From owner-chemistry@ccl.net Wed Apr  7 07:52:01 2010
From: "Guenter Grethe ggrethe|a|comcast.net" <owner-chemistry .. server.ccl.net>
To: CCL
Subject: CCL: Extended abstract submission for Pacifichem2010
Message-Id: <-41611-100406194957-14358-v6xXTkHzr5CdUy2eDZ1Kiw .. server.ccl.net>
X-Original-From: "Guenter  Grethe" <ggrethe#comcast.net>
Date: Tue, 6 Apr 2010 19:49:55 -0400


Sent to CCL by: "Guenter  Grethe" [ggrethe#%#comcast.net]

Final Call  Deadline for Abstract Submission Extended to April 12th, 2010

Announcing an upcoming symposium at Pacifichem 2010 in the Topic Area of Biological Chemistry.

Polypharmacology for Drug Discovery  (#90)

Coordinating Symposium Organizer: Guenter Grethe
Co-Organizers: Rajarshi Guha, Richard Horuk, Tsuneaki Sakata

Synopsis:
The symposium will address a broad range of topics covering both experimental and computation approaches. The latter include determination of off-target effects based on complete or partial knowledge of the membership of a protein target to a network, methods to identify network choke points and the design of drugs that target multiple proteins in a network or even multiple networks. Additionally, we solicit contributions that consider the dynamics of biological networks with respect to drug discovery, the use of network information for the repurposing of drugs, high-throughput screening and case studies highlighting the use of systems-level information to guide drug discovery. In the experimental area, methods discussing proteomics and chemical biology, especially those oriented towards perturbation and manipulation of biological networks will be included. Contributions describing the dynamics of biological networks with respect to drug discovery, the use of network information for the repurposing of drugs and high-throughput screening will be considered. Case studies highlighting the use of systems-level information to guide discovery with a focus on the therapeutic use of promiscuous drugs targeting GPCRs are solicited.

If you plan to present a paper either orally or as a poster, please go to http://pacifichem.abstractcentral.com/ and follow the instructions for abstract submission.  You have to establish an account in order to submit an abstract.  Extended abstract submission will close on April 12, 2010.  Feel free to contact me if you have any questions.

With best regards,
Guenter Grethe


From owner-chemistry@ccl.net Wed Apr  7 08:29:00 2010
From: "Jason Swails jason.swails^gmail.com" <owner-chemistry|a|server.ccl.net>
To: CCL
Subject: CCL: Negative NMODE
Message-Id: <-41612-100406121946-1440-QFVkWDEHn2hdPvFzobcALA|a|server.ccl.net>
X-Original-From: Jason Swails <jason.swails!^!gmail.com>
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Date: Tue, 6 Apr 2010 11:17:15 -0400
MIME-Version: 1.0


Sent to CCL by: Jason Swails [jason.swails|-|gmail.com]

Hello,

When you're doing normal mode analysis, the entropy for each species
should certainly be positive.  However, when you take a difference of
positive numbers, anything can happen :).  If you're performing your
calculations on a relatively large system, however, keep in mind that
you will have many vibrational degrees of freedom which in turn gives
rise to a very large value for vibrational energy calculations.
Taking differences of two large numbers to get a small number is a
challenge faced in virtually every aspect of computational chemistry
and plays havoc with your precision.

Also keep in mind that configurational entropy is not accounted for by
a nmode analysis.  Also be aware of the limitations of whatever
free-energy calculation you're doing and the assumptions made by the
method (especially MM/PB(GB)SA).

Finally, that said, a negative DELTA S binding is what I would expect,
as that implies that the unbound state has a higher entropy than the
bound state (which makes sense).

All the best,
Jason

On Tue, Apr 6, 2010 at 7:35 AM, Kshatresh Dutta Dubey
kshatresh*gmail.com <owner-chemistry(~)ccl.net> wrote:
> Dear All,
> During the calculation of binding free energy i got negative entropic
> contribution (NMODE= negative). Can entropic contributions be negative, and
> what is the significance of it?
> Every help is welcome. Thanks in advance.
> Regards
> kshatresh



-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032


From owner-chemistry@ccl.net Wed Apr  7 13:17:00 2010
From: "SUBHADEEP SAHA saha.subhadeep|-|gmail.com" <owner-chemistry[]server.ccl.net>
To: CCL
Subject: CCL:G: charge calculation using gaussian
Message-Id: <-41613-100407022102-30046-3pq3f2Yh7sdBPp9bfPdpuw[]server.ccl.net>
X-Original-From: SUBHADEEP SAHA <saha.subhadeep**gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Date: Wed, 7 Apr 2010 10:44:46 +0530
MIME-Version: 1.0


Sent to CCL by: SUBHADEEP SAHA [saha.subhadeep|,|gmail.com]

Dear all,
  I need to calculate charge on each atom of a cluster extrated from a
crystal using gaussian 03.
In the input file I have written "sp hf/6-31g geom=connectivity Pop=CHelpG"

But it is showing an error for Copper atom,
"GetVDW:  no radius for atom  28 atomic number  29"

Can anyone of you  help me out?
-- 
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


From owner-chemistry@ccl.net Wed Apr  7 13:52:00 2010
From: "David Livingstone davel,,chemquestuk.com" <owner-chemistry_+_server.ccl.net>
To: CCL
Subject: CCL: Essential books in computational chemistry (drug design)
Message-Id: <-41614-100407051921-25440-ETc9kVj+VqHwexQEb/3djg_+_server.ccl.net>
X-Original-From: "David Livingstone" <davel]*[chemquestuk.com>
Content-type: Multipart/Alternative; boundary="Alt-Boundary-23031.1093957"
Date: Wed, 07 Apr 2010 09:45:57 +0100
MIME-Version: 1.0


Sent to CCL by: "David Livingstone" [davel(~)chemquestuk.com]
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Sorry to be so tardy in replying to this.

My book on data analysis (a Practical Guide to Scientific Data Analysis,
Wiley, 2009) covers many of the techniques used in QSAR - indeed many of
the examples are from the field of drug design. This is a "how it works"
and "how to do it" book.

I don't know what exactly is in Yvonne Martin's book but I would guess
that this is complementary. Here is a link to Wiley's website:

http://eu.wiley.com/WileyCDA/WileyTitle/productCd-0470851538.html

On 15 Mar 2010 at 15:35, Senthil Natesan sen.natesan]^ wrote:

> Greetings. It will be very helpful  if you could recommend a few
> essential (authoritative in its area) books in the following areas
> 
> 1) Molecular dynamics simulation
> 2) Molecular recognition
> 3) QM/MM calculations
> 4) QSAR
> 5) ADMET
> 
> Books published after 2000 would be great as it would cover the latest
> developments.
> 
> Thanks everyone for your time and valuable recommendations.

-- 
D.J. Livingstone                ChemQuest
                       Delamere House, 1 Royal Crescent,
                       Sandown. Isle of Wight UK PO36 8LZ 

Phone: +44 (0)1983 406832
e-mail davel ~~ chemquestuk.com     www.chemquestuk.com
------------------------------------------------------------------


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<body>
<div align="left"><font face="Arial"><span style=" font-size:12pt">Sorry to be so tardy in replying to this.</span></font></div>
<div align="left"><font face="Arial"><span style=" font-size:12pt"><br />
</span></font></div>
<div align="left"><font face="Arial"><span style=" font-size:12pt">My book on data analysis (a Practical Guide to Scientific Data Analysis,</span></font></div>
<div align="left"><font face="Arial"><span style=" font-size:12pt">Wiley, 2009) covers many of the techniques used in QSAR - indeed many of</span></font></div>
<div align="left"><font face="Arial"><span style=" font-size:12pt">the examples are from the field of drug design. This is a &quot;how it works&quot;</span></font></div>
<div align="left"><font face="Arial"><span style=" font-size:12pt">and &quot;how to do it&quot; book.</span></font></div>
<div align="left"><font face="Arial"><span style=" font-size:12pt"><br />
</span></font></div>
<div align="left"><font face="Arial"><span style=" font-size:12pt">I don't know what exactly is in Yvonne Martin's book but I would guess</span></font></div>
<div align="left"><font face="Arial"><span style=" font-size:12pt">that this is complementary. Here is a link to Wiley's website:</span></font></div>
<div align="left"><font face="Arial"><span style=" font-size:12pt"><br />
</span></font></div>
<div align="left"><font face="Arial" color="#008000"><span style=" font-size:12pt"><u>http://eu.wiley.com/WileyCDA/WileyTitle/productCd-0470851538.html</u></span></font></div>
<div align="left"><font face="Arial"><span style=" font-size:12pt"><br />
</span></font></div>
<div align="left"><font face="Arial"><span style=" font-size:12pt">On 15 Mar 2010 at 15:35, Senthil Natesan sen.natesan]^ wrote:</span></font></div>
<div align="left"><font face="Arial"><span style=" font-size:12pt"><br />
</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span style=" font-size:12pt">&gt; Greetings. It will be very helpful&#160; if you could recommend a few</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span style=" font-size:12pt">&gt; essential (authoritative in its area) books in the following areas</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span style=" font-size:12pt">&gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span style=" font-size:12pt">&gt; 1) Molecular dynamics simulation</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span style=" font-size:12pt">&gt; 2) Molecular recognition</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span style=" font-size:12pt">&gt; 3) QM/MM calculations</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span style=" font-size:12pt">&gt; 4) QSAR</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span style=" font-size:12pt">&gt; 5) ADMET</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span style=" font-size:12pt">&gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span style=" font-size:12pt">&gt; Books published after 2000 would be great as it would cover the latest</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span style=" font-size:12pt">&gt; developments.</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span style=" font-size:12pt">&gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span style=" font-size:12pt">&gt; Thanks everyone for your time and valuable recommendations.</span></font></div>
<div align="left"><font face="Arial"><span style=" font-size:12pt"><br />
</span></font></div>
<div align="left"><font face="Arial"><span style=" font-size:12pt">-- </span></font></div>
<div align="left"><font face="Arial"><span style=" font-size:12pt">D.J. Livingstone&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; ChemQuest</span></font></div>
<div align="left"><font face="Arial"><span style=" font-size:12pt">&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; Delamere House, 1 Royal Crescent,</span></font></div>
<div align="left"><font face="Arial"><span style=" font-size:12pt">&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; Sandown. Isle of Wight UK PO36 8LZ </span></font></div>
<div align="left"><font face="Arial"><span style=" font-size:12pt"><br />
</span></font></div>
<div align="left"><font face="Arial"><span style=" font-size:12pt">Phone: +44 (0)1983 406832</span></font></div>
<div align="left"><font face="Arial"><span style=" font-size:12pt">e-mail davel ~~ chemquestuk.com&#160;&#160;&#160;&#160; www.chemquestuk.com</span></font></div>
<div align="left"><font face="Arial"><span style=" font-size:12pt">------------------------------------------------------------------</span></font></div>
<div align="left">&nbsp;&nbsp;</div>
</body>
</html>

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From owner-chemistry@ccl.net Wed Apr  7 14:27:01 2010
From: "Ol Ga eurisco1]~[pochta.ru" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL:G: charge calculation using gaussian
Message-Id: <-41615-100407140251-14416-0suc63RftYd/zU2oPr6aLQ++server.ccl.net>
X-Original-From: "Ol  Ga" <eurisco1/a\pochta.ru>
Date: Wed, 7 Apr 2010 14:02:50 -0400


Sent to CCL by: "Ol  Ga" [eurisco1---pochta.ru]
Dear SUBHADEEP SAHA,

You need van der Waals radius of Copper atom: 140  pm (http://www.webelements.com/copper/atom_sizes.html)
and route 
sp hf/6-31g geom=connectivity Pop=(ReadRadii,CHelpG)

> From http://www.gaussian.com/g_tech/g_ur/k_population.htm
ReadRadii
Read in alternative radii (in Angstroms) for each element for use in fitting potentials. These are read as pairs of atomic symbol and radius, terminated by a blank line.

But EPS methodology gives unreliable charges. For instance, look here
http://www.sciforum.net/presentation/245
test of some methodologies to assign partial charges .



Sincerely,
Ol Ga


>Sent to CCL by: SUBHADEEP SAHA [saha.subhadeep|,|gmail.com]

>Dear all,
> I need to calculate charge on each atom of a cluster extrated from a
crystal using gaussian 03.
In the input file I have written "sp hf/6-31g geom=connectivity Pop=CHelpG"

But it is showing an error for Copper atom,
"GetVDW: no radius for atom 28 atomic number 29"

Can anyone of you help me out?
--  
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


From owner-chemistry@ccl.net Wed Apr  7 21:29:00 2010
From: "Ramachandran Chelat rcchelat.=-=.rediffmail.com" <owner-chemistry=-=server.ccl.net>
To: CCL
Subject: CCL: Temperature and pressure in Q-Chem
Message-Id: <-41616-100407144418-8670-o1jdWB5QdN/fspc21uLlbg=-=server.ccl.net>
X-Original-From: "Ramachandran  Chelat" <rcchelat,+,rediffmail.com>
Date: Wed, 7 Apr 2010 14:44:09 -0400


Sent to CCL by: "Ramachandran  Chelat" [rcchelat,+,rediffmail.com]
Dear CCL users,
Could you please tell me how to set the temperature and pressure keywords in Q-chem program with an example input file?
Thanks in advance,
Rama


From owner-chemistry@ccl.net Wed Apr  7 22:04:00 2010
From: "Decai Yu decai-yu%a%northwestern.edu" <owner-chemistry|*|server.ccl.net>
To: CCL
Subject: CCL:G: 3d Orbtial using Gaussian
Message-Id: <-41617-100407180834-8063-1uPJ2Vd5O2A4mhgKxk7buw|*|server.ccl.net>
X-Original-From: "Decai Yu" <decai-yu-.-northwestern.edu>
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Date: Wed, 7 Apr 2010 17:08:30 -0500
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Sent to CCL by: "Decai Yu" [decai-yu[A]northwestern.edu]
Dear All,
 
In the Gaussian calculations, the d orbitals look like XX, YY, ZZ, XY,
XZ, YZ. How do I convert them into the 5 independent d orbitals (XY,
XZ,YZ,X2-Y2,
 Z2)? I would appreciate any help on this.
 
Regards,
 
Decai Yu