From owner-chemistry@ccl.net Mon Sep 27 05:13:01 2010
From: "Sayan Mondal sayanmondal.ncbs[#]gmail.com" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL: TDDFT- transition dipole moment
Message-Id: <-42840-100927051135-23992-GnEPs5laP+5HJKFl1IeilA++server.ccl.net>
X-Original-From: Sayan Mondal <sayanmondal.ncbs_._gmail.com>
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Date: Mon, 27 Sep 2010 14:41:25 +0530
MIME-Version: 1.0


Sent to CCL by: Sayan Mondal [sayanmondal.ncbs^gmail.com]
On 9/23/10, Sayan Mondal <sayanmondal.ncbs**gmail.com> wrote:
> Hi Sagarika,
>
> For a detail implementation of the subject, you can read the book titled
> "Time-Dependent Density Functional Theory"
> edited by Marques, M.A.L.; Ullrich, C.A.; Nogueira, F.; Rubio, A.;
> Burke, K.; Gross, E.K.U.
> http://www.springer.com/physics/book/978-3-540-35422-2
>
> Also take a look at the recent review on TD-DFT by M.E.Casida
> "Time-dependent density-functional theory for molecules and molecular
> solids"
> http://dx.doi.org/10.1016/j.theochem.2009.08.018
> and the references there in.
>
> sayan
>
>
> On 9/23/10, Sagarika Dev sagarika.dev(0)gmail.com
> <owner-chemistry**ccl.net> wrote:
>>
>> Sent to CCL by: "Sagarika  Dev" [sagarika.dev]_[gmail.com]
>> Dear Dr. Allouche
>>  I can visualise the transition dipole moment vector by Gabedit. Thank
>> you
>> very much. Can you suggest me a good text book to get more in depth
>> knowledge about TDDFT theory.
>> regards
>> Sagarika>>
>>
>>
>
>
> --
> Sayan Mondal
> Graduate Student
> Dr. Mrinalini Puranik's Lab
> National Centre for Biological Sciences, TIFR
> Bangalore - 560065
> INDIA
> Ph:  +91-080-2366 6161
> Fax: +91-080-2363 6662
>


-- 
Sayan Mondal
Graduate Student
Dr. Mrinalini Puranik's Lab
National Centre for Biological Sciences, TIFR
Bangalore - 560065
INDIA
Ph:  +91-080-2366 6161
Fax: +91-080-2363 6662


From owner-chemistry@ccl.net Mon Sep 27 11:15:01 2010
From: "SUBHADEEP SAHA saha.subhadeep#%#gmail.com" <owner-chemistry:_:server.ccl.net>
To: CCL
Subject: CCL: problem with freezing atoms and bonds
Message-Id: <-42841-100927111032-23736-w9QiE/cgay6amZgSuphQyA:_:server.ccl.net>
X-Original-From: SUBHADEEP SAHA <saha.subhadeep]*[gmail.com>
Content-Type: multipart/alternative; boundary=001636164a2bdf3b6e04913f2009
Date: Mon, 27 Sep 2010 20:40:27 +0530
MIME-Version: 1.0


Sent to CCL by: SUBHADEEP SAHA [saha.subhadeep[a]gmail.com]
--001636164a2bdf3b6e04913f2009
Content-Type: text/plain; charset=ISO-8859-1

Dear all,

I am trying to optimize(b3lyp/6-31g) a structure freezing almost 20 atoms
and 30 bonds.Now the problem  is crashing after a running number of steps
giving the following error



Iteration100 RMS(Cart)=  0.00000470 RMS(Int)=  0.01035587
 New curvilinear step not converged.
 Error imposing constraints



I checked the final configuration and got that the some of the groups(which
are from the frozen bonds only,suppose I have frozen the C-H bonds of CH3
groups) moves away from initial configuration after feeling some favorable
interaction elsewhere.

I have checked CCL archive but did not get any satisfactory solution to
optimizing the structure keeping the constrains(Whatever I have provided)
same.

Can anyone please suggest a solution?

Thanks in advance...


-- 
Regards,
Subhadeep Saha
C/O Dr.Rahul Banerjee
Materials and Physical Chemistry Division
National Chemical Laboratory
Dr. Homi Bhabha Road
Pune:411008
Maharasthra
India
Ph:+91-20-2590-2387
     +91-20-2590-2535
     +91-20-2590-2598

--001636164a2bdf3b6e04913f2009
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Dear all,<br><br>I am trying to optimize(b3lyp/6-31g) a structure
freezing almost 20 atoms and 30 bonds.Now the problem=A0 is crashing
after a running number of steps=A0 giving the following error<br><br><br><b=
r>
Iteration100 RMS(Cart)=3D=A0 0.00000470 RMS(Int)=3D=A0 0.01035587<br>=A0New=
 curvilinear step not converged.<br>=A0Error imposing constraints<br><br><b=
r><br>I
checked the final configuration and got that the some of the
groups(which are from the frozen bonds only,suppose I have frozen the
C-H bonds of CH3 groups) moves away from initial configuration after
feeling some favorable interaction elsewhere.<br>
<br>I have checked CCL archive but did not get any satisfactory solution to=
 optimizing the structure keeping the constrains(Whatever I have provided) =
same.<br>
<br>Can anyone please suggest a solution?<br><br>Thanks in advance...<br><b=
r clear=3D"all"><br>-- <br>Regards,<br>Subhadeep Saha<br>C/O Dr.Rahul Baner=
jee<br>Materials and Physical Chemistry Division<br>National Chemical Labor=
atory<br>
Dr. Homi Bhabha Road<br>Pune:411008<br>Maharasthra<br>India<br>Ph:+91-20-25=
90-2387<br>=A0 =A0=A0 +91-20-2590-2535<br>=A0 =A0=A0 +91-20-2590-2598<br>

--001636164a2bdf3b6e04913f2009--


From owner-chemistry@ccl.net Mon Sep 27 11:50:00 2010
From: "SUBHADEEP SAHA saha.subhadeep*gmail.com" <owner-chemistry-x-server.ccl.net>
To: CCL
Subject: CCL: problem with fixing a bond
Message-Id: <-42842-100927110405-22706-NObekvkw8PtvcC2CnVWvvw-x-server.ccl.net>
X-Original-From: SUBHADEEP SAHA <saha.subhadeep]![gmail.com>
Content-Type: multipart/alternative; boundary=0015175cdddaa4463004913f080b
Date: Mon, 27 Sep 2010 20:33:40 +0530
MIME-Version: 1.0


Sent to CCL by: SUBHADEEP SAHA [saha.subhadeep.:.gmail.com]
--0015175cdddaa4463004913f080b
Content-Type: text/plain; charset=ISO-8859-1

Dear all,

I am trying to optimize(b3lyp/6-31g) a structure freezing almost 20 atoms
and 30 bonds.Now the problem  is crashing after a running number of steps
giving the following error



Iteration100 RMS(Cart)=  0.00000470 RMS(Int)=  0.01035587
 New curvilinear step not converged.
 Error imposing constraints



I checked the final configuration and got that the some of the groups(which
are from the frozen bonds only,suppose I have frozen the C-H bonds of CH3
groups) moves away from initial configuration after feeling some favorable
interaction elsewhere.

I have checked CCL archives"
http://server.ccl.net/cgi-bin/ccl/message-new?2003+05+23+007".But did not
get any satisfactory solution to optimizing the structure keeping the
constrains(Whatever I have provided) same.

Can anyone please suggest a solution?

Thanks in advance...


Regards,
Subhadeep Saha
C/O Dr.Rahul Banerjee
Materials and Physical Chemistry Division
National Chemical Laboratory
Dr. Homi Bhabha Road
Pune:411008
Maharasthra
India
Ph:+91-20-2590-2387
     +91-20-2590-2535
     +91-20-2590-2598

--0015175cdddaa4463004913f080b
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

<br clear=3D"all">Dear all,<br><br>I am trying to optimize(b3lyp/6-31g) a s=
tructure freezing almost 20 atoms and 30 bonds.Now the problem=A0 is crashi=
ng after a running number of steps=A0 giving the following error<br><br><br=
><br>
Iteration100 RMS(Cart)=3D=A0 0.00000470 RMS(Int)=3D=A0 0.01035587<br>=A0New=
 curvilinear step not converged.<br>=A0Error imposing constraints<br><br><b=
r><br>I checked the final configuration and got that the some of the groups=
(which are from the frozen bonds only,suppose I have frozen the C-H bonds o=
f CH3 groups) moves away from initial configuration after feeling some favo=
rable interaction elsewhere.<br>
<br>I have checked CCL archives&quot;<a href=3D"http://server.ccl.net/cgi-b=
in/ccl/message-new?2003+05+23+007">http://server.ccl.net/cgi-bin/ccl/messag=
e-new?2003+05+23+007</a>&quot;.But did not get any satisfactory solution to=
 optimizing the structure keeping the constrains(Whatever I have provided) =
same.<br>
<br>Can anyone please suggest a solution?<br><br>Thanks in advance...<br><b=
r><br>Regards,<br>Subhadeep Saha<br>C/O Dr.Rahul Banerjee<br>Materials and =
Physical Chemistry Division<br>National Chemical Laboratory<br>Dr. Homi Bha=
bha Road<br>
Pune:411008<br>Maharasthra<br>India<br>Ph:+91-20-2590-2387<br>=A0 =A0=A0 +9=
1-20-2590-2535<br>=A0 =A0=A0 +91-20-2590-2598<br>

--0015175cdddaa4463004913f080b--


From owner-chemistry@ccl.net Mon Sep 27 17:02:00 2010
From: "Phil McHale pmchale,cambridgesoft.com" <owner-chemistry/./server.ccl.net>
To: CCL
Subject: CCL: 2011 Herman Skolnik Award Winner Announced
Message-Id: <-42843-100927120357-18573-o6QdU0kPSCDdHYuddmRVVA/./server.ccl.net>
X-Original-From: "Phil  McHale" <pmchale/./cambridgesoft.com>
Date: Mon, 27 Sep 2010 12:03:56 -0400


Sent to CCL by: "Phil  McHale" [pmchale : cambridgesoft.com]
Professor Dr. Alexander (Sandy) Lawson will be the recipient of the 2011 Herman Skolnik Award presented by the ACS Division of Chemical Information (CINF). The award recognizes outstanding contributions to and achievements in the theory and practice of chemical information science and related disciplines. The prize consists of a $3,000 honorarium and a plaque. The winner will also be invited to present an award symposium at the Fall 2011 ACS Meeting.

Sandy Lawson is recognized as a pioneer and far-sighted visionary in the fields of chemical structure handling, database searching, chemical nomenclature, reading machines, and linking text and structural information. He has made numerous innovative contributions, often struggling with the limitations of nascent technology, to develop early prototypes to validate concepts, which sometimes only bore fruit when the technology caught up with his ideas. Sandy has spent a large part of his career associated with "Beilstein," initially working with the Beilstein Handbook. As early aids to searching in Beilstein, he developed the Lawson Number and the SANDRA program. He was instrumental in the creation and development of the electronic Beilstein Database, including both the organization, data structure, and indexing, and also the development of the powerful CrossFire search engine and interface, capable of handling millions of molecules, reactions, and properties. 

Sandy has a deep and abiding interest in chemical nomenclature and has been active on IUPAC Committees for Publications, Databases, and Structural Representation, including Division VIII Chemical Nomenclature of Organic Structures. His expertise lead him and his team to develop the first commercial program for generating systematic names from structures, AUTONOM, and then its counterpart, to generate structures from names. More recently Sandy has been involved in the consolidation of Beilstein, Gmelin, and Patent Chemistry Database into a unified database with modern and chemist-friendly interface, Reaxys. In his current role within Reed Elsevier, and in earlier organizations, he pioneered building bridges between the structured world of molecules and reactions in databases and the looser but nonetheless related realm of text in journals, and the early DYMOND Linking project presaged later developments such as Project Prospect from the Royal Society of Chemistry.

Sandy Lawson received a B.Sc. from the University of St. Andrews, and a Ph.D. and D.I.C. from the University of London. He did post-graduate work at the Universities of Kent and Mainz, and was an extramural professor at the latter. He has been awarded the Irvine Medal (1966), Forrester Prize (1966), Gold Medal (1985, for Sandra), EuroCase IT Prizewinner (1997, for CrossFire), and the CSA Trust Mike Lynch Award (2008). He has continued to pursue his love of cheminformatics research and development through a series of organizations, including the Beilstein Institute, Beilstein Informationssysteme GmbH, MDL Information Systems GmbH, Elsevier Information Systems GmbH, and latterly Elsevier Properties SA in Neuchtel. 

Sandy Lawson is among the handful of truly excellent cheminformatics scientists at work today, and is widely and thoroughly respected. He is a gentleman's scientist with a tremendous understanding of chemistry and computers. He embodies the best qualities of cheminformatics and is truly worthy of this award. 


Phil McHale
Chair, CINF Awards Committee


From owner-chemistry@ccl.net Mon Sep 27 17:37:00 2010
From: "Jim Kress ccl_nospam=kressworks.com" <owner-chemistry*server.ccl.net>
To: CCL
Subject: CCL: problem with fixing a bond
Message-Id: <-42844-100927155448-6707-7PsYfBPBEsHUvUKgHqKZRw*server.ccl.net>
X-Original-From: "Jim Kress" <ccl_nospam^^kressworks.com>
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Date: Mon, 27 Sep 2010 15:54:31 -0400
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Sent to CCL by: "Jim Kress" [ccl_nospam{}kressworks.com]
This is a multi-part message in MIME format.

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What software are you using and what do your input and output files look
like?

 

Jim

 

> From: owner-chemistry+ccl_nospam==kressworks.com[-]ccl.net
[mailto:owner-chemistry+ccl_nospam==kressworks.com[-]ccl.net] On Behalf Of
SUBHADEEP SAHA saha.subhadeep*gmail.com
Sent: Monday, September 27, 2010 11:04 AM
To: Kress, Jim 
Subject: CCL: problem with fixing a bond

 


Dear all,

I am trying to optimize(b3lyp/6-31g) a structure freezing almost 20 atoms
and 30 bonds.Now the problem  is crashing after a running number of steps
giving the following error



Iteration100 RMS(Cart)=  0.00000470 RMS(Int)=  0.01035587
 New curvilinear step not converged.
 Error imposing constraints



I checked the final configuration and got that the some of the groups(which
are from the frozen bonds only,suppose I have frozen the C-H bonds of CH3
groups) moves away from initial configuration after feeling some favorable
interaction elsewhere.

I have checked CCL
archives"http://server.ccl.net/cgi-bin/ccl/message-new?2003+05+23+007".But
did not get any satisfactory solution to optimizing the structure keeping
the constrains(Whatever I have provided) same.

Can anyone please suggest a solution?

Thanks in advance...


Regards,
Subhadeep Saha
C/O Dr.Rahul Banerjee
Materials and Physical Chemistry Division
National Chemical Laboratory
Dr. Homi Bhabha Road
Pune:411008
Maharasthra
India
Ph:+91-20-2590-2387
     +91-20-2590-2535
     +91-20-2590-2598


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<p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>What software are you using and what do your input and =
output
files look like?<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Jim<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

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0in 0in 0in'>

<p class=3DMsoNormal><b><span =
style=3D'font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span>=
</b><span
style=3D'font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
owner-chemistry+ccl_nospam=3D=3Dkressworks.com[-]ccl.net
[mailto:owner-chemistry+ccl_nospam=3D=3Dkressworks.com[-]ccl.net] <b>On =
Behalf Of </b>SUBHADEEP
SAHA saha.subhadeep*gmail.com<br>
<b>Sent:</b> Monday, September 27, 2010 11:04 AM<br>
<b>To:</b> Kress, Jim <br>
<b>Subject:</b> CCL: problem with fixing a bond<o:p></o:p></span></p>

</div>

<p class=3DMsoNormal><o:p>&nbsp;</o:p></p>

<p class=3DMsoNormal><br clear=3Dall>
Dear all,<br>
<br>
I am trying to optimize(b3lyp/6-31g) a structure freezing almost 20 =
atoms and
30 bonds.Now the problem&nbsp; is crashing after a running number of
steps&nbsp; giving the following error<br>
<br>
<br>
<br>
Iteration100 RMS(Cart)=3D&nbsp; 0.00000470 RMS(Int)=3D&nbsp; =
0.01035587<br>
&nbsp;New curvilinear step not converged.<br>
&nbsp;Error imposing constraints<br>
<br>
<br>
<br>
I checked the final configuration and got that the some of the =
groups(which are
> from the frozen bonds only,suppose I have frozen the C-H bonds of CH3 =
groups)
moves away from initial configuration after feeling some favorable =
interaction
elsewhere.<br>
<br>
I have checked CCL archives&quot;<a
href=3D"http://server.ccl.net/cgi-bin/ccl/message-new?2003+05+23+007">htt=
p://server.ccl.net/cgi-bin/ccl/message-new?2003+05+23+007</a>&quot;.But
did not get any satisfactory solution to optimizing the structure =
keeping the
constrains(Whatever I have provided) same.<br>
<br>
Can anyone please suggest a solution?<br>
<br>
Thanks in advance...<br>
<br>
<br>
Regards,<br>
Subhadeep Saha<br>
C/O Dr.Rahul Banerjee<br>
Materials and Physical Chemistry Division<br>
National Chemical Laboratory<br>
Dr. Homi Bhabha Road<br>
Pune:411008<br>
Maharasthra<br>
India<br>
Ph:+91-20-2590-2387<br>
&nbsp; &nbsp;&nbsp; +91-20-2590-2535<br>
&nbsp; &nbsp;&nbsp; +91-20-2590-2598<o:p></o:p></p>

</div>

</body>

</html>

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From owner-chemistry@ccl.net Mon Sep 27 21:27:00 2010
From: "Andrew Orry andy- -molsoft.com" <owner-chemistry{:}server.ccl.net>
To: CCL
Subject: CCL: Denovo ligand design: tools
Message-Id: <-42845-100927190609-25605-NCClskVcKmBrfACOX/VCYA{:}server.ccl.net>
X-Original-From: Andrew Orry <andy||molsoft.com>
Content-Transfer-Encoding: 7bit
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Date: Mon, 27 Sep 2010 16:06:00 -0700
MIME-Version: 1.0


Sent to CCL by: Andrew Orry [andy_-_molsoft.com]

Sangeetha,

Please consider MolSoft's ICM-Chemist-Pro ( 
http://www.molsoft.com/icm-chemist-pro.html ) software for this. This 
package includes a 3D ligand editor which allows you to interactively de 
novo design  a ligand, dock fragments, and build linkers. The package 
comes with scoring and ligand strain calculation to evaluate the ligand. 
There is a user guide here 
http://www.molsoft.com/gui/icm-chemist-pro-tutorials.html  with links to 
the manual and video demos.

Thanks,
Andrew

-- 
Andrew Orry Ph.D.
Senior Research Scientist
MolSoft LLC
3366 North Torrey Pines Court
Suite 300
La Jolla
CA 92037
Tel: 858-625-2000 x108
Fax: 828-625-2888
www.molsoft.com


On 9/24/2010 3:49 AM, SANGEETHA SUBRAMANIAM srdshigella]^[gmail.com wrote:
> Sent to CCL by: "SANGEETHA  SUBRAMANIAM" [srdshigella,,gmail.com]
> Dear Members,
>
> Can you please suggest the software available for denovo-ligand designing (both academic and commercial). Your information would be greatly appreciated.
>
> Thanks
> Sangeetha.>