From owner-chemistry@ccl.net Thu Aug  2 10:29:01 2012
From: "Oellien, F (Frank) frank.oellien(a)msd.de" <owner-chemistry---server.ccl.net>
To: CCL
Subject: CCL: GCC2012 Last Call For Paper / Extended Deadline
Message-Id: <-47302-120802035210-4936-aoybm8YKoraG/1IlD8zxMA---server.ccl.net>
X-Original-From: "Oellien, F (Frank)" <frank.oellien*|*msd.de>
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Date: Thu, 2 Aug 2012 09:51:56 +0200
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Sent to CCL by: "Oellien, F (Frank)" [frank.oellien(a)msd.de]
LAST CALL FOR PAPERS / EXTENDED DEADLINE
8th German Conference on Chemoinformatics (GCC2012)
Hotel 'Der Achtermann', Goslar, Germany
11 - 13 November 2012

Dear Colleagues,

The CIC division of the German Chemical Society announces the 8. German Conference on Chemoinformatics (GCC2012) (http://www.gdch.de/gcc2012) to be held in Goslar, Germany, November 11 - 13, 2012. We wish to attract both industrial and academic scientists in this field. The scientific program will include plenary lectures as well as presentation of posters, projects and software. The conference language is English.

We are inviting the submission of abstracts for talks, posters and free software contributions in the following plenary sessions:
* Chemoinformatics and Drug Discovery
* Chemical Information, Patents, and Databases
* Molecular Modelling
* Computational Material Science and Nanotechnology

In addition other highlights in the field of Computational Chemistry are also welcome.

There is a limited number of scholarships available. Applications have to be send to the German Chemical Society until September 1, 2012.

The deadline for the submissions of oral contributions has been extended to August 19, 2012. The submission deadline for posters and free software session contributions is September 1, 2012.

Please visit our online submission form on http://www.gdch.de/gcc2012 to submit your abstract.

Invited Speakers this year are:
* Andreas Bender, University of Cambridge/UK
* Lucio Colombi Ciacchi, Bremen/DE
* Gregory Landrum, Novartis, Basel/CH
* Randall Marcinko, Mei, Stanford/US
* Klaus-Jürgen Schleifer, BASF, Ludwigshafen/DE
* Rebecca Wade, HITS, Heidelberg/DE
* Engelbert Zass, ETH, Zurich/CH

Visit the conference website at http://www.gdch.de/gcc2012 for more information.

Frank Oellien
Chairman GDCh CIC Division

Dr. Frank Oellien
Computational Sciences / Molecular Discovery Sciences
MSD Animal Health Germany

E-Mail: frank.oellien~!~msd.de
Phone: +49 (6130) 948 365
Fax: +49 (6130) 948 517

Intervet Innovation GmbH
Zur Propstei
55270 Schwabenheim, Germany
www.msd-animal-health.com 


Hinweis: Diese Email wird von einem Unternehmen der deutschen MSD-Gruppe versandt. Hierzu gehören folgende Vertriebsunternehmen:

Humanarzneimittel:

MSD Sharp & Dohme GmbH, Lindenplatz 1, 85540 Haar; HR München B 6194
Geschäftsführer: Hanspeter Quodt (Vors.), Dr. Claus Dollinger, Dr. Thomas Lang, Dr. Veit Stoll
Aufsichtsratsvorsitzender: Dr. Axel Breitstadt

Tierarzneimittel:

Intervet Deutschland GmbH, Feldstr. 1a, 85716 Unterschleißheim; HR München B 138151
Geschäftsführer: Dr. Daniel Sicher, Christoph Kölsch

Weitere Unternehmen der deutschen MSD-Gruppe siehe http://info.msd.de/pflichtangaben


From owner-chemistry@ccl.net Thu Aug  2 11:04:01 2012
From: "AMBAR BANERJEE ambarpchem^gmail.com" <owner-chemistry||server.ccl.net>
To: CCL
Subject: CCL:G: visualization of MO,s from GAMESS(US) job
Message-Id: <-47303-120802051131-9619-JSfeA78kOgd9k7u4iZ8KCA||server.ccl.net>
X-Original-From: "AMBAR  BANERJEE" <ambarpchem ~~ gmail.com>
Date: Thu, 2 Aug 2012 05:11:29 -0400


Sent to CCL by: "AMBAR  BANERJEE" [ambarpchem.^.gmail.com]
i was using GAMESS-(US) to do some rhf calculations. i need to visualize the MO's using some freely available graphical interface. please help me. is it possible to generate gaussian cube files from gamess dat files?


From owner-chemistry@ccl.net Thu Aug  2 11:39:01 2012
From: "Sandhya Rai sandhyachemistry30##gmail.com" <owner-chemistry]=[server.ccl.net>
To: CCL
Subject: CCL: Problem in running the post processing code for proline in Quantum Espresso
Message-Id: <-47304-120802090417-13795-0FoYjQPENpbYaMqwcRt87w]=[server.ccl.net>
X-Original-From: Sandhya Rai <sandhyachemistry30{=}gmail.com>
Content-Type: multipart/alternative; boundary=f46d04447383328c9804c6480c1d
Date: Thu, 2 Aug 2012 18:33:51 +0530
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Sent to CCL by: Sandhya Rai [sandhyachemistry30-#-gmail.com]
--f46d04447383328c9804c6480c1d
Content-Type: text/plain; charset=ISO-8859-1

Dear All,

I am a new user of Quantum Espresso. I am trying to plot the charge density
of proline after performing the 'scf' and 'nscf' calculations.
But I am getting the following error:

 Program POST-PROC v.4.3.2  starts on  2Aug2012 at 18:25:55

     This program is part of the open-source Quantum ESPRESSO suite
     for quantum simulation of materials; please cite
         "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
          URL http://www.quantum-espresso.org",
     in publications or presentations arising from this work. More details
at
     http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO

     Parallel version (MPI), running on     4 processors
     R & G space division:  proc/pool =    4
    * Message from routine read_file:*
*     file /home1/supriya/Quantum_espresso_proline/tmp/proline_scf.save not
guaranteed to be safe for post-processing*
~
The input file that I am giving is:
&INPUTPP
                      prefix = 'proline_scf' ,
                      outdir =
'/home1/supriya/Quantum_espresso_proline/tmp' ,
                     filplot = 'prolinecharge' ,
                    plot_num = 0,
              spin_component = 0 ,
 /
 &PLOT
                       nfile = 1 ,
                   filepp(1) = 'prolinecharge',
                   weight(1) = 1.0,
                     fileout = 'proline.pp.gnu' ,
                       iflag = 2 ,
               output_format = 0 ,
                       e1(1) = 1.0,
                       e1(2) = 0.0,
                       e1(3) = 0.0,
                       e2(1) = 0.0,
                       e2(2) = 0.0,
                       e2(3) = 1.0,
                          nx = 56 ,
                          ny = 40 ,
 /




-- 
Sandhya Rai
Pursuing Ph.D
Centre of Computational Natural Sciences & Bioinformatics
International Institute of Information & Technology
Gachibowli, Hyderabad.

--f46d04447383328c9804c6480c1d
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Content-Transfer-Encoding: quoted-printable

Dear All,<div><br></div><div>I am a new user of Quantum Espresso. I am tryi=
ng to plot the charge density of proline after performing the &#39;scf&#39;=
 and &#39;nscf&#39; calculations.</div><div>But I am getting the following =
error:=A0</div>


<div><div><br></div><div>=A0Program POST-PROC v.4.3.2 =A0starts on =A02Aug2=
012 at 18:25:55</div><div><br></div><div>=A0 =A0 =A0This program is part of=
 the open-source Quantum ESPRESSO suite</div><div>=A0 =A0 =A0for quantum si=
mulation of materials; please cite</div>


<div>=A0 =A0 =A0 =A0 =A0&quot;P. Giannozzi et al., J. Phys.:Condens. Matter=
 21 395502 (2009);</div><div>=A0 =A0 =A0 =A0 =A0 URL <a href=3D"http://www.=
quantum-espresso.org" target=3D"_blank">http://www.quantum-espresso.org</a>=
&quot;,</div><div>=A0 =A0 =A0in publications or presentations arising from =
this work. More details at</div>


<div>=A0 =A0 =A0<a href=3D"http://www.quantum-espresso.org/wiki/index.php/C=
iting_Quantum-ESPRESSO" target=3D"_blank">http://www.quantum-espresso.org/w=
iki/index.php/Citing_Quantum-ESPRESSO</a></div><div><br></div><div>=A0 =A0 =
=A0Parallel version (MPI), running on =A0 =A0 4 processors</div>


<div>=A0 =A0 =A0R &amp; G space division: =A0proc/pool =3D =A0 =A04</div><d=
iv>=A0 =A0 <b>=A0Message from routine read_file:</b></div><div><b>=A0 =A0 =
=A0file /home1/supriya/Quantum_espresso_proline/tmp/proline_scf.save not gu=
aranteed to be safe for post-processing</b></div>


<div>~ =A0=A0</div><div>The input file that I am giving is:=A0</div><div>&a=
mp;INPUTPP</div><div>=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 prefix =3D=
 &#39;proline_scf&#39; ,</div><div>=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =
=A0 outdir =3D &#39;/home1/supriya/Quantum_espresso_proline/tmp&#39; ,</div=
>

<div>=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0filplot =3D &#39;prolinecha=
rge&#39; ,</div><div>=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 plot_num =3D 0=
,</div><div>=A0 =A0 =A0 =A0 =A0 =A0 =A0 spin_component =3D 0 ,</div><div>=
=A0/</div><div>=A0&amp;PLOT</div><div>=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =
=A0 =A0 =A0nfile =3D 1 ,</div>

<div>=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0filepp(1) =3D &#39;prolinecharg=
e&#39;,</div><div>=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0weight(1) =3D 1.0,=
</div><div>=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0fileout =3D &#39;prol=
ine.pp.gnu&#39; ,</div><div>=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=
iflag =3D 2 ,</div>

<div>=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0output_format =3D 0 ,</div><div>=A0 =A0=
 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0e1(1) =3D 1.0,</div><div>=A0 =A0 =
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0e1(2) =3D 0.0,</div><div>=A0 =A0 =A0=
 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0e1(3) =3D 0.0,</div><div>=A0 =A0 =A0 =
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0e2(1) =3D 0.0,</div>

<div>=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0e2(2) =3D 0.0,</div><di=
v>=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0e2(3) =3D 1.0,</div><div>=
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 nx =3D 56 ,</div><div>=
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 ny =3D 40 ,</div><div>=
=A0/</div><div><br></div><div><br>

</div><div>=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=
 =A0 =A0 =A0</div><div><br></div>-- <br>Sandhya Rai<br>Pursuing Ph.D<br>Cen=
tre of Computational Natural Sciences &amp; Bioinformatics<br>
International Institute of Information &amp; Technology<br>Gachibowli, Hyde=
rabad.<br><br>
</div>

--f46d04447383328c9804c6480c1d--


From owner-chemistry@ccl.net Thu Aug  2 15:01:00 2012
From: "Andrew Yeung andrew.yeung/./chem.tamu.edu" <owner-chemistry a server.ccl.net>
To: CCL
Subject: CCL:G: visualization of MO,s from GAMESS(US) job
Message-Id: <-47305-120802121006-28833-uJ8whunyHaJgTKLcq1f0qg a server.ccl.net>
X-Original-From: Andrew Yeung <andrew.yeung**chem.tamu.edu>
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Date: Thu, 02 Aug 2012 11:09:53 -0500
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Sent to CCL by: Andrew Yeung [andrew.yeung(!)chem.tamu.edu]
With Gaussian, my favorite so far has been Avogadro. This program 
accepts Gamess too, I believe.

Avogadro crashes every now and then, but when it works, it's wonderful. 
If the basis set is printed, it can generate MOs from log files instead 
of fchk files.

It creates nice pictures when you export it to POV-Ray, and it cleans up 
the POV-Ray files if you ask it to. It is also able to generate vector 
graphics in the form of pdf, svg, & eps.

Andrew Yeung
Donald J. Darensbourg Research Group
Department of Chemistry, Texas A&M University
3255 TAMU
College Station, TX 77843-3255

Tel: 979 845 4837

On 2012-08-02 4:11 AM, AMBAR BANERJEE ambarpchem^gmail.com wrote:
> Sent to CCL by: "AMBAR  BANERJEE" [ambarpchem.]-[.gmail.com]
> i was using GAMESS-(US) to do some rhf calculations. i need to visualize the MO's using some freely available graphical interface. please help me. is it possible to generate gaussian cube files from gamess dat files?>
>


From owner-chemistry@ccl.net Thu Aug  2 15:36:00 2012
From: "David Gallagher gallagher.da#gmail.com" <owner-chemistry*_*server.ccl.net>
To: CCL
Subject: CCL: ACS Workshop, Next Generation Molecular Modeling & QSAR
Message-Id: <-47306-120802132213-30230-i8jMrYjTsk0+0klqhf6rpA*_*server.ccl.net>
X-Original-From: David Gallagher <gallagher.da(0)gmail.com>
Content-Type: multipart/alternative;
 boundary="------------070303030005070502040904"
Date: Thu, 02 Aug 2012 10:22:09 -0700
MIME-Version: 1.0


Sent to CCL by: David Gallagher [gallagher.da!^!gmail.com]
This is a multi-part message in MIME format.
--------------070303030005070502040904
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*ACS Workshop:**  Next Generation Molecular Modeling & QSAR**
Presenters: *Prof. Tim Clark & Prof & Prof. Jürgen Brickmann*
Venue: *Room 104A, Pennsylvania Convention Center*
*                               (ACS meeting, Philadelphia, PA, USA)*
Time: *6pm - 8pm, Tuesday 21st August 2012*

Background and introduction:
*Professor Tim Clark will start by providing an introduction to two 
next-generation molecular modeling tools. "SAR-caddle" is a web-based 
tool for building & applying robust QSAR/QSPR models with applicability 
domain analysis & 3D visualization, and "caddle" is a web-based 
molecular modeling system with advanced flexible workflows and 
protocols, and interactive 3D-visualization.  These new tools require 
only a suitable browser on a desktop computer, laptop, tablet or smart 
phone (no local installation).*

Hand-on training session:
*This will be followed by a hands-on training session with SAR-caddle & 
caddle, so please bring your own  laptop or tablet.  No software 
installation is necessary as the tools are all web-based.

*Registration:*  The workshop is free but seats are limited so please 
preregister by Email toWorkshop_+_CACheResearch.com 
<mailto:workshop_+_cacheresearch.com?subject=ACS%20Workshop%20Registration,%20Next%20Generation%20Molecular%20Modeling%20and%20QSAR&body=Please%20include%20name,%20affiliation%20and%20location:>, 
and include name, affiliation, and location.

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<html>
  <head>

    <meta http-equiv="content-type" content="text/html; charset=ISO-8859-1">
  </head>
  <body bgcolor="#FFFFFF" text="#000000">
    <font style="color: rgb(0, 0, 0); font-style: normal; font-variant:
      normal; font-weight: normal; letter-spacing: normal; line-height:
      normal; orphans: 2; text-align: -webkit-left; text-indent: 0px;
      text-transform: none; white-space: normal; widows: 2;
      word-spacing: 0px; -webkit-text-size-adjust: auto;
      -webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
      255); font-size: 13px; " color="#000000" face="Arial"><b>ACS
        Workshop:</b></font><font style="font-style: normal;
      font-variant: normal; font-weight: normal; letter-spacing: normal;
      line-height: normal; orphans: 2; text-align: -webkit-left;
      text-indent: 0px; text-transform: none; white-space: normal;
      widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto;
      -webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
      255); font-size: 13px; " color="#0000A0" face="Arial"><b>&nbsp; Next
        Generation Molecular Modeling &amp; QSAR</b></font><font
      style="color: rgb(0, 0, 0); font-style: normal; font-variant:
      normal; font-weight: normal; letter-spacing: normal; line-height:
      normal; orphans: 2; text-align: -webkit-left; text-indent: 0px;
      text-transform: none; white-space: normal; widows: 2;
      word-spacing: 0px; -webkit-text-size-adjust: auto;
      -webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
      255); font-size: 13px; " color="#000000" face="Arial"><b><br>
        Presenters:&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;<span class="Apple-converted-space">&nbsp;</span></b>Prof.
      Tim Clark &amp; Prof &amp; Prof. J&uuml;rgen Brickmann<b><br>
        Venue:&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;<span class="Apple-converted-space">&nbsp;</span></b>Room
      104A, Pennsylvania Convention Center<b><br>
      </b>&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; (ACS meeting, Philadelphia, PA,
      USA)<b><br>
        Time:&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;<span class="Apple-converted-space">&nbsp;</span></b>6pm
      - 8pm, Tuesday 21st August 2012<b><br>
        <br>
        Background and introduction:&nbsp;<span class="Apple-converted-space">&nbsp;</span><br>
      </b>Professor Tim Clark will start by providing an introduction to
      two next-generation molecular modeling tools. "SAR-caddle" is a
      web-based tool for building &amp; applying robust QSAR/QSPR models
      with applicability domain analysis &amp; 3D visualization, and
      "caddle" is a web-based molecular modeling system with advanced
      flexible workflows and protocols, and interactive
      3D-visualization.&nbsp; These new tools require only a suitable browser
      on a desktop computer, laptop, tablet or smart phone (no local
      installation).<b><br>
        <br>
        Hand-on training session:&nbsp;<span class="Apple-converted-space">&nbsp;</span><br>
      </b>This will be followed by a hands-on training session with
      SAR-caddle &amp; caddle, so please bring your own&nbsp; laptop or
      tablet.&nbsp; No software installation is necessary as the tools are
      all web-based.<br>
      <br>
      <b>Registration:</b>&nbsp; The workshop is free but seats are limited
      so please preregister by Email to<span
        class="Apple-converted-space">&nbsp;</span><a
href="mailto:workshop_+_cacheresearch.com?subject=ACS%20Workshop%20Registration,%20Next%20Generation%20Molecular%20Modeling%20and%20QSAR&amp;body=Please%20include%20name,%20affiliation%20and%20location:">Workshop_+_CACheResearch.com</a>,
      and include name, affiliation, and location.</font>
  </body>
</html>

--------------070303030005070502040904--


From owner-chemistry@ccl.net Thu Aug  2 21:46:01 2012
From: "Jonas Baltrusaitis jasius_1[-]yahoo.com" <owner-chemistry ~ server.ccl.net>
To: CCL
Subject: CCL: solid state TDDFT
Message-Id: <-47307-120802214453-705-ULOBJtRtTCXmwBGFO6yQRQ ~ server.ccl.net>
X-Original-From: "Jonas  Baltrusaitis" <jasius_1++yahoo.com>
Date: Thu, 2 Aug 2012 21:44:46 -0400


Sent to CCL by: "Jonas  Baltrusaitis" [jasius_1===yahoo.com]
Dear all,

anybody know of software packages that would be able to perform solid state TDDFT in any form, e.g. I am interested in surface slab+adsorbed molecule TDDFT optimization. Probably, there is much more to this question since that involves performing any element (metal, for example) TDDFT which is probably superhard to do but I figure I would give it a chance and ask

thanks

Jonas Baltrusaitis
university of Iowa