From owner-chemistry@ccl.net Tue Feb  3 01:56:00 2009
From: "Sue L chsue2004(~)yahoo.com" <owner-chemistry||server.ccl.net>
To: CCL
Subject: CCL:G: Broken Symmetry Singlet Excited State
Message-Id: <-38539-090203015411-30759-3OIKaVGVXUgZw/fRa4qjUw||server.ccl.net>
X-Original-From: "Sue  L" <chsue2004++yahoo.com>
Date: Tue, 3 Feb 2009 01:54:06 -0500


Sent to CCL by: "Sue  L" [chsue2004..yahoo.com]
Hi, 

I am running a DFT open-shell singlet calculation using Gaussian 03 to obtain a broken symmetry singlet excited state. Does anyone know whether the electronic energy calculated at the end based on the annihilated wave function or not? 

Thank you very much!

Best regards,
Sue


From owner-chemistry@ccl.net Tue Feb  3 06:30:00 2009
From: "hirdesh kumar hirdeshs8]_[gmail.com" <owner-chemistry(a)server.ccl.net>
To: CCL
Subject: CCL: Target identification for reported inhibitor
Message-Id: <-38540-090203062710-27272-YSQxUxpm3s55GYyHw/saDg(a)server.ccl.net>
X-Original-From: hirdesh kumar <hirdeshs8[*]gmail.com>
Content-Type: multipart/alternative; boundary=001485f01b28f89b8f046201f2bf
Date: Tue, 3 Feb 2009 16:56:57 +0530
MIME-Version: 1.0


Sent to CCL by: hirdesh kumar [hirdeshs8 * gmail.com]
--001485f01b28f89b8f046201f2bf
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit

Hi All;
I have a molecule in my hand which is well reported antitubercular drug but
the respective target protein is not known! Can anyone suggest me how can i
find the target for this ligand?

--001485f01b28f89b8f046201f2bf
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit

Hi All;<br>I have a molecule in my hand which is well reported antitubercular drug but the respective target protein is not known! Can anyone suggest me how can i find the target for this ligand?<br clear="all"><br><br>

--001485f01b28f89b8f046201f2bf--


From owner-chemistry@ccl.net Tue Feb  3 07:50:00 2009
From: "David A. Case case^^biomaps.rutgers.edu" <owner-chemistry^^^server.ccl.net>
To: CCL
Subject: CCL: Source codes for ligand docking softwares
Message-Id: <-38541-090202110600-21529-1b0gFmq+9LKAduNV6os+8g^^^server.ccl.net>
X-Original-From: "David A. Case" <case#,#biomaps.rutgers.edu>
Content-Disposition: inline
Content-Type: text/plain; charset=us-ascii
Date: Mon, 2 Feb 2009 10:03:29 -0500
MIME-Version: 1.0


Sent to CCL by: "David A. Case" [case#,#biomaps.rutgers.edu]

On Thu, Jan 29, 2009, Skull Crossbones wrote
> 
> 
> Can anyone provide names of some ligand docking softwares, for which the
> source codes are available.

See UCSF DOCK: http://dock.compbio.ucsf.edu/

...dave case


From owner-chemistry@ccl.net Tue Feb  3 09:01:00 2009
From: "Zhong jie Liang zjliang=-=mail.shcnc.ac.cn" <owner-chemistry---server.ccl.net>
To: CCL
Subject: CCL: the charge problem in ONIOM method in Gaussian
Message-Id: <-38542-090203080734-17478-mfsPZe4eJ7ug6tGqeFLgDQ---server.ccl.net>
X-Original-From: "Zhong jie Liang" <zjliang()mail.shcnc.ac.cn>
Date: Tue, 3 Feb 2009 08:07:30 -0500


Sent to CCL by: "Zhong jie Liang" [zjliang#mail.shcnc.ac.cn]
Dear experts,
  I have had a  question  for a long time  in  the QM/MM method calculations. That is how  to  get  the  whole charge  on the real system.
I just calculated every atom charge on total with Excel,and the result is  
-8.5876.That is even not integer. How  should  I do ?
  Wish to get your answer very much!







                                            ZhongjieLiang
                                      zjliang|-|mail.shcnc.ac.cn
                          Shanghai Institute of Materia Medica


From owner-chemistry@ccl.net Tue Feb  3 10:35:00 2009
From: "Maxim Kholin maxim.kholin=-=q-pharm.com" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL: Target identification for reported inhibitor
Message-Id: <-38543-090203102133-21293-dV52eDtOJryM05l2RRF0Xw-#-server.ccl.net>
X-Original-From: Maxim Kholin <maxim.kholin- -q-pharm.com>
Content-Type: multipart/alternative; boundary=0016e65bc1ceb4c94f046205380c
Date: Tue, 3 Feb 2009 18:21:12 +0300
MIME-Version: 1.0


Sent to CCL by: Maxim Kholin [maxim.kholin|-|q-pharm.com]
--0016e65bc1ceb4c94f046205380c
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit

Hi,
We are doing that for many customers, including Top Pharma Performing a
mechanism of action exploration by using a proprietary representative panel
of proteins covering virtually all human proteome to identify active
clusters of the binding sites. A list of the proteins with the binding sites
highly homological to the representative proteins found to be active will be
provided together with explanation of the proteins function.
Feel free to contact us.

-- 
Maxim Kholin
Business Development Director
Quantum Pharmaceuticals
Tel. +7(499) 150 8332
Fax  +7(499) 156 156 1
125171, 6a Kosmonavta Volkova, off. # 606
Moscow,  Russia
maxim.kholin-*-q-pharm.com
www.q-pharm.com
www.q-lead.com

2009/2/3 hirdesh kumar hirdeshs8]_[gmail.com <owner-chemistry-*-ccl.net>

> Hi All;
> I have a molecule in my hand which is well reported antitubercular drug but
> the respective target protein is not known! Can anyone suggest me how can i
> find the target for this ligand?
>
>
>

--0016e65bc1ceb4c94f046205380c
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Hi,<br>We are doing that for many customers, including Top Pharma <span sty=
le=3D"font-size: 10pt; font-family: sans-serif;" lang=3D"EN-US"><span><span=
 style=3D"font-family: &quot;Times New Roman&quot;; font-style: normal; fon=
t-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal=
; font-size-adjust: none; font-stretch: normal;">P</span></span></span><spa=
n style=3D"font-size: 10pt; font-family: sans-serif;" lang=3D"EN-US">erform=
ing a mechanism of action exploration by using a proprietary representative
panel of proteins covering virtually all human proteome to identify active
clusters of the binding sites. A list of the proteins with the binding site=
s
highly homological to the representative proteins found to be active will b=
e
provided together with explanation of the proteins function. </span><br>Fee=
l free to contact us.<br><br>-- <br>Maxim Kholin<br>Business Development Di=
rector <br>Quantum Pharmaceuticals<br>Tel. +7(499) 150 8332<br>Fax &nbsp;+7=
(499) 156 156 1<br>
125171, 6a Kosmonavta Volkova, off. # 606<br>
Moscow, &nbsp;Russia<br><a href=3D"mailto:maxim.kholin-*-q-pharm.com" target=
=3D"_blank">maxim.kholin-*-q-pharm.com</a><br><a href=3D"http://www.q-pharm.c=
om/" target=3D"_blank">www.q-pharm.com</a><br><a href=3D"http://www.q-lead.=
com/" target=3D"_blank">www.q-lead.com</a> <br>
<br><div class=3D"gmail_quote">2009/2/3 hirdesh kumar hirdeshs8]_[<a href=
=3D"http://gmail.com" target=3D"_blank">gmail.com</a> <span dir=3D"ltr">&lt=
;<a href=3D"mailto:owner-chemistry-*-ccl.net" target=3D"_blank">owner-chemist=
ry-*-ccl.net</a>&gt;</span><br>

<blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid rgb(204, =
204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi All;<br>I have=
 a molecule in my hand which is well reported antitubercular drug but the r=
espective target protein is not known! Can anyone suggest me how can i find=
 the target for this ligand?<br clear=3D"all">

<br><br>
</blockquote></div><br><br clear=3D"all"><br><br> <br><br>

--0016e65bc1ceb4c94f046205380c--


From owner-chemistry@ccl.net Tue Feb  3 11:09:00 2009
From: "Alexander Klenner klenner[a]bioinformatik.uni-frankfurt.de" <owner-chemistry-,-server.ccl.net>
To: CCL
Subject: CCL: Target identification for reported inhibitor
Message-Id: <-38544-090203082543-24985-eKs0HrPPeKh2L1eJ1ZBKBA-,-server.ccl.net>
X-Original-From: Alexander Klenner <klenner]=[bioinformatik.uni-frankfurt.de>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Tue, 03 Feb 2009 13:16:52 +0100
MIME-Version: 1.0


Sent to CCL by: Alexander Klenner [klenner|-|bioinformatik.uni-frankfurt.de]
hirdesh kumar hirdeshs8]_[gmail.com schrieb:
> Hi All;
> I have a molecule in my hand which is well reported antitubercular 
> drug but the respective target protein is not known! Can anyone 
> suggest me how can i find the target for this ligand?
>
>
Hi,

a quite general approach would be to map your ligand onto other ligands 
(e.g similarity search) from which you do know the target. What you need 
therefore is a database that contains ligands and their  respectives 
targets.  If your are lucky your ligand will be mapped into a certain 
cluster of known ligands that target a specific protein.  That could be 
a first hint for your target, also you can check if this target makes 
sense regarding the antitubercular effect.

Cheers,

Alex

-- 
Alexander Klenner, Dipl.-Bioinf.
Johann Wolfgang Goethe-University Frankfurt
Department of Biosciences
Siesmayerstrasse 70
D-60323 Frankfurt
Tel: +49 (0) 69 798 24879
Fax: +49 (0) 69 798 24880
klenner a bioinformatik.uni-frankfurt.de


From owner-chemistry@ccl.net Tue Feb  3 13:00:01 2009
From: "Jean-Christophe Poully poully=galilee.univ-paris13.fr" <owner-chemistry]_[server.ccl.net>
To: CCL
Subject: CCL: the charge problem in ONIOM method in Gaussian
Message-Id: <-38545-090203110828-7285-1lXP93zWATjWcqWbiIZ5WA]_[server.ccl.net>
X-Original-From: Jean-Christophe Poully <poully,,galilee.univ-paris13.fr>
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain; charset="iso-8859-1"; format=flowed
Date: Tue, 03 Feb 2009 17:08:29 +0100
Mime-Version: 1.0


Sent to CCL by: Jean-Christophe Poully [poully_+_galilee.univ-paris13.fr]

Dear Zhongjie,

It is rather simple to know the charge of the=20
real system, it is the net charge of your=20
molecule that you must know by advance. It is a=20
bit more complicated to get the charge and=20
multiplicity of the model system, especially=20
beware of the link atoms!! Don't put an atom=20
linked by two high layer atoms in the low layer,=20
Oniom would be confused and you would end up with an unpaired electron.

Hope it helps,

Jean-Christophe Poully



At 14:07 03/02/2009, you wrote:

>Sent to CCL by: "Zhong jie Liang" [zjliang#mail.shcnc.ac.cn]
>Dear experts,
>   I have had a  question  for a long=20
> time  in  the QM/MM method calculations. That=20
> is how  to  get  the  whole charge  on the real system.
>I just calculated every atom charge on total with Excel,and the result is
>-8.5876.That is even not integer. How  should  I do ?
>   Wish to get your answer very much!
>
>
>
>
>
>
>
>                                             ZhongjieLiang
>                                       zjliang=3D-=3Dmail.shcnc.ac.cn
>                           Shanghai Institute of Materia Medica
>
>
>
>-=3D This is automatically added to each message by the mailing script =3D-Jean-Christophe Poully

Doctorant dans l'=E9quipe AMIBES
Laboratoire de Physique des Lasers
Institut Galil=E9e
99, avenue JB Cl=E9ment
93430 VILLETANEUSE

Bureau B002
0149403853=20


From owner-chemistry@ccl.net Tue Feb  3 13:37:00 2009
From: "Harry Stern hstern16(-)mac.com" <owner-chemistry .. server.ccl.net>
To: CCL
Subject: CCL: comp chem in NY Times
Message-Id: <-38546-090203124853-1748-46SE5f8Q5QZTUXYuIMsitw .. server.ccl.net>
X-Original-From: Harry Stern <hstern16. .. .mac.com>
Content-type: multipart/alternative;
 boundary="Boundary_(ID_dvW7Mt3DRy48ZPvLtCB2IQ)"
Date: Tue, 03 Feb 2009 11:48:22 -0500
MIME-version: 1.0


Sent to CCL by: Harry Stern [hstern16(0)mac.com]

--Boundary_(ID_dvW7Mt3DRy48ZPvLtCB2IQ)
Content-type: text/plain; charset=US-ASCII; format=flowed
Content-transfer-encoding: 7BIT

http://www.nytimes.com/2009/02/03/science/03boron.html

- - - -
Harry A. Stern
Assistant Professor, Department of Chemistry
University of Rochester
RC Box 270216
Rochester, NY 14627-0216
(585) 275-8804


--Boundary_(ID_dvW7Mt3DRy48ZPvLtCB2IQ)
Content-type: text/html; charset=US-ASCII
Content-transfer-encoding: quoted-printable

<html><body style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; =
-webkit-line-break: after-white-space; "><div style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal =
normal normal 12px/normal Helvetica; "><a =
href=3D"http://www.nytimes.com/2009/02/03/science/03boron.html">http://www=
.nytimes.com/2009/02/03/science/03boron.html</a></div><div =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; font: normal normal normal 12px/normal Helvetica; =
"><br></div><div apple-content-edited=3D"true"><div> <p style=3D"margin: =
0.0px 0.0px 0.0px 0.0px"><font face=3D"Helvetica" size=3D"3" =
style=3D"font: 12.0px Helvetica">- - - -</font></p> <p style=3D"margin: =
0.0px 0.0px 0.0px 0.0px"><font face=3D"Helvetica" size=3D"3" =
style=3D"font: 12.0px Helvetica">Harry A. Stern</font></p> <p =
style=3D"margin: 0.0px 0.0px 0.0px 0.0px"><font face=3D"Helvetica" =
size=3D"3" style=3D"font: 12.0px Helvetica">Assistant Professor, =
Department of Chemistry</font></p> <p style=3D"margin: 0.0px 0.0px 0.0px =
0.0px"><font face=3D"Helvetica" size=3D"3" style=3D"font: 12.0px =
Helvetica">University of Rochester</font></p> <p style=3D"margin: 0.0px =
0.0px 0.0px 0.0px"><font face=3D"Helvetica" size=3D"3" style=3D"font: =
12.0px Helvetica">RC Box 270216</font></p> <p style=3D"margin: 0.0px =
0.0px 0.0px 0.0px"><font face=3D"Helvetica" size=3D"3" style=3D"font: =
12.0px Helvetica">Rochester, NY 14627-0216</font></p> <p style=3D"margin: =
0.0px 0.0px 0.0px 0.0px"><font face=3D"Helvetica" size=3D"3" =
style=3D"font: 12.0px Helvetica">(585) 275-8804</font></p> </div> =
</div><br></body></html>=

--Boundary_(ID_dvW7Mt3DRy48ZPvLtCB2IQ)--


From owner-chemistry@ccl.net Tue Feb  3 20:56:01 2009
From: "Zhong jie Liang zjliang]^[mail.shcnc.ac.cn" <owner-chemistry- -server.ccl.net>
To: CCL
Subject: CCL:G: the charge problem in ONIOM method in Gaussian
Message-Id: <-38547-090203205320-18146-DxdKPOLl1d7iGEkkLkiDbw- -server.ccl.net>
X-Original-From: "Zhong jie Liang" <zjliang-$-mail.shcnc.ac.cn>
Date: Tue, 3 Feb 2009 20:53:17 -0500


Sent to CCL by: "Zhong jie Liang" [zjliang..mail.shcnc.ac.cn]
Dear Jean-Christophe,
  Thanks for your answer very much.But I still have the problem .
  That is how to get the net charge. I know it is easy to get the net charge with Sybyl software. But the charge Sybyl uses is diffenrent from the charge used in GaussianView software, especially that Sybyl adds different charge types on the protein residues and ligands,which affects the result.I don't know if GaussianView can get the net charge on the whole molecule easily.This is not a big problem,but I want to make it clearly.
Wish your answer.Thanks.










                                            ZhongjieLiang
                                         zjliang++mail.shcnc.ac.cn
                                   Shanghai Institute of Materia Medica


From owner-chemistry@ccl.net Tue Feb  3 23:24:00 2009
From: "D Joshua Dibble ddibble() uci.edu" <owner-chemistry~!~server.ccl.net>
To: CCL
Subject: CCL:G: Problem with an NBO calculation.
Message-Id: <-38548-090203230107-21899-FK7Fr8glX/P0fgdkOYwDHA~!~server.ccl.net>
X-Original-From: "D Joshua Dibble" <ddibble---uci.edu>
Date: Tue, 3 Feb 2009 23:01:04 -0500


Sent to CCL by: "D Joshua Dibble" [ddibble . uci.edu]
Hello,

I am unable to complete an NBO calculation, particularly the NBO deletion routing.  The header to the input file is as follows:

%chk=axial.chk
%mem=1000MB
%NProcShared=2
# b3lyp/6-311g(d,p) pop=(savenbo,nbodel) geom=connectivity iop(5/48=10000)
scf=tight 

The output is:

N-N= 1.094452818274D+03 E-N=-3.791025927973D+03  KE= 6.929502473477D+02
NtrOpn-Old failed.
Error termination via Lnk1e in /modfac/apps//g03/l607.exe at Tue Feb  3 19:11:22 2009.
Job cpu time:  0 days  0 hours 16 minutes 51.1 seconds.
File lengths (MBytes):  RWF=     99 Int=      0 D2E=      0 Chk=      5 Scr=      1 



Running Gaussian 03 E.01, NBO version 3.

Does anyone know what this error means?

Thank you for your time,
D. Joshua Dibble
ddibble|*|uci.edu