From owner-chemistry@ccl.net Wed May 12 07:38:00 2010
From: "rinu iyer rinuiyer{:}gmail.com" <owner-chemistry#,#server.ccl.net>
To: CCL
Subject: CCL: simulation
Message-Id: <-41842-100512062718-5046-Ot1ZYHIXyWKeIkAhrqneBg#,#server.ccl.net>
X-Original-From: rinu iyer <rinuiyer|*|gmail.com>
Content-Type: multipart/alternative; boundary=000e0cd182a4ce5c71048662a968
Date: Wed, 12 May 2010 15:27:00 +0530
MIME-Version: 1.0


Sent to CCL by: rinu iyer [rinuiyer::gmail.com]
--000e0cd182a4ce5c71048662a968
Content-Type: text/plain; charset=ISO-8859-1

dear subscribers,
         i am using gromacs . i want to run a calculation in which i want to
place a molecule in the centre during the generation of the box to do
molecular dynamics simulation. the molecule is surrounded by solvents.
can u tell me please how to run this calculation.

Thanks in advance
K.R.Ramya
research fellow
Indian Institute of science,Pune
Tower, Sai Trinity Building, Sutarwadi Road, Pashan,
Pune 411021, INDIA

--000e0cd182a4ce5c71048662a968
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

<div>dear subscribers,</div>
<div>=A0=A0=A0=A0=A0=A0=A0=A0 i am using gromacs . i want to run a calculat=
ion in which i want to place a molecule in the centre during the generation=
 of the box to do molecular dynamics simulation. the molecule is surrounded=
 by solvents. </div>

<div>can u tell me please how to run this calculation.</div>
<div>=A0</div>
<div>Thanks in advance</div>
<div>K.R.Ramya</div>
<div>research fellow</div>
<div>Indian Institute of science,Pune</div>
<div>Tower, Sai Trinity Building, Sutarwadi Road, Pashan,<br>Pune 411021, I=
NDIA<br></div>

--000e0cd182a4ce5c71048662a968--


From owner-chemistry@ccl.net Wed May 12 09:17:00 2010
From: "Vincent Leroux vincent.leroux,+,loria.fr" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL: Hints for computer purchasing
Message-Id: <-41843-100511145835-29116-jaRMt2Lxnfm0DFxJjsoppQ(0)server.ccl.net>
X-Original-From: Vincent Leroux <vincent.leroux(!)loria.fr>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=windows-1252
Date: Tue, 11 May 2010 20:58:23 +0200
MIME-Version: 1.0


Sent to CCL by: Vincent Leroux [vincent.leroux[a]loria.fr]
Hi Massimo,

For $6000 I would personally go for a small cluster of 8 nodes, 1 4-core
CPU each. Try to get entry-level motherboards from Asus or Gigabyte
(reliable brands) with no fancy features and integrated graphic circuit,
solid power supplies (I mean, reliable brand like Seasonic, Antec,
Enermax, Fortron, and the ~400 W models, not the 800 W "made for gamers"
ones), 4 GB memory per node, low capacity hard drive (or no hard drive
at all for the nodes if you feel like you can install and use dedicated
Linux distributions like PelicanHPC).

A rough estimate (these are the prices you can get quite easily in France):
8 4-core CPUs (e.g. Intel Q8300) ~ 1200 €
8 motherboards (e.g. Gigabyte GA-G31M-ES2L) ~ 400 €
8 cases with included power supply (e.g. Antec NSK 6580 430W - avoid the
"first price, no brand" ones *at all costs*) ~ 800 €
8 4 GB DDR2 RAM kits (2x2 GB) ~ 1000 €
8 hard drives (e.g. Seagate 7200.12 250 GB) ~ 400 €
1 16*Gigabit switch + cables ~ 100 €
One or several good UPS devices, if the power sockets in the building
are not protected already ~ 500 €

I would also suggest backup spare parts, just in case: 2 hard drives, 2
power supplies, 2 12 cm fans, 1 motherboard, 1 RAM kit. Do not forget to
make sure the cluster is placed in a well-cooled dedicated room, without
the cases being stacked together: when such setups are pushed at full
power, things can get really warm and noisy...

Of course I assume you are not afraid of building your own computer
setup from the spare parts!

VL



Le 11/05/10 14:17, Massimo Ottonelli massimo],[chimica.unige.it a ιcrit :
> 
> Sent to CCL by: Massimo Ottonelli [massimo],[chimica.unige.it]
> 
>  Dear all,
>     maybe I am a little bit off-topic but I would like to have your
> hints for the better  purchasing
>     of a "workstation" focused on quantum chemical calulations with the
> bugget of about 6000$.
> 
>    Regards,
>   Massimohttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences:
> http://server.ccl.net/chemistry/announcements/conferences/> 
> 
>


From owner-chemistry@ccl.net Wed May 12 09:52:00 2010
From: "Mike Towler mdt26#%#cam.ac.uk" <owner-chemistry.@.server.ccl.net>
To: CCL
Subject: CCL: Quantum Monte Carlo summer school, Tuscany - final call
Message-Id: <-41844-100512080008-13179-PfZ1xEZNe/RXbdly124K3w.@.server.ccl.net>
X-Original-From: "Mike  Towler" <mdt26..@..cam.ac.uk>
Date: Wed, 12 May 2010 08:00:06 -0400


Sent to CCL by: "Mike  Towler" [mdt26]~[cam.ac.uk]
Dear all,

There are still some places available at the forthcoming Cambridge University quantum Monte Carlo summer school at the Apuan Alps Centre for Physics in Vallico Sotto, Tuscany next August (details below).

If you or anyone you know would like to attend, please get in touch with me
as soon as you can.

Best wishes,
Mike Towler

+------------------------------------------------------------------------+
|Dr. Mike Towler (mdt26 at cam.ac.uk) Theory of Condensed Matter (Rm 529)|
|  Cavendish Laboratory, University of Cambridge, Cambridge  CB3 0HE, UK |
|Tel. +44-(0)1223-337378 OR -334256 (College)     Fax. +44-(0)1223-337356|
+----------------------: www.tcm.phy.cam.ac.uk/~mdt26 :------------------+

                   SUMMER SCHOOL ANNOUNCEMENT

         "Quantum Monte Carlo and the CASINO program V"
         ===============================================

              Sun 1st August - Sun 8th August 2010
 Apuan Alps Centre for Physics :-: TTI, Vallico Sotto, Tuscany, Italy

             http://www.vallico.net/tti/tti.html

           A4 POSTER FOR THE SCHOOL AVAILABLE HERE :
        http://www.tcm.phy.cam.ac.uk/~mdt26/poster.png


The fifth international summer school in the series "Quantum Monte Carlo
and the CASINO program" will take place during August 2010 at the TTI
monastery in the Tuscan Apuan Alps in Italy, organized and hosted by
members of Cambridge University physics department's Theory of Condensed
Matter Group. The aim of the school is to give students a thorough
introduction to quantum Monte Carlo as a method for performing
high-quality calculations of the electronic structure of atoms, molecules,
and materials. The course is designed for young quantum chemists or
theoretical physicists who have no previous experience with this
technique, though anyone interested is welcome to take part.

The monastery is a unique venue where the community spirit and magnificent
location have inspired memorable workshops in the past. It is a delightful
16th century building incorporating an ancient church, and is situated in
the isolated but spectacular setting of the Tuscan mountain village of
Vallico Sotto. The church is fully equipped with relevant presentation and
computer technology, and all accommodation is on-site.  As with all events
at the Institute, formal lectures are restricted to the mornings, and
participants are given the freedom and space to think and to contemplate
and discuss the issues at hand. In addition to hands-on exercises, a
programme of healthy recreational activities will be organized in the
afternoons, and it is hoped that by following this strict regime, together
with breathing clean mountain air and by preparing and sampling fine
Tuscan cuisine, the participant will be able to return home mentally and
physically refreshed as well as better informed.

Describing the complex behaviour of materials at the atomic level requires
a sophisticated description of the correlated motion of the electrons.
Quantum Monte Carlo (QMC) is an increasingly popular and explicitly
many-body method with the unusual capability of yielding highly accurate
results whilst also exhibiting a very favourable scaling of computational
cost with system size. Over the last eighteen years, the Cambridge group
have been researching QMC methods and we have created a powerful, general
computer program - CASINO - to carry out the calculations. The school will
focus both on the basic theory of QMC and on more advanced practical
techniques, and will include a thorough introduction to the CASINO
program. A background in density functional theory or similar - though not
essential - is normally thought to be useful.

Instructors will include the main authors of the CASINO program (Dr. Mike
Towler, Dr. Neil Drummond and Dr. Pablo Lopez Rios) assisted by Robert Lee.

Participants would normally need to book a flight to Pisa airport from
where onward transportation will be arranged (though other destinations
are possible). Details of previous schools - including photographs - are
available under the PUBLIC EVENTS link on the TTI web site.

Interested students should email Mike Towler (mdt26 at cam.ac.uk) for
registration and further details.


From owner-chemistry@ccl.net Wed May 12 10:27:00 2010
From: "Basma Ghazal basmaghazal**ymail.com" <owner-chemistry^_^server.ccl.net>
To: CCL
Subject: CCL: Effect of sulphate ions on the preparation of the enzyme
Message-Id: <-41845-100512064437-7137-IzrrMKdTDfXTv5SN35uc8A^_^server.ccl.net>
X-Original-From: Basma Ghazal <basmaghazal ~ ymail.com>
Content-Type: multipart/alternative; boundary="0-1032246702-1273657816=:80183"
Date: Wed, 12 May 2010 02:50:16 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: Basma Ghazal [basmaghazal[a]ymail.com]
--0-1032246702-1273657816=:80183
Content-Type: text/plain; charset=us-ascii



Hello, 
Because I am still beginner in the field I need the advices in the
following items:
The PDB structure that I use
for docking have two sulphate ions, one of them is very close to the active
site and make interaction with it is residue. The other is far from it.
1-If I
removed the sulfate ions from the pocket containing the active site am I need
to do partial optimization of this part?Because removing them give more compact pocket by partial optimization.
2-Instead, I think to add
two water molecules in the same places of two sulfate ions, do you think this
way will compensate the removing of sulfate ions to avoid the conformational
change during the docking? 
3- Butthe sulfate ions are charged and replacement them by explicit water molecules may not be equivalent, right? 
I
look forward to any response.
Thanks, 
Basma



      
--0-1032246702-1273657816=:80183
Content-Type: text/html; charset=us-ascii

<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:bookman old style,new york,times,serif;font-size:18pt"><br><meta http-equiv="Content-Type" content="text/html; charset=utf-8"><meta name="ProgId" content="Word.Document"><meta name="Generator" content="Microsoft Word 11"><meta name="Originator" content="Microsoft Word 11"><link rel="File-List" href="file:///C:%5CDOCUME%7E1%5CXPPRESP3%5CLOCALS%7E1%5CTemp%5Cmsohtml1%5C01%5Cclip_filelist.xml"><!--[if gte mso 9]><xml>
 <w:WordDocument>
  <w:View>Normal</w:View>
  <w:Zoom>0</w:Zoom>
  <w:PunctuationKerning/>
  <w:ValidateAgainstSchemas/>
  <w:SaveIfXMLInvalid>false</w:SaveIfXMLInvalid>
  <w:IgnoreMixedContent>false</w:IgnoreMixedContent>
  <w:AlwaysShowPlaceholderText>false</w:AlwaysShowPlaceholderText>
  <w:Compatibility>
   <w:BreakWrappedTables/>
   <w:SnapToGridInCell/>
   <w:WrapTextWithPunct/>
   <w:UseAsianBreakRules/>
   <w:DontGrowAutofit/>
  </w:Compatibility>
  <w:BrowserLevel>MicrosoftInternetExplorer4</w:BrowserLevel>
 </w:WordDocument>
</xml><![endif]--><!--[if gte mso 9]><xml>
 <w:LatentStyles DefLockedState="false" LatentStyleCount="156">
 </w:LatentStyles>
</xml><![endif]--><style>
<!--
 /* Font Definitions */
 ^font-face
	{font-family:"Bookman Old Style";
	panose-1:2 5 6 4 5 5 5 2 2 4;
	mso-font-charset:0;
	mso-generic-font-family:roman;
	mso-font-pitch:variable;
	mso-font-signature:647 0 0 0 159 0;}
 /* Style Definitions */
 p.MsoNormal, li.MsoNormal, div.MsoNormal
	{mso-style-parent:"";
	margin:0in;
	margin-bottom:.0001pt;
	text-align:right;
	mso-pagination:widow-orphan;
	direction:rtl;
	unicode-bidi:embed;
	font-size:12.0pt;
	font-family:"Times New Roman";
	mso-fareast-font-family:"Times New Roman";}
^page Section1
	{size:8.5in 11.0in;
	margin:1.0in 1.25in 1.0in 1.25in;
	mso-header-margin:.5in;
	mso-footer-margin:.5in;
	mso-paper-source:0;}
div.Section1
	{page:Section1;}
-->
</style><!--[if gte mso 10]>
<style>
 /* Style Definitions */
 table.MsoNormalTable
	{mso-style-name:"Table Normal";
	mso-tstyle-rowband-size:0;
	mso-tstyle-colband-size:0;
	mso-style-noshow:yes;
	mso-style-parent:"";
	mso-padding-alt:0in 5.4pt 0in 5.4pt;
	mso-para-margin:0in;
	mso-para-margin-bottom:.0001pt;
	mso-pagination:widow-orphan;
	font-size:10.0pt;
	font-family:"Times New Roman";
	mso-ansi-language:#0400;
	mso-fareast-language:#0400;
	mso-bidi-language:#0400;}
</style>
<![endif]-->

<p class="MsoNormal" style="text-align: left; direction: ltr; unicode-bidi: embed;"><span style="font-family: &quot;Bookman Old Style&quot;; color: blue;">Hello, <br>
Because I am still&nbsp;beginner in the field I need the advices in the
following items:<o:p></o:p></span></p>

<p class="MsoNormal" style="text-align: left; direction: ltr; unicode-bidi: embed;"><span style="font-family: &quot;Bookman Old Style&quot;; color: blue;">The PDB structure that I use
for docking have two sulphate ions, one of them is very close to the active
site and make interaction with it is residue. The other is far from it.<br>
1-</span><span style="font-family: &quot;Bookman Old Style&quot;; color: black;"> If I
removed the sulfate ions from the pocket containing the active site am I need
to do partial optimization of this part</span><span style="font-family: &quot;Bookman Old Style&quot;; color: blue;">?</span><span style="font-family: &quot;Bookman Old Style&quot;; color: black;">
Because removing them give more compact pocket by partial optimization.<br>
</span><span style="font-family: &quot;Bookman Old Style&quot;; color: blue;">2-</span><span style="font-family: &quot;Bookman Old Style&quot;; color: black;"> Instead, I think to add
two water molecules in the same places of two sulfate ions, do you think this
way will compensate the removing of sulfate ions to avoid the conformational
change during the docking? <br>
</span><span style="font-family: &quot;Bookman Old Style&quot;; color: blue;">3- But</span><span style="font-family: &quot;Bookman Old Style&quot;; color: black;"> the sulfate ions are <u>charged</u>
and replacement them by explicit water molecules may not be equivalent, </span><span style="font-family: &quot;Bookman Old Style&quot;; color: blue;">right? <o:p></o:p></span></p>

<p class="MsoNormal" style="text-align: left; line-height: 150%; direction: ltr; unicode-bidi: embed;"><span style="font-family: &quot;Bookman Old Style&quot;; color: black;">I
look forward to any response.<br>
</span><span style="font-family: &quot;Bookman Old Style&quot;; color: blue;">Thanks, <br>
Basma<o:p></o:p></span></p>

<br><div id="bandoo_adv"><a href="http://www.bandoo.com/wp/ie.php?plg=ie&amp;ad2=0&amp;subs=yahoo&amp;elm=sign"><img src="http://triggers.wp.bandoo.com/signature_001.gif" border="0"></a></div></div><br>







      </body></html>
--0-1032246702-1273657816=:80183--


From owner-chemistry@ccl.net Wed May 12 11:01:00 2010
From: "Comp Chem Group compchemgroup1^gmail.com" <owner-chemistry!=!server.ccl.net>
To: CCL
Subject: CCL: Binding Enthalpy in vacuum and solvent
Message-Id: <-41846-100512092917-32689-kUVK9JsSt7gUrbvj1Qs8pg!=!server.ccl.net>
X-Original-From: "Comp Chem Group " <compchemgroup1\a/gmail.com>
Date: Wed, 12 May 2010 09:29:15 -0400


Sent to CCL by: "Comp Chem Group " [compchemgroup1 a gmail.com]
Dear All,
By surveying on "Interaction Enthalpy" of transition metal complex in vacuum and solvent (PCM or other model), I found in all cases that the enthalpy change in vacuum is larger than that solvent. For example, if delta H in vacuum= -1000 kcal/mol, in solvent= -200 kcal/mol. Could anyone explain why? 
Regards,
CCG1


From owner-chemistry@ccl.net Wed May 12 13:54:01 2010
From: "James Prudhomme jprudhomme_._healthtech.com" <owner-chemistry%a%server.ccl.net>
To: CCL
Subject: CCL: CHI's Structure-Based Drug Design: Register by May 14
Message-Id: <-41847-100512124809-18816-mHhZ81fx1BepI80WDFk49w%a%server.ccl.net>
X-Original-From: "James  Prudhomme" <jprudhomme%a%healthtech.com>
Date: Wed, 12 May 2010 12:48:08 -0400


Sent to CCL by: "James  Prudhomme" [jprudhomme-x-healthtech.com]
Dear Group,

My company, Cambridge Healthtech Institute, cordially invites you to attend its 10th anniversary event:

STRUCTURE-BASED DRUG DESIGN:
Multidisciplinary Innovations and Structural Insights to Enhance Drug Discovery

June 23-25, 2010
Royal Sonesta Hotel, Cambridge, MA

Register by May 14 and Save up to $200
www.healthtech.com/sbd

In this program, we wish to highlight some recent breakthrough stories and successes using SBDD driven by medicinal chemistry, computational and biophysical approaches. This conference continues to offer both new attendees and alumni insights into the latest work of community thought-leaders as well as invaluable networking opportunities.

Topics Include:
- Selectivity Optimization: Using Structure to Optimize Selectivity
- In Silico Discovery of Small Molecule Binders
- New Computational Methods in SBDD
- Targeting of Protein-Protein Interactions
- New Advances in Docking
- Impact of SBDD on Small Molecule Drug Discovery
- GPCR Drug Discovery
- Workshop: Therapeutic Target Space: Methods for Druggability Assessment

Speakers and delegates represent both industry & academia.  By attending, you will interact and share ideas in a comfortable setting while participating in roundtable discussions, case studies, networking luncheon, cocktail reception, and an exhibit/poster hall.

View the full agenda and register at www.healthtech.com/SBD or call 781-972-5400.

Interested in Sponsoring and/or Exhibiting?
Contact Katelin Fitzgerald at 781-972-5458, kfitzgerald.:.healthtech.com

Group Discounts are Available
Contact David Cunningham at 781-972-5472, cunningham.:.healthtech.com

Regards,

James Prudhomme
Cambridge Healthtech Institute