From owner-chemistry@ccl.net Mon Apr  4 03:15:00 2011
From: "Lars Goerigk lars.goerigk-$-uni-muenster.de" <owner-chemistry{:}server.ccl.net>
To: CCL
Subject: CCL: Physisorption and Density Functionals
Message-Id: <-44277-110404030802-1523-wB81pc24DuBRxegz3oKD+Q{:}server.ccl.net>
X-Original-From: Lars Goerigk <lars.goerigk-x-uni-muenster.de>
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Date: Mon, 04 Apr 2011 09:07:50 +0200 (CEST)
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Sent to CCL by: Lars Goerigk [lars.goerigk!^!uni-muenster.de]
Dear Sanjay,

dispersion corrected (DFT-D3) semi-local density functionals like B97-D,
TPSS, BLYP, and revPBE perform very well (typical error for interaction
energies of 5-10%) for many non-covalent interactions including those in
alkane dimers. For
larger systems properly polarized triple-zeta basis sets without counterpoise
corrections are sufficient. Also DFT-D3 gradients for geometry optimizations
are availabe.  You might have a look to the following references and
references therein:

S. Grimme, Density functional theory with London dispersion corrections,
WIREs Comput. Mol. Sci., 1 (2011), 211-228.

S. Grimme and J. Antony and S. Ehrlich and H. Krieg, J. Chem. Phys., 132
(2010), 154104.

L. Goerigk and S. Grimme, Phys. Chem. Chem. Phys., 13 (2011), 6670-6688.

DFT-D3 has been implemented meanwhile in many major QC program packages
including TURBOMOLE but can also be downloaded as a stand-alone program
> from http://toc.uni-muenster.de/DFTD3/

With best wishes,

Lars Goerigk
Theoretical Organic Chemistry
University of Münster
Germany


From owner-chemistry@ccl.net Mon Apr  4 03:57:00 2011
From: "qiancheng shen qianchengshen()gmail.com" <owner-chemistry-x-server.ccl.net>
To: CCL
Subject: CCL: Convert Molecule Structure to IUPAC
Message-Id: <-44278-110404035419-19251-98BATifLAWO6+3brC2uz7g-x-server.ccl.net>
X-Original-From: qiancheng shen <qianchengshen]|[gmail.com>
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Date: Mon, 4 Apr 2011 15:54:13 +0800
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Sent to CCL by: qiancheng shen [qianchengshen^_^gmail.com]
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Hello everyone,

        I wondered there exists any opensource toolkit to convert Molecule
Structure (such as *.mol,*.smi) to IUPAC name?
        I tried OPSIN, but it seems only to be able to convert IUPAC name to
structure.

Thanks in advance.

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<span class=3D"Apple-style-span" style=3D"border-collapse: collapse; font-f=
amily: arial, sans-serif; font-size: 13px; ">Hello everyone,<div><br><div><=
div>=A0=A0 =A0 =A0 =A0I wondered there exists any opensource toolkit to con=
vert Molecule Structure (such as *.mol,*.smi) to IUPAC name?</div>
<div>=A0=A0 =A0 =A0 =A0I tried OPSIN, but it seems only to be able to conve=
rt IUPAC name to structure.</div><div><br></div><div>Thanks in advance.</di=
v></div></div></span>

--000e0cd71a6acacfae04a0131040--


From owner-chemistry@ccl.net Mon Apr  4 06:58:00 2011
From: "Chris Swain swain(0)mac.com" <owner-chemistry===server.ccl.net>
To: CCL
Subject: CCL: Convert Molecule Structure to IUPAC
Message-Id: <-44279-110404065719-13345-ni9WRYepUmChYWfkLaqFHw===server.ccl.net>
X-Original-From: Chris Swain <swain::mac.com>
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Date: Mon, 04 Apr 2011 11:57:08 +0100
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Sent to CCL by: Chris Swain [swain.^.mac.com]

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Might be worth looking at

http://cactus.nci.nih.gov/chemical/structure

Chris
On 4 Apr 2011, at 08:54, qiancheng shen qianchengshen()gmail.com wrote:

> Hello everyone,
> 
>         I wondered there exists any opensource toolkit to convert Molecule Structure (such as *.mol,*.smi) to IUPAC name?
>         I tried OPSIN, but it seems only to be able to convert IUPAC name to structure.
> 
> Thanks in advance.


--Boundary_(ID_sEw8CR1mBra0kXA+J5oEhg)
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<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Might be worth looking at<div><br></div><div><a href="http://cactus.nci.nih.gov/chemical/structure">http://cactus.nci.nih.gov/chemical/structure</a></div><div><br></div><div>Chris<br><div><div>On 4 Apr 2011, at 08:54, qiancheng shen qianchengshen()<a href="http://gmail.com">gmail.com</a> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; ">Hello everyone,</span><div style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; "><br><div><div>&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;I wondered there exists any opensource toolkit to convert Molecule Structure (such as *.mol,*.smi) to IUPAC name?</div>
<div>&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;I tried OPSIN, but it seems only to be able to convert IUPAC name to structure.</div><div><br></div><div>Thanks in advance.</div></div></div>
</blockquote></div><br></div></body></html>

--Boundary_(ID_sEw8CR1mBra0kXA+J5oEhg)--


From owner-chemistry@ccl.net Mon Apr  4 07:50:00 2011
From: "Serdar Bado?lu sbadoglu|*|gazi.edu.tr" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL: Convert Molecule Structure to IUPAC
Message-Id: <-44280-110404073556-29252-LS5YaTn8HICpOQ/6h6zyNA+*+server.ccl.net>
X-Original-From: "Serdar Bado?lu" <sbadoglu(-)gazi.edu.tr>
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Date: Mon, 4 Apr 2011 11:28:57 -0000


Sent to CCL by: "Serdar Bado?lu" [sbadoglu_._gazi.edu.tr]
Hi,

You can use MarvinSketch.

> Hello everyone,
> 
>         I wondered there exists any opensource toolkit to convert Molecule
> Structure (such as *.mol,*.smi) to IUPAC name?
>         I tried OPSIN, but it seems only to be able to convert IUPAC name to
> structure.
> 
> Thanks in advance.
> 

-- 
Serdar BADOGLU
Gazi University
Department of Physics


From owner-chemistry@ccl.net Mon Apr  4 09:19:00 2011
From: "Roscioni O.M. omr(-)soton.ac.uk" <owner-chemistry:-:server.ccl.net>
To: CCL
Subject: CCL: Script - Dipole moment
Message-Id: <-44281-110404053005-21211-BbgGIWqRr2KLrAsDdmnSfQ:-:server.ccl.net>
X-Original-From: "Roscioni O.M." <omr]*[soton.ac.uk>
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Date: Mon, 4 Apr 2011 10:29:25 +0100
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Sent to CCL by: "Roscioni O.M." [omr:-:soton.ac.uk]
Here it is. Save this script and use it to read your pdbqt file (I assume you are using a unix-like ambient). You should verify that the x y z and q fields are correct (I have assumed that they are the same as a normal PDB file).

#!/usr/bin/awk -f
BEGIN{
   # atomic unit of length in angstrom.
   a0=0.52917720859;
   # 1 D (debye) in atomic units.
   debye=2.54174630771028;
}

# Main program
{
  IGNORECASE = 1
  if ($1=="atom"||$1=="hetatm"){
    x=substr($0,31,8)
    y=substr($0,39,8)
    z=substr($0,47,8)
    q=substr($0,71,6)
    dx+=q*x;
    dy+=q*y;
    dz+=q*z;
  }
}

END {
    dip=sqrt(dx**2+dy**2+dz**2);
    print  "Dipole moment in Debye:\n";
    printf "Dtotal: %12.6f\n",dip/a0*debye;
    printf "Dx:     %12.6f\n",dx/a0*debye;
    printf "Dy:     %12.6f\n",dy/a0*debye;
    printf "Dz:     %12.6f\n\n",dz/a0*debye;
    print  "Dipole moment in e*Angs:\n";
    printf "Dtotal: %12.6f\n",dip;
    printf "Dx:     %12.6f\n",dx;
    printf "Dy:     %12.6f\n",dy;
    printf "Dz:     %12.6f\n",dz;
}

#Cheers,
#otello
________________________________________
> From: owner-chemistry+omr==soton.ac.uk- -ccl.net [owner-chemistry+omr==soton.ac.uk- -ccl.net] On Behalf Of Eliac Brown Eliacbrown]^[yahoo.com [owner-chemistry- -ccl.net]
Sent: 02 April 2011 01:08
To: Roscioni O.M.
Subject: CCL: Script - Dipole moment

Sent to CCL by: "Eliac  Brown" [Eliacbrown|*|yahoo.com]
Dear all
I was wondering if anyone could support me with a software or script can be
used to calculate the dipole moment of small molecules in the pdbqt formate.
Thanks in advance
Eliachttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

From owner-chemistry@ccl.net Mon Apr  4 12:52:01 2011
From: "zouzou adnani zinebeladnani{:}hotmail.com" <owner-chemistry{}server.ccl.net>
To: CCL
Subject: CCL: .cif file of alpha iron
Message-Id: <-44282-110404124928-21432-Bl9ALGYG3m+t8Zz/bUm/ng{}server.ccl.net>
X-Original-From: "zouzou  adnani" <zinebeladnani*o*hotmail.com>
Date: Mon, 4 Apr 2011 12:49:26 -0400


Sent to CCL by: "zouzou  adnani" [zinebeladnani-.-hotmail.com]
hi everyone; 
I'm working with crystal programme for the first time, I need a cif file of the alpha iron to extract all the cristallographic data needed to launch my job.
I would be thankful if anyone can give me a link to get this cif file
regards


From owner-chemistry@ccl.net Mon Apr  4 14:14:00 2011
From: "Abu Asaduzzaman a.asaduzzaman[-]gmail.com" <owner-chemistry_-_server.ccl.net>
To: CCL
Subject: CCL: .cif file of alpha iron
Message-Id: <-44283-110404141128-25252-8/D/dF8hDclIKDUE5T3HnA_-_server.ccl.net>
X-Original-From: Abu Asaduzzaman <a.asaduzzaman-,-gmail.com>
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Date: Mon, 4 Apr 2011 13:11:20 -0500
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Sent to CCL by: Abu Asaduzzaman [a.asaduzzaman]![gmail.com]
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http://rruff.geo.arizona.edu/AMS/minerals/Iron-alpha

On Mon, Apr 4, 2011 at 11:49 AM, zouzou adnani zinebeladnani{:}hotmail.com <
owner-chemistry[A]ccl.net> wrote:

>
> Sent to CCL by: "zouzou  adnani" [zinebeladnani-.-hotmail.com]
> hi everyone;
> I'm working with crystal programme for the first time, I need a cif file of
> the alpha iron to extract all the cristallographic data needed to launch my
> job.
> I would be thankful if anyone can give me a link to get this cif file
> regards>
>
>

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<a href=3D"http://rruff.geo.arizona.edu/AMS/minerals/Iron-alpha">http://rru=
ff.geo.arizona.edu/AMS/minerals/Iron-alpha</a><br><br><div class=3D"gmail_q=
uote">On Mon, Apr 4, 2011 at 11:49 AM, zouzou adnani zinebeladnani{:}<a hre=
f=3D"http://hotmail.com">hotmail.com</a> <span dir=3D"ltr">&lt;<a href=3D"m=
ailto:owner-chemistry[A]ccl.net">owner-chemistry[A]ccl.net</a>&gt;</span> wrote=
:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex;"><br>
Sent to CCL by: &quot;zouzou =A0adnani&quot; [zinebeladnani-.-<a href=3D"ht=
tp://hotmail.com" target=3D"_blank">hotmail.com</a>]<br>
hi everyone;<br>
I&#39;m working with crystal programme for the first time, I need a cif fil=
e of the alpha iron to extract all the cristallographic data needed to laun=
ch my job.<br>
I would be thankful if anyone can give me a link to get this cif file<br>
regards<br>
<br>
<br>
<br>
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