From owner-chemistry@ccl.net Tue Jun  5 02:23:00 2007
From: "Jerome Kieffer jerome.Kieffer,+,terre-adelie.org" <owner-chemistry(!)server.ccl.net>
To: CCL
Subject: CCL: Running GAMESS on Intel Celeron Processors
Message-Id: <-34416-070605021701-26990-htAEnkSeTC6LrSGHsG67Mw(!)server.ccl.net>
X-Original-From: Jerome Kieffer <jerome.Kieffer*o*terre-adelie.org>
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Date: Tue, 5 Jun 2007 07:47:11 +0200
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Sent to CCL by: Jerome Kieffer [jerome.Kieffer|a|terre-adelie.org]

Celeron processor ar just intel Pentium (2,3,4...) with part (all) of
the cache memory descativated. They are able to run the same programs,
they are just less efficient thus slower.

-- 
Jérôme KIEFFER


From owner-chemistry@ccl.net Tue Jun  5 04:51:01 2007
From: "Alex A. Granovsky gran%x%classic.chem.msu.su" <owner-chemistry.@.server.ccl.net>
To: CCL
Subject: CCL: Running GAMESS on Intel Celeron Processors
Message-Id: <-34417-070605034826-23965-0E/fSw9VbnPfRrKuwPUHqw.@.server.ccl.net>
X-Original-From: "Alex A. Granovsky" <gran~~classic.chem.msu.su>
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Date: Tue, 5 Jun 2007 11:18:05 +0400
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Sent to CCL by: "Alex A. Granovsky" [gran%a%classic.chem.msu.su]
Hi,

there are several different types of Celeron processors.
The first ones were based on Pentium II core, and you need Pentium II optimized PC GAMESS version for them.
Next, there were Celerons based on Pentium III core, so you need Pentium III optimized PC GAMESS version for these Celerons.
Finally, latest Celerons were based on Pentium 4 core. Use Pentium 4 optimized PC GAMESS binaries to run calculations on these
processors.
You can just run the generic Pentium version and look at the beginning of the output to find what is the most appropriate PC GAMESS
version for you.

Best regards,
Alex Granovsky



----- Original Message -----
> From: "Mustafa Hussein mustafa.hussein86]|[yahoo.com" <owner-chemistry*_*ccl.net>
To: "Granovsky, Alex, A. " <gran*_*classic.chem.msu.su>
Sent: Tuesday, June 05, 2007 4:11 AM
Subject: CCL: Running GAMESS on Intel Celeron Processors


>
> Sent to CCL by: "Mustafa  Hussein" [mustafa.hussein86%%yahoo.com]
> Hi,
>
> My PC has an Intel Celeron Processor. I have checked the specifications on hardware requirements for running GAMESS. I found no
thing stated on Celeron Processors. Does this mean GAMESS can not be run on such processors?
>
> If so, I am gonna change my processor, really.
>
> Any help is appreciated
>
> Thanks
>
> Mustafa>
>
>
>


From owner-chemistry@ccl.net Tue Jun  5 08:44:01 2007
From: "Gerard Pujadas gerard.pujadas]-[gmail.com" <owner-chemistry#,#server.ccl.net>
To: CCL
Subject: CCL: Any computational method to predict binding affinities of metals for different PROTEINS?
Message-Id: <-34418-070605043957-30478-2MTQrrCjPpMNMDctfVFAzQ#,#server.ccl.net>
X-Original-From: "Gerard Pujadas" <gerard.pujadas:_:gmail.com>
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Sent to CCL by: "Gerard Pujadas" [gerard.pujadas(a)gmail.com]
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Dear CCL list members,

I wonder if there is any computational method that I can use to predict if
when adding Zn2+ to a solution that contains the same concentration of two
different proteins, the ions will bind, preferably, to one of the two
proteins.

With many thanks in advances

Yours sincerely,

Gerard

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<br><br><br>Dear CCL list members,<br><br>I wonder if there is any computational method that I can use to predict if when adding Zn2+ to a solution that contains the same concentration of two different proteins, the ions will bind, preferably,  to one of the two proteins.
<br><br>With many thanks in advances<br><br>Yours sincerely,<br><span class="sg"><br>Gerard<br>
</span><br><br>

------=_Part_3926_20520855.1181029133167--


From owner-chemistry@ccl.net Tue Jun  5 09:19:00 2007
From: "Sergio Emanuel Galembeck segalemb(-)usp.br" <owner-chemistry_+_server.ccl.net>
To: CCL
Subject: CCL:G: about AIM calculation
Message-Id: <-34419-070605090724-17902-ikryZ2gvg3Rl/HVn9qkhGQ_+_server.ccl.net>
X-Original-From: Sergio Emanuel Galembeck <segalemb],[usp.br>
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Sent to CCL by: Sergio Emanuel Galembeck [segalemb**usp.br]
Dear Guermoune,

    I suggest to use 6D 10F keywords, because AIM only
do coerent results with cartesian GTOs.

           Best regards,

                  Sergio Galembeck

Citando "GUERMOUNE ABDELADIM lguermoune]_[hotmail.com"  
<owner-chemistry]|[ccl.net>:

>
> Sent to CCL by: "GUERMOUNE  ABDELADIM" [lguermoune..hotmail.com]
> Hello,
> I am beginner with the program of AIM2000 analysis.
> First I have create file wfn from the Gaussian98
> using words key
> P B3LYP/6-311+G** output=wfn density=current
> then I treated file wfn by the AIM2000 program to localize
> the critical points, the density and laplacian.
> But the results don't seem to me coherent, for example
> when the density increases laplacian can take a positive
> value, and it can take a negative value when the density
> decrease. In my structure I have specially a metallic
> center: iron, and two borons with hydrogens in bridged position.
> I wish to know if there is another manner to improve my file
> result wfn or any others suggestions.
> Thanks.>
>
>
>


From owner-chemistry@ccl.net Tue Jun  5 15:50:01 2007
From: "Peter Rose prose001###san.rr.com" <owner-chemistry-.-server.ccl.net>
To: CCL
Subject: CCL: Any computational method to predict binding affinities of metals for different PROTEINS?
Message-Id: <-34420-070605152810-9145-uBzmZ/PfiyWeJUxBjZFh3w-.-server.ccl.net>
X-Original-From: "Peter Rose" <prose001_._san.rr.com>
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Date: Tue, 5 Jun 2007 09:20:23 -0700
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Sent to CCL by: "Peter Rose" [prose001%%san.rr.com]
This is a multi-part message in MIME format.

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Here are a couple of recent papers that identify metal binding motifs on a
qualitative basis:

 

Richard Thilakaraj , Krishnan Raghunathan , Sharmila Anishetty, and Gautam
Pennathur, 

In silico identification of putative metal binding motifs, Bioinformatics
2007 23(3):267-271.

 

Passerini A, Andreini C, Menchetti S, Rosato A, Frasconi P., 

Predicting zinc binding at the proteome level, BMC Bioinformatics 2007 Feb
5, 8-39

The software implementing the predictor is freely available at:
http://zincfinder.dsi.unifi.it

 

Peter Rose, Ph.D.

InSilicoChem, Inc.

 

  _____  

> From: owner-chemistry---ccl.net [mailto:owner-chemistry---ccl.net] 
Sent: Tuesday, June 05, 2007 12:39 AM
To: Rose, Peter W 
Subject: CCL: Any computational method to predict binding affinities of
metals for different PROTEINS?

 




Dear CCL list members,

I wonder if there is any computational method that I can use to predict if
when adding Zn2+ to a solution that contains the same concentration of two
different proteins, the ions will bind, preferably, to one of the two
proteins. 

With many thanks in advances

Yours sincerely,

Gerard




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<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
11.0pt;font-family:Arial;color:black'>Here are a couple of recent papers =
that
identify metal binding motifs on a qualitative =
basis:<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
11.0pt;font-family:Arial;color:black'><o:p>&nbsp;</o:p></span></font></p>=


<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
11.0pt;font-family:Arial;color:black'>Richard Thilakaraj , Krishnan =
Raghunathan
, Sharmila Anishetty, and Gautam Pennathur, =
<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
11.0pt;font-family:Arial;color:black'>In silico identification of =
putative
metal binding motifs, Bio<st1:PersonName =
w:st=3D"on">info</st1:PersonName>rmatics
2007 23(3):267-271.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
11.0pt;font-family:Arial;color:black'><o:p>&nbsp;</o:p></span></font></p>=


<p class=3DMsoNormal><span class=3Dti><font size=3D2 color=3Dblack =
face=3DArial><span
style=3D'font-size:11.0pt;font-family:Arial;color:black'>Passerini A, =
Andreini C,
Menchetti S, Rosato A, Frasconi P., <o:p></o:p></span></font></span></p>

<p class=3DMsoNormal><span class=3Dti><font size=3D2 color=3Dblack =
face=3DArial><span
style=3D'font-size:11.0pt;font-family:Arial;color:black'>Predicting zinc =
binding
at the proteome level, BMC Bio<st1:PersonName =
w:st=3D"on">info</st1:PersonName>rmatics
2007 Feb 5, 8-39<o:p></o:p></span></font></span></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
11.0pt;font-family:Arial;color:black'>The software implementing the =
predictor
is freely available at: =
http://zincfinder.dsi.unifi.it<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
11.0pt;font-family:Arial;color:black'><o:p>&nbsp;</o:p></span></font></p>=


<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
11.0pt;font-family:Arial;color:black'>Peter Rose, =
Ph.D.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
11.0pt;font-family:Arial;color:black'>InSilicoChem, =
Inc.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<div>

<div class=3DMsoNormal align=3Dcenter style=3D'text-align:center'><font =
size=3D3
face=3D"Times New Roman"><span style=3D'font-size:12.0pt'>

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<p class=3DMsoNormal><b><font size=3D2 face=3DTahoma><span =
style=3D'font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font =
size=3D2
face=3DTahoma><span style=3D'font-size:10.0pt;font-family:Tahoma'>
owner-chemistry---ccl.net [mailto:owner-chemistry---ccl.net] <br>
<b><span style=3D'font-weight:bold'>Sent:</span></b> Tuesday, June 05, =
2007 12:39
AM<br>
<b><span style=3D'font-weight:bold'>To:</span></b> Rose, Peter W =
<br>
<b><span style=3D'font-weight:bold'>Subject:</span></b> CCL: Any =
computational
method to predict binding affinities of metals for different =
PROTEINS?</span></font><o:p></o:p></p>

</div>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal style=3D'margin-bottom:12.0pt'><font size=3D3
face=3D"Times New Roman"><span style=3D'font-size:12.0pt'><br>
<br>
<br>
Dear CCL list members,<br>
<br>
I wonder if there is any computational method that I can use to predict =
if when
adding Zn2+ to a solution that contains the same concentration of two =
different
proteins, the ions will bind, preferably, to one of the two proteins. =
<br>
<br>
With many thanks in advances<br>
<br>
Yours sincerely,<br>
<br>
<span class=3Dsg>Gerard</span><br>
<br>
<o:p></o:p></span></font></p>

</div>

</body>

</html>

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From owner-chemistry@ccl.net Tue Jun  5 19:15:01 2007
From: "Mustafa Hussein mustafa.hussein86]|[yahoo.com" <owner-chemistry|*|server.ccl.net>
To: CCL
Subject: CCL: Papers on Quantum Chemical Topology
Message-Id: <-34421-070605191235-22700-+YVzjECyFSU3Z2bx3YfBcw|*|server.ccl.net>
X-Original-From: "Mustafa  Hussein" <mustafa.hussein86,+,yahoo.com>
Date: Tue, 5 Jun 2007 19:12:31 -0400


Sent to CCL by: "Mustafa  Hussein" [mustafa.hussein86!^!yahoo.com]
Hi,

I am preparing a review article on the theory of Atoms in Molecules and Quantum Chemical Topology (QCT). I need some papers on the application of QCT to biomacromolecular properties.

Any help is appreciated.

Thanks,

Mustafa