From owner-chemistry@ccl.net Mon Aug  9 09:30:00 2010
From: "Serdar Bado?lu sbadoglu\a/gazi.edu.tr" <owner-chemistry!^!server.ccl.net>
To: CCL
Subject: CCL:G: charged atoms in neutral molecule
Message-Id: <-42481-100809092415-5608-WmQEvv2jlar82RvkNCpBvg!^!server.ccl.net>
X-Original-From: "Serdar Bado?lu" <sbadoglu]|[gazi.edu.tr>
Content-Type: text/plain; charset="iso-8859-9" 
Date: Mon, 9 Aug 2010 13:23:55 -0000


Sent to CCL by: "Serdar Bado?lu" [sbadoglu**gazi.edu.tr]
Hi,

Suppose that I want to optimize then calculate several properties of a
molecule which has 30 atoms, including one oxygen cation and one nitrogen
anion, and the rest of the atoms are neutral. Do I need to specify those
ions in the Gaussian input file? If so, how can I do that? That's what I
need to know.

Regards.

-- 
Serdar BADOGLU
Gazi University
Department of Physics


From owner-chemistry@ccl.net Mon Aug  9 10:04:00 2010
From: "Gabriel Urquiza urquizagabes[A]gmail.com" <owner-chemistry=server.ccl.net>
To: CCL
Subject: CCL: PDB coordinates tranformation
Message-Id: <-42482-100809091859-2277-I7FamLqNVrMKDXxvZSjveg=server.ccl.net>
X-Original-From: Gabriel Urquiza <urquizagabes---gmail.com>
Content-Type: multipart/alternative; boundary=001485f28010a7a409048d63db75
Date: Mon, 9 Aug 2010 10:18:53 -0300
MIME-Version: 1.0


Sent to CCL by: Gabriel Urquiza [urquizagabes%gmail.com]
--001485f28010a7a409048d63db75
Content-Type: text/plain; charset=ISO-8859-1

Greetings CCLers.

I am trying to make some surveys about the structures of some channel
proteins and it would really help if the Z axis coincided with the pore of
the channel and passed along the middle point among the atoms. The problem,
evidently, is that such properties are usually absent in any PDB. So I was
wondering if there would be any program able to let me manipulate the
coordinate reference of a pdb file.

Thank you for your time.

Gabriel Urquiza

--001485f28010a7a409048d63db75
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

<div class=3D"gmail_quote">Greetings CCLers.<div><br></div><div>I am trying=
 to make some surveys about the structures of some channel proteins and it =
would really help if the Z axis coincided with the pore of the channel and =
passed along the middle point among the atoms. The problem, evidently, is t=
hat such properties are usually absent in any PDB. So I was wondering if th=
ere would be any program able to let me manipulate the coordinate reference=
 of a pdb file.</div>

<div><br></div><div>Thank you for your time.</div><div><br></div><font colo=
r=3D"#888888"><div>Gabriel Urquiza</div>
</font></div><br>

--001485f28010a7a409048d63db75--


From owner-chemistry@ccl.net Mon Aug  9 10:40:01 2010
From: "Uwe Huniar huniar]*[cosmologic.de" <owner-chemistry#server.ccl.net>
To: CCL
Subject: CCL: Free COSMOtherm Workshop
Message-Id: <-42483-100809095321-1237-e4Bkp5nbhfnJLohwE8HzrQ#server.ccl.net>
X-Original-From: Uwe Huniar <huniar^_^cosmologic.de>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-15; format=flowed
Date: Mon, 09 Aug 2010 15:53:05 +0200
MIME-Version: 1.0


Sent to CCL by: Uwe Huniar [huniar]*[cosmologic.de]
Dear colleagues,

We offer a COSMOtherm workshop for our academic customers or scientists
who are interested in our COSMOtherm software on a regular basis. The
workshop is free of charge.

Our next workshop is scheduled on Tuesday 14th of September 2010.

If you or your colleagues are interested, we will be glad to welcome you
in our office in Leverkusen, Germany.

We will adjust the content of the training to the needs of all
participants as far as possible.

For more information and contact details for registration visit
http://www.cosmologic.de/cttraining

Regards,

(on behalf of) Jens Reinisch

-- 
------------------------------------------------------------------------------
COSMOlogic GmbH & Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany
web     http://www.cosmologic.com


From owner-chemistry@ccl.net Mon Aug  9 11:15:01 2010
From: "Serge Gorelsky gorelsky|,|gmail.com" <owner-chemistry]![server.ccl.net>
To: CCL
Subject: CCL:G: charged atoms in neutral molecule
Message-Id: <-42484-100809110729-10432-zxcczLYp0krpCIk8gIodMg]![server.ccl.net>
X-Original-From: Serge Gorelsky <gorelsky],[gmail.com>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=UTF-8
Date: Mon, 9 Aug 2010 11:07:18 -0400
MIME-Version: 1.0


Sent to CCL by: Serge Gorelsky [gorelsky:gmail.com]
> Suppose that I want to optimize then calculate several properties of a
> molecule which has 30 atoms, including one oxygen cation and one nitrogen
> anion, and the rest of the atoms are neutral. Do I need to specify those
> ions in the Gaussian input file? If so, how can I do that? That's what I
> need to know.

You specify charged or neutral parts by building a GUESS=CARDS initial
guess input file (http://www.gaussian.com/g_tech/g_ur/k_guess.htm)
that correspond to your desired charge distribution. Building such
initial guess for Gaussian or GAMESS calculations is fully automated
if you use the AOMix software (www.sg-chem.net). You can find all the
necessary details about the procedure in Appendix II of the AOMix
manual.
-- 
Best regards,
  Serge Gorelsky


From owner-chemistry@ccl.net Mon Aug  9 11:50:03 2010
From: "Carlos Alberto Ortega Zu iga caoz96()yahoo.es" <owner-chemistry ~~ server.ccl.net>
To: CCL
Subject: CCL: Information about charges in ligands in docking studies
Message-Id: <-42485-100809112850-2140-Y+BcEPFgVlzS+g+aYwPsLQ ~~ server.ccl.net>
X-Original-From: "Carlos Alberto Ortega Zu  iga" <caoz96,,yahoo.es>
Date: Mon, 9 Aug 2010 11:28:48 -0400


Sent to CCL by: "Carlos Alberto Ortega Zu  iga" [caoz96{:}yahoo.es]
Dear CCL users,

I have a doubt about the charges that i must use, when i do a docking ligand-protein.

The procedure i do is the following:

I optimize the ligand with DFT level, to obtain the structure of molecule more relaxed.

I use DOCK program for the docking.

But i dont know what charges i must use when i do the docking, because the optimization offer me charges Mulliken and the software of docking use other charges, like Gasteiger-Hckel. Then what charges recomend me? And why? There are references that say this?

I really thanks your help and info.


From owner-chemistry@ccl.net Mon Aug  9 13:20:01 2010
From: "Jeffrey N Woodford jeffwoodford2,gmail.com" <owner-chemistry a server.ccl.net>
To: CCL
Subject: CCL: Computational Chemistry and Renewable Energy
Message-Id: <-42486-100809124643-14822-9gb7/NdBnW6V+dBNkavomg a server.ccl.net>
X-Original-From: "Jeffrey N Woodford" <jeffwoodford2_+_gmail.com>
Date: Mon, 9 Aug 2010 12:46:39 -0400


Sent to CCL by: "Jeffrey N Woodford" [jeffwoodford2(0)gmail.com]
All:
I've been approached by a publisher to edit a volume on "Computational Chemistry and Renewable Energy".  (I interpret this topic rather broadly.)  So before I put a lot of effort into a book proposal on this topic, I thought I'd throw it out to the list to see if there would be any interest in this type of book, more specifically:

1. Would you be interested in purchasing a book like this for your collection or for your institution's library holdings?
2. Would you be interested in submitting a chapter to a volume like this?
3. Would you be interested in co-editing this book?  Since I'm a QM guy, it would be best if co-editors were in a complementary area.

Thanks for your feedback!

-Jeff 

Jeffrey N. Woodford
Assistant Professor of Chemistry
Missouri Western State University


From owner-chemistry@ccl.net Mon Aug  9 13:55:01 2010
From: "Jim Kress ccl_nospam+/-kressworks.com" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL: PDB coordinates tranformation
Message-Id: <-42487-100809120552-7501-D7zuo+GS+2jQeIZKLozYSQ+*+server.ccl.net>
X-Original-From: "Jim Kress" <ccl_nospam^kressworks.com>
Content-Language: en-us
Content-Type: multipart/alternative;
	boundary="----=_NextPart_000_0004_01CB37BB.3098E690"
Date: Mon, 9 Aug 2010 12:05:36 -0400
MIME-Version: 1.0


Sent to CCL by: "Jim Kress" [ccl_nospam(a)kressworks.com]
This is a multi-part message in MIME format.

------=_NextPart_000_0004_01CB37BB.3098E690
Content-Type: text/plain;
	charset="us-ascii"
Content-Transfer-Encoding: 7bit

ChemCraft might.

 

http://www.chemcraftprog.com/info.html

 

Jim

 

> From: owner-chemistry+ccl_nospam==kressworks.com_+_ccl.net
[mailto:owner-chemistry+ccl_nospam==kressworks.com_+_ccl.net] On Behalf Of
Gabriel Urquiza urquizagabes[A]gmail.com
Sent: Monday, August 09, 2010 9:19 AM
To: Kress, Jim 
Subject: CCL: PDB coordinates tranformation

 

Greetings CCLers.

 

I am trying to make some surveys about the structures of some channel
proteins and it would really help if the Z axis coincided with the pore of
the channel and passed along the middle point among the atoms. The problem,
evidently, is that such properties are usually absent in any PDB. So I was
wondering if there would be any program able to let me manipulate the
coordinate reference of a pdb file.

 

Thank you for your time.

 

Gabriel Urquiza

 


------=_NextPart_000_0004_01CB37BB.3098E690
Content-Type: text/html;
	charset="us-ascii"
Content-Transfer-Encoding: quoted-printable

<html xmlns:v=3D"urn:schemas-microsoft-com:vml" =
xmlns:o=3D"urn:schemas-microsoft-com:office:office" =
xmlns:w=3D"urn:schemas-microsoft-com:office:word" =
xmlns:m=3D"http://schemas.microsoft.com/office/2004/12/omml" =
xmlns=3D"http://www.w3.org/TR/REC-html40">

<head>
<meta http-equiv=3DContent-Type content=3D"text/html; =
charset=3Dus-ascii">
<meta name=3DGenerator content=3D"Microsoft Word 12 (filtered medium)">
<style>
<!--
 /* Font Definitions */
 _+_font-face
	{font-family:"Cambria Math";
	panose-1:2 4 5 3 5 4 6 3 2 4;}
_+_font-face
	{font-family:Calibri;
	panose-1:2 15 5 2 2 2 4 3 2 4;}
_+_font-face
	{font-family:Tahoma;
	panose-1:2 11 6 4 3 5 4 4 2 4;}
 /* Style Definitions */
 p.MsoNormal, li.MsoNormal, div.MsoNormal
	{margin:0in;
	margin-bottom:.0001pt;
	font-size:12.0pt;
	font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
	{mso-style-priority:99;
	color:blue;
	text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
	{mso-style-priority:99;
	color:purple;
	text-decoration:underline;}
span.EmailStyle17
	{mso-style-type:personal-reply;
	font-family:"Calibri","sans-serif";
	color:#1F497D;}
.MsoChpDefault
	{mso-style-type:export-only;}
_+_page WordSection1
	{size:8.5in 11.0in;
	margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
	{page:WordSection1;}
-->
</style>
<!--[if gte mso 9]><xml>
 <o:shapedefaults v:ext=3D"edit" spidmax=3D"1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
 <o:shapelayout v:ext=3D"edit">
  <o:idmap v:ext=3D"edit" data=3D"1" />
 </o:shapelayout></xml><![endif]-->
</head>

<body lang=3DEN-US link=3Dblue vlink=3Dpurple>

<div class=3DWordSection1>

<p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>ChemCraft might.<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'>http://www.chemcraftprog.com/info.html<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>

<div style=3D'border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt =
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>Gabriel
Urquiza urquizagabes[A]gmail.com<br>
<b>Sent:</b> Monday, August 09, 2010 9:19 AM<br>
<b>To:</b> Kress, Jim <br>
<b>Subject:</b> CCL: PDB coordinates tranformation<o:p></o:p></span></p>

</div>

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

<div>

<p class=3DMsoNormal>Greetings CCLers.<o:p></o:p></p>

<div>

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

</div>

<div>

<p class=3DMsoNormal>I am trying to make some surveys about the =
structures of
some channel proteins and it would really help if the Z axis coincided =
with the
pore of the channel and passed along the middle point among the atoms. =
The
problem, evidently, is that such properties are usually absent in any =
PDB. So I
was wondering if there would be any program able to let me manipulate =
the
coordinate reference of a pdb file.<o:p></o:p></p>

</div>

<div>

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

</div>

<div>

<p class=3DMsoNormal>Thank you for your time.<o:p></o:p></p>

</div>

<div>

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

</div>

<div>

<p class=3DMsoNormal><span style=3D'color:#888888'>Gabriel =
Urquiza<o:p></o:p></span></p>

</div>

</div>

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

</div>

</body>

</html>

------=_NextPart_000_0004_01CB37BB.3098E690--


From owner-chemistry@ccl.net Mon Aug  9 14:30:00 2010
From: "Jim Kress ccl_nospam]*[kressworks.com" <owner-chemistry]~[server.ccl.net>
To: CCL
Subject: CCL: PDB coordinates tranformation
Message-Id: <-42488-100809125246-19729-C85t6km/arj/+S/oavk9/g]~[server.ccl.net>
X-Original-From: "Jim Kress" <ccl_nospam!A!kressworks.com>
Content-Language: en-us
Content-Type: multipart/alternative;
	boundary="----=_NextPart_000_0011_01CB37C1.BE254340"
Date: Mon, 9 Aug 2010 12:52:33 -0400
MIME-Version: 1.0


Sent to CCL by: "Jim Kress" [ccl_nospam,+,kressworks.com]
This is a multi-part message in MIME format.

------=_NextPart_000_0011_01CB37C1.BE254340
Content-Type: text/plain;
	charset="us-ascii"
Content-Transfer-Encoding: 7bit

ChemCraft might.

 

http://www.chemcraftprog.com/

 

Jim

 

> From: owner-chemistry+ccl_nospam==kressworks.com^^ccl.net
[mailto:owner-chemistry+ccl_nospam==kressworks.com^^ccl.net] On Behalf Of
Gabriel Urquiza urquizagabes[A]gmail.com
Sent: Monday, August 09, 2010 9:19 AM
To: Kress, Jim 
Subject: CCL: PDB coordinates tranformation

 

Greetings CCLers.

 

I am trying to make some surveys about the structures of some channel
proteins and it would really help if the Z axis coincided with the pore of
the channel and passed along the middle point among the atoms. The problem,
evidently, is that such properties are usually absent in any PDB. So I was
wondering if there would be any program able to let me manipulate the
coordinate reference of a pdb file.

 

Thank you for your time.

 

Gabriel Urquiza

 


------=_NextPart_000_0011_01CB37C1.BE254340
Content-Type: text/html;
	charset="us-ascii"
Content-Transfer-Encoding: quoted-printable

<html xmlns:v=3D"urn:schemas-microsoft-com:vml" =
xmlns:o=3D"urn:schemas-microsoft-com:office:office" =
xmlns:w=3D"urn:schemas-microsoft-com:office:word" =
xmlns:m=3D"http://schemas.microsoft.com/office/2004/12/omml" =
xmlns=3D"http://www.w3.org/TR/REC-html40">

<head>
<meta http-equiv=3DContent-Type content=3D"text/html; =
charset=3Dus-ascii">
<meta name=3DGenerator content=3D"Microsoft Word 12 (filtered medium)">
<style>
<!--
 /* Font Definitions */
 ^^font-face
	{font-family:"Cambria Math";
	panose-1:2 4 5 3 5 4 6 3 2 4;}
^^font-face
	{font-family:Calibri;
	panose-1:2 15 5 2 2 2 4 3 2 4;}
^^font-face
	{font-family:Tahoma;
	panose-1:2 11 6 4 3 5 4 4 2 4;}
 /* Style Definitions */
 p.MsoNormal, li.MsoNormal, div.MsoNormal
	{margin:0in;
	margin-bottom:.0001pt;
	font-size:12.0pt;
	font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
	{mso-style-priority:99;
	color:blue;
	text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
	{mso-style-priority:99;
	color:purple;
	text-decoration:underline;}
span.EmailStyle17
	{mso-style-type:personal-reply;
	font-family:"Calibri","sans-serif";
	color:#1F497D;}
.MsoChpDefault
	{mso-style-type:export-only;
	font-size:10.0pt;}
^^page WordSection1
	{size:8.5in 11.0in;
	margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
	{page:WordSection1;}
-->
</style>
<!--[if gte mso 9]><xml>
 <o:shapedefaults v:ext=3D"edit" spidmax=3D"1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
 <o:shapelayout v:ext=3D"edit">
  <o:idmap v:ext=3D"edit" data=3D"1" />
 </o:shapelayout></xml><![endif]-->
</head>

<body lang=3DEN-US link=3Dblue vlink=3Dpurple>

<div class=3DWordSection1>

<p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>ChemCraft might.<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'>http://www.chemcraftprog.com/<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>

<div style=3D'border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt =
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>Gabriel
Urquiza urquizagabes[A]gmail.com<br>
<b>Sent:</b> Monday, August 09, 2010 9:19 AM<br>
<b>To:</b> Kress, Jim <br>
<b>Subject:</b> CCL: PDB coordinates tranformation<o:p></o:p></span></p>

</div>

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

<div>

<p class=3DMsoNormal>Greetings CCLers.<o:p></o:p></p>

<div>

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

</div>

<div>

<p class=3DMsoNormal>I am trying to make some surveys about the =
structures of
some channel proteins and it would really help if the Z axis coincided =
with the
pore of the channel and passed along the middle point among the atoms. =
The
problem, evidently, is that such properties are usually absent in any =
PDB. So I
was wondering if there would be any program able to let me manipulate =
the
coordinate reference of a pdb file.<o:p></o:p></p>

</div>

<div>

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

</div>

<div>

<p class=3DMsoNormal>Thank you for your time.<o:p></o:p></p>

</div>

<div>

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

</div>

<div>

<p class=3DMsoNormal><span style=3D'color:#888888'>Gabriel =
Urquiza<o:p></o:p></span></p>

</div>

</div>

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

</div>

</body>

</html>

------=_NextPart_000_0011_01CB37C1.BE254340--


From owner-chemistry@ccl.net Mon Aug  9 15:05:01 2010
From: "Daniel Glossman-Mitnik dglossman^gmail.com" <owner-chemistry]|[server.ccl.net>
To: CCL
Subject: CCL: Computational Chemistry and Renewable Energy
Message-Id: <-42489-100809140602-25546-sGpDLK6s7hQEu9gfCShCAg]|[server.ccl.net>
X-Original-From: Daniel Glossman-Mitnik <dglossman:+:gmail.com>
Content-Type: multipart/alternative; boundary=0015174c0f76e3592e048d67dd37
Date: Mon, 9 Aug 2010 12:05:50 -0600
MIME-Version: 1.0


Sent to CCL by: Daniel Glossman-Mitnik [dglossman(-)gmail.com]
--0015174c0f76e3592e048d67dd37
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

Dear Jeffrey:

My answer is a big YES to all
I will be very interested in collaborating with you in this rpoject.

Best regards,

Daniel

***************************************************************************=
************************************
Dr. Daniel Glossman-Mitnik
Centro de Investigaci=C3=B3n en Materiales Avanzados, SC
Departamento de Simulaci=C3=B3n Computacional y Modelado Molecular
Miguel de Cervantes 120 - Comp. Ind. Chihuahua - Chihuahua, Chih 31109,
Mexico
Phone: +52 614 4391151   Secretary/FAX: +52 614 4391130    Lab: +52 614
4394805
E-mail:  daniel.glossman^cimav.edu.mx          dglossman^gmail.com
WWW:  http://www.cimav.edu.mx/cv/daniel.glossman
              http://blogs.cimav.edu.mx/daniel.glossman
***************************************************************************=
************************************


2010/8/9 Jeffrey N Woodford jeffwoodford2,gmail.com <owner-chemistry^ccl.ne=
t
>

>
> Sent to CCL by: "Jeffrey N Woodford" [jeffwoodford2(0)gmail.com]
> All:
> I've been approached by a publisher to edit a volume on "Computational
> Chemistry and Renewable Energy".  (I interpret this topic rather broadly.=
)
>  So before I put a lot of effort into a book proposal on this topic, I
> thought I'd throw it out to the list to see if there would be any interes=
t
> in this type of book, more specifically:
>
> 1. Would you be interested in purchasing a book like this for your
> collection or for your institution's library holdings?
> 2. Would you be interested in submitting a chapter to a volume like this?
> 3. Would you be interested in co-editing this book?  Since I'm a QM guy, =
it
> would be best if co-editors were in a complementary area.
>
> Thanks for your feedback!
>
> -Jeff
>
> Jeffrey N. Woodford
> Assistant Professor of Chemistry
> Missouri Western State University
>
>
>
> -=3D This is automatically added to each message by the mailing script =
=3D->
>
>

--0015174c0f76e3592e048d67dd37
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

Dear Jeffrey:<br><br>My answer is a big YES to all<br>I will be very intere=
sted in collaborating with you in this rpoject.<br><br>Best regards,<br><br=
>Daniel<br><br clear=3D"all">**********************************************=
*****************************************************************<br>
Dr. Daniel Glossman-Mitnik<br>Centro de Investigaci=C3=B3n en Materiales Av=
anzados, SC<br>Departamento de Simulaci=C3=B3n Computacional y Modelado Mol=
ecular<br>Miguel de Cervantes 120 - Comp. Ind. Chihuahua - Chihuahua, Chih =
31109, Mexico<br>
Phone: +52 614 4391151=C2=A0=C2=A0 Secretary/FAX: +52 614 4391130=C2=A0 =C2=
=A0 Lab: +52 614 4394805<br>E-mail:=C2=A0 <a href=3D"mailto:daniel.glossman=
^cimav.edu.mx">daniel.glossman^cimav.edu.mx</a>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =
=C2=A0 <a href=3D"mailto:dglossman^gmail.com">dglossman^gmail.com</a><br>
WWW:=C2=A0 <a href=3D"http://www.cimav.edu.mx/cv/daniel.glossman">http://ww=
w.cimav.edu.mx/cv/daniel.glossman</a><br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=
 =C2=A0 =C2=A0 <a href=3D"http://blogs.cimav.edu.mx/daniel.glossman">http:/=
/blogs.cimav.edu.mx/daniel.glossman</a><br>
***************************************************************************=
************************************<br>
<br><br><div class=3D"gmail_quote">2010/8/9 Jeffrey N Woodford jeffwoodford=
2,<a href=3D"http://gmail.com">gmail.com</a> <span dir=3D"ltr">&lt;<a href=
=3D"mailto:owner-chemistry^ccl.net">owner-chemistry^ccl.net</a>&gt;</span><=
br><blockquote class=3D"gmail_quote" style=3D"margin: 0pt 0pt 0pt 0.8ex; bo=
rder-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
Sent to CCL by: &quot;Jeffrey N Woodford&quot; [jeffwoodford2(0)<a href=3D"=
http://gmail.com" target=3D"_blank">gmail.com</a>]<br>
All:<br>
I&#39;ve been approached by a publisher to edit a volume on &quot;Computati=
onal Chemistry and Renewable Energy&quot;. =C2=A0(I interpret this topic ra=
ther broadly.) =C2=A0So before I put a lot of effort into a book proposal o=
n this topic, I thought I&#39;d throw it out to the list to see if there wo=
uld be any interest in this type of book, more specifically:<br>

<br>
1. Would you be interested in purchasing a book like this for your collecti=
on or for your institution&#39;s library holdings?<br>
2. Would you be interested in submitting a chapter to a volume like this?<b=
r>
3. Would you be interested in co-editing this book? =C2=A0Since I&#39;m a Q=
M guy, it would be best if co-editors were in a complementary area.<br>
<br>
Thanks for your feedback!<br>
<br>
-Jeff<br>
<br>
Jeffrey N. Woodford<br>
Assistant Professor of Chemistry<br>
Missouri Western State University<br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
<br<br=<br<br>
<br>
E-mail to subscribers: <a href=3D"mailto:CHEMISTRY^ccl.net">CHEMISTRY^ccl.n=
et</a> or use:<br>
 =C2=A0 =C2=A0 =C2=A0<a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_mes=
sage" target=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a>=
<br>
<br>
E-mail to administrators: <a href=3D"mailto:CHEMISTRY-REQUEST^ccl.net">CHEM=
ISTRY-REQUEST^ccl.net</a> or use<br>
 =C2=A0 =C2=A0 =C2=A0<a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_mes=
sage" target=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a>=
<br>
<br>
Subscribe/Unsubscribe:<br>
 =C2=A0 =C2=A0 =C2=A0<a href=3D"http://www.ccl.net/chemistry/sub_unsub.shtm=
l" target=3D"_blank">http://www.ccl.net/chemistry/sub_unsub.shtml</a><br>
<br>
Before posting, check wait time at: <a href=3D"http://www.ccl.net" target=
=3D"_blank">http://www.ccl.net</a><br>
<br>
Job: <a href=3D"http://www.ccl.net/jobs" target=3D"_blank">http://www.ccl.n=
et/jobs</a><br>
Conferences: <a href=3D"http://server.ccl.net/chemistry/announcements/confe=
rences/" target=3D"_blank">http://server.ccl.net/chemistry/announcements/co=
nferences/</a><br>
<br>
Search Messages: <a href=3D"http://www.ccl.net/chemistry/searchccl/index.sh=
tml" target=3D"_blank">http://www.ccl.net/chemistry/searchccl/index.shtml</=
a><br>
<br<br>
 =C2=A0 =C2=A0 =C2=A0<a href=3D"http://www.ccl.net/spammers.txt" target=3D"=
_blank">http://www.ccl.net/spammers.txt</a><br>
<br>
RTFI: <a href=3D"http://www.ccl.net/chemistry/aboutccl/instructions/" targe=
t=3D"_blank">http://www.ccl.net/chemistry/aboutccl/instructions/</a><br>
<br>
<br>
</blockquote></div><br>

--0015174c0f76e3592e048d67dd37--


From owner-chemistry@ccl.net Mon Aug  9 16:57:00 2010
From: "Roy Kim rkim],[nvidia.com" <owner-chemistry/a\server.ccl.net>
To: CCL
Subject: CCL: Try NVIDIA GPUs for Free on MD Codes
Message-Id: <-42490-100809134527-3080-0umWMV8o7aUCxFfDLEuBbQ/a\server.ccl.net>
X-Original-From: "Roy  Kim" <rkim(a)nvidia.com>
Date: Mon, 9 Aug 2010 13:45:25 -0400


Sent to CCL by: "Roy  Kim" [rkim:+:nvidia.com]
If you are an AMBER, GROMACS, or NAMD user, you can enjoy tremendous computational capabilities by running your code on GPUs. 

NVIDIA is now offering a limited time program called "The GPU Test Drive" where a user can remotely log into a personal supercomputer for free, run sample models, and even run their own models.  

For more information, visit www.nvidia.com/MD_Test_Drive or contact me at rkim],[nvidia.com.

Regards,

Roy Kim
rkim],[nvidia.com
NVIDIA Tesla Product Manager


From owner-chemistry@ccl.net Mon Aug  9 18:01:01 2010
From: "Brian Salter-Duke b_duke+/-bigpond.net.au" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL:G: charged atoms in neutral molecule
Message-Id: <-42491-100809174053-20005-cOBquQuQpXRLm9QpGhPTDQ-#-server.ccl.net>
X-Original-From: Brian Salter-Duke <b_duke{}bigpond.net.au>
Content-Disposition: inline
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=iso-8859-1
Date: Tue, 10 Aug 2010 07:39:38 +1000
MIME-Version: 1.0


Sent to CCL by: Brian Salter-Duke [b_duke(-)bigpond.net.au]
On Mon, Aug 09, 2010 at 11:07:18AM -0400, Serge Gorelsky gorelsky|,|gmail.com wrote:
> 
> Sent to CCL by: Serge Gorelsky [gorelsky:gmail.com]
> > Suppose that I want to optimize then calculate several properties of a
> > molecule which has 30 atoms, including one oxygen cation and one nitrogen
> > anion, and the rest of the atoms are neutral. Do I need to specify those
> > ions in the Gaussian input file? If so, how can I do that? That's what I
> > need to know.
> 
> You specify charged or neutral parts by building a GUESS=CARDS initial
> guess input file (http://www.gaussian.com/g_tech/g_ur/k_guess.htm)
> that correspond to your desired charge distribution. Building such
> initial guess for Gaussian or GAMESS calculations is fully automated
> if you use the AOMix software (www.sg-chem.net). You can find all the
> necessary details about the procedure in Appendix II of the AOMix
> manual.

You really should not need to go to all that trouble. Any normal guess
for the initial orbitals should do.

Brian.

> -- 
> Best regards,
>   Serge Gorelsky> 

-- 
                Brian Salter-Duke (Brian Duke)       
      626 Melbourne Rd, Spotswood, VIC, 3015, Australia. 
      Email: b_duke%%bigbond.net.au    Phone: 03-93992847
Web: http://www.salter-duke.bigpondhosting.com/brian/index.htm


From owner-chemistry@ccl.net Mon Aug  9 19:02:00 2010
From: "Serge Gorelsky gorelsky(~)gmail.com" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL: charged atoms in neutral molecule
Message-Id: <-42492-100809190056-19480-DQzx0McggNhffU1SgV3iQA**server.ccl.net>
X-Original-From: Serge Gorelsky <gorelsky#%#gmail.com>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=UTF-8
Date: Mon, 9 Aug 2010 19:00:47 -0400
MIME-Version: 1.0


Sent to CCL by: Serge Gorelsky [gorelsky]![gmail.com]
> You really should not need to go to all that trouble. Any normal guess
> for the initial orbitals should do.
>
> Brian.

yes, many people assume that this should be the case. And as a result,
> from time to time one gets the wrong (excited) electronic state to
calculate instead of looking at the true ground state and those even
make to publications to present a record for all to see. The most
common example of the situation when "normal guess"  fails is bi- or
multi-nuclear transition metal complexes with antiferromagnetic
coupling.

"Normal guess" does not know chemistry!
-- 
Regards,
  Serge Gorelsky


From owner-chemistry@ccl.net Mon Aug  9 20:58:01 2010
From: "Brian Salter-Duke b_duke*|*bigpond.net.au" <owner-chemistry]_[server.ccl.net>
To: CCL
Subject: CCL: charged atoms in neutral molecule
Message-Id: <-42493-100809205211-3410-Ph8lMWaIPUMF4XZgN1PYMA]_[server.ccl.net>
X-Original-From: Brian Salter-Duke <b_duke:_:bigpond.net.au>
Content-Disposition: inline
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=iso-8859-1
Date: Tue, 10 Aug 2010 10:50:58 +1000
MIME-Version: 1.0


Sent to CCL by: Brian Salter-Duke [b_duke : bigpond.net.au]
On Mon, Aug 09, 2010 at 07:00:47PM -0400, Serge Gorelsky gorelsky(~)gmail.com wrote:
> 
> Sent to CCL by: Serge Gorelsky [gorelsky]![gmail.com]
> > You really should not need to go to all that trouble. Any normal guess
> > for the initial orbitals should do.
> >
> > Brian.
> 
> yes, many people assume that this should be the case. And as a result,
> > from time to time one gets the wrong (excited) electronic state to
> calculate instead of looking at the true ground state and those even
> make to publications to present a record for all to see. The most
> common example of the situation when "normal guess"  fails is bi- or
> multi-nuclear transition metal complexes with antiferromagnetic
> coupling.

Of course, such systems may well be a problem, as indeed almost all
transition metal calculations may be a problem. However, it sounded like
the OP was talking about an amino acid, and a standard Huckel or whatever
guess is usually OK there.
 
> "Normal guess" does not know chemistry!

It can do in some cases.

Brian.

> -- 
> Regards,
>   Serge Gorelsky> 

-- 
                Brian Salter-Duke (Brian Duke)       
      626 Melbourne Rd, Spotswood, VIC, 3015, Australia. 
      Email: b_duke-.-bigbond.net.au    Phone: 03-93992847
Web: http://www.salter-duke.bigpondhosting.com/brian/index.htm


From owner-chemistry@ccl.net Mon Aug  9 22:56:00 2010
From: "Jeff Woodford jeffwoodford2^-^gmail.com" <owner-chemistry .. server.ccl.net>
To: CCL
Subject: CCL: AMD/Intel 6-core comparison
Message-Id: <-42494-100809225431-18167-YdLAKeclsz81pc6UEe4i3A .. server.ccl.net>
X-Original-From: Jeff Woodford <jeffwoodford2[-]gmail.com>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset="UTF-8"
Date: Mon, 09 Aug 2010 21:53:03 -0500
Mime-Version: 1.0


Sent to CCL by: Jeff Woodford [jeffwoodford2 ~ gmail.com]
All:
I'm in the market to buy some new hardware for QM calculations
(generally GAMESS-US), and I'm looking to buy a 6-core chip, either AMD
Phenom II X6 or Intel Core i7 970.  Just looking at the specs, the AMD
looks to be the better buy, but my experience with 6-core chips is
nonexistent.  Does anyone here have any experience with doing QM
computations on either of these?  How do they compare?

Thanks for your input!

-Jeff

Jeffrey N. Woodford
Assistant Professor of Chemistry
Missouri Western State University