcp.u-psud.fr]
This is an answer to R. Ribeiro.
Dear collegue,
In his book (p. 419) C. Cramer shows the PMF curve of, say, a dimer of 
Cl- in water.
This dimer is known to display two minimas at large and short distances.
The two cavities are the cavities of the two Cl-!
At large distance the two cavities are two separated spheres,
at some distance they begin to interpenetrate. This is the issue
mentioned in Cramer's book.
Pierre Archirel
LCP, Universite d'Orsay, France

__________________________________________________________

 Pierre Archirel
 Groupe de Chimie Théorique
 Laboratoire de Chimie Physique      Tel: 01 69 15 63 86
 Bat 349                             Fax: 01 69 15 61 88
 91405 Orsay Cedex
 France                   pierre.archirel()lcp.u-psud.fr
__________________________________________________________


From owner-chemistry@ccl.net Mon Oct 20 11:29:01 2008
From: "Raphael Ribeiro raphaelri a hotmail.com" <owner-chemistry-,-server.ccl.net>
To: CCL
Subject: CCL: Answer to : PMF with implicit Solvent
Message-Id: <-37954-081020111430-23586-wXyCtGP3xji3lkSM5J/xXA-,-server.ccl.net>
X-Original-From: "Raphael  Ribeiro" <raphaelri|,|hotmail.com>
Date: Mon, 20 Oct 2008 11:14:26 -0400


Sent to CCL by: "Raphael  Ribeiro" [raphaelri##hotmail.com]
Dear Pierre,
 
Thank you for your answer, now I can understand the curve. I thought the PMF curve referred to solute and solvent molecules, not two solute molecules and that is why I could not understand some issues. Now it makes sense to me, I mean a curve of PMF between solute and solvent, in a implicit description of the solvent, would be a decreasing curve just like the potential electrostatic energy curve (as there is no consideration of entropic effects), so there is no way of getting an accurate PMF (solute x solvent) if there are no explicit solvent molecules.


--------------------------------------------------------------------------------

> From: owner-chemistry*ccl.net
> To: raphaelri*hotmail.com
> Subject: CCL: Answer to : PMF with implicit Solvent
> Date: Mon, 20 Oct 2008 16:03:45 +0200
> 
> 
> Sent to CCL by: Pierre Archirel [pierre.archirel*o*lcp.u-psud.fr]
> This is an answer to R. Ribeiro.
> Dear collegue,
> In his book (p. 419) C. Cramer shows the PMF curve of, say, a dimer of 
> Cl- in water.
> This dimer is known to display two minimas at large and short distances.
> The two cavities are the cavities of the two Cl-!
> At large distance the two cavities are two separated spheres,
> at some distance they begin to interpenetrate. This is the issue
> mentioned in Cramer's book.
> Pierre Archirel
> LCP, Universite d'Orsay, France
> 
> __________________________________________________________
> 
> Pierre Archirel
> Groupe de Chimie Thorique
> Laboratoire de Chimie Physique Tel: 01 69 15 63 86
> Bat 349 Fax: 01 69 15 61 88
> 91405 Orsay Cedex
> France pierre.archirel.*.lcp.u-psud.fr
> __________________________________________________________> 
>


From owner-chemistry@ccl.net Mon Oct 20 12:50:00 2008
From: "Melissa melchem{}gmail.com" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL:G: fluorescence spectra
Message-Id: <-37955-081020124649-12498-/o8P1ibP953CLaG6M4rXRw^server.ccl.net>
X-Original-From: "Melissa" <melchem,,gmail.com>
Content-Type: multipart/alternative;
	boundary="----=_NextPart_000_009C_01C932C2.A3AE4080"
Date: Mon, 20 Oct 2008 14:46:30 -0200
MIME-Version: 1.0


Sent to CCL by: "Melissa" [melchem++gmail.com]
Esta i uma mensagem em varias partes no formato MIME.

------=_NextPart_000_009C_01C932C2.A3AE4080
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable


Dear John McKelvey and David Gallagher,

Thank you very much for yours replies, they were very enlightening.

Best regards,

Melissa


-------------------------------------------------------------------------=
-------------------------------------


=20
On Thu, Oct 9, 2008 at 1:21 PM, Melissa melchem{:}gmail.com =
<owner-chemistry[*]ccl.net> wrote:

  Dear CCL readers,

  I would like to know how to calculate fluorescence spectra of organic =
molecules using g03? Could anyone please help me.

  Thanks in advance,

  Melissa


------=_NextPart_000_009C_01C932C2.A3AE4080
Content-Type: text/html;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=3DContent-Type =
content=3Dtext/html;charset=3Diso-8859-1>
<META content=3D"MSHTML 6.00.6000.16735" name=3DGENERATOR></HEAD>
<BODY id=3DMailContainerBody=20
style=3D"PADDING-RIGHT: 10px; PADDING-LEFT: 10px; PADDING-TOP: 15px"=20
bgColor=3D#ffffff leftMargin=3D0 topMargin=3D0 CanvasTabStop=3D"true"=20
name=3D"Compose message area">
<DIV><FONT color=3D#000080></FONT>&nbsp;</DIV>
<DIV style=3D"FONT: 10pt Tahoma">
<DIV>
<DIV><FONT color=3D#000080 size=3D3>Dear John McKelvey and David=20
Gallagher,</FONT></DIV>
<DIV><FONT color=3D#000080></FONT><FONT size=3D3></FONT>&nbsp;</DIV>
<DIV><FONT color=3D#000080 size=3D3>Thank you&nbsp;very much =
for&nbsp;yours replies,=20
they were very enlightening.</FONT></DIV>
<DIV><FONT color=3D#000080 size=3D3></FONT>&nbsp;</DIV>
<DIV><FONT color=3D#000080 size=3D3>Best regards,</FONT></DIV>
<DIV><FONT color=3D#000080 size=3D3></FONT>&nbsp;</DIV>
<DIV><FONT color=3D#000080 size=3D3>Melissa</FONT></DIV>
<DIV><FONT color=3D#000080></FONT>&nbsp;</DIV>
<DIV><FONT color=3D#000080></FONT>&nbsp;</DIV><FONT color=3D#000080=20
size=3D3>----------------------------------------------------------------=
----------------------------------------------</FONT><BR></DIV>
<DIV style=3D"BACKGROUND: #f5f5f5">
<DIV style=3D"font-color: black"><FONT face=3D"Times New Roman" =
color=3D#000080=20
size=3D3></FONT><BR>&nbsp;</DIV></DIV></DIV>
<DIV dir=3Dltr>
<DIV class=3Dgmail_quote>On Thu, Oct 9, 2008 at 1:21 PM, Melissa =
melchem{:}<A=20
title=3D"http://gmail.com&#10;CTRL + Clique para seguir o link"=20
href=3D"http://gmail.com" target=3D_blank>gmail.com</A> <SPAN =
dir=3Dltr>&lt;<A=20
title=3D"mailto:owner-chemistry[*]ccl.net&#10;CTRL + Clique para seguir =
o link"=20
href=3D"mailto:owner-chemistry[*]ccl.net"=20
target=3D_blank>owner-chemistry[*]ccl.net</A>&gt;</SPAN> wrote:<BR>
<BLOCKQUOTE class=3Dgmail_quote=20
style=3D"PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: =
rgb(204,204,204) 1px solid">
  <DIV style=3D"PADDING-RIGHT: 10px; PADDING-LEFT: 10px; PADDING-TOP: =
15px"=20
  name=3D"Compose message area" bgcolor=3D"#ffffff">
  <DIV><FONT color=3D#000000>Dear CCL readers,</FONT></DIV>
  <DIV><FONT color=3D#000000></FONT>&nbsp;</DIV>
  <DIV><FONT color=3D#000000>I would like to know&nbsp;how to calculate =
<FONT=20
  face=3DTimes-Roman size=3D2><FONT face=3DTimes-Roman size=3D2><FONT=20
  size=3D3>fluorescence </FONT></FONT></FONT>spectra of organic=20
  molecules&nbsp;using g03? Could anyone please help me.</FONT></DIV>
  <DIV><FONT color=3D#000080></FONT>&nbsp;</DIV>
  <DIV><FONT color=3D#000000>Thanks in advance<FONT=20
  color=3D#000080>,</FONT><BR></FONT></DIV><FONT color=3D#888888>
  <DIV><FONT=20
color=3D#000000>Melissa</FONT></DIV></FONT></DIV></BLOCKQUOTE></DIV><BR><=
/DIV></BODY></HTML>

------=_NextPart_000_009C_01C932C2.A3AE4080--


From owner-chemistry@ccl.net Mon Oct 20 16:37:01 2008
From: "James Gary Prudhomme jprudhomme*o*healthtech.com" <owner-chemistry]^[server.ccl.net>
To: CCL
Subject: CCL: Call for Speakers: Structure-Based Drug Design
Message-Id: <-37956-081020163332-27712-3nLX7QiRR61WocKSm1n0gw]^[server.ccl.net>
X-Original-From: "James Gary Prudhomme" <jprudhomme],[healthtech.com>
Date: Mon, 20 Oct 2008 16:33:28 -0400


Sent to CCL by: "James Gary Prudhomme" [jprudhomme[a]healthtech.com]
CALL FOR SPEAKER PROPOSALS 

Cambridge Healthtech Institute's Ninth Annual 
STRUCTURE-BASED DRUG DESIGN 
June 4-5, 2009 | Royal Sonesta Hotel | Cambridge, Massachusetts 

Submit a speaker proposal at www.healthtech.com/sbd/es.aspx
Deadline for submission: November 9, 2008

In this program, we wish to highlight some recent breakthrough stories and successes using SBDD driven by medicinal chemistry, computational and biophysical approaches. All proposals are subject to review by the Scientific Advisory Committee to ensure the overall quality of the conference program. 

Deadline to submit a speaker proposal is November 9, 2008.

For more information, please contact: 
Micah Lieberman
Executive Director, Conferences
Cambridge Healthtech Institute
250 First Ave, Suite 300
Needham, MA 02494
Tel: 541-482-4709
E-mail: mlieberman(-)pharmaseries.com