From owner-chemistry@ccl.net Mon Mar 28 04:49:01 2011
From: "Gerd Neudert gneudert^web.de" <owner-chemistry-x-server.ccl.net>
To: CCL
Subject: CCL: RMSD Calculation
Message-Id: <-44229-110328044633-14680-ABF2GAhZuZHbPu87plEQGA-x-server.ccl.net>
X-Original-From: "Gerd  Neudert" <gneudert(_)web.de>
Date: Mon, 28 Mar 2011 04:46:31 -0400


Sent to CCL by: "Gerd  Neudert" [gneudert a web.de]
You can use fconv:
http://pc1664.pharmazie.uni-marburg.de/drugscore/download.php
For example 'fconv -rmsd docking.mol2 --s=cryst.mol2' could do the job (other options are available)

>Von: "Nancy nancy5villa]~[gmail.com" <owner-chemistry^ccl.net>
>Gesendet: 27.03.2011 03:26:23
>
>Hi All,
>I need to determine the RMSD of a small molecule cocrystallized ligand, >against a large number of predicted docked conformations. Please let me know >what is the best method for doing this.
>Thank you very much,
>Nancy


From owner-chemistry@ccl.net Mon Mar 28 12:22:00 2011
From: "Emilio Xavier Esposito emilio.esposito],[gmail.com" <owner-chemistry .. server.ccl.net>
To: CCL
Subject: CCL: COMP's Denver ACS meeting abstract deadline: April 4th, 2011
Message-Id: <-44230-110328115101-16234-FODmIU5Hak10QmcKSfHBig .. server.ccl.net>
X-Original-From: Emilio Xavier Esposito <emilio.esposito^_^gmail.com>
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Sent to CCL by: Emilio Xavier Esposito [emilio.esposito:gmail.com]
Hi
The COMP Programming Board would like to remind you that abstract
submissions for the COMP technical meeting at Denver ACS meeting close
on Monday, April 4th, 2011. Information about the following COMP
programming topics are below:

- COMP Symposia at the Denver ACS meeting
- Graduate Student and Post Doc Image Contest
- Organize a symposium within COMP in 2012

Thank you for your time
Emilio Xavier Esposito
Michael Feig
Melissa Landon
Jeffry D Madura
Eric V Patterson
Yufeng Jane Tseng
Scott A Wildman
The COMP Programming Board


*COMP Symposia at the Denver ACS meeting*
The COMP Programming Board has expanded the contributed presentation
portion of the technical program for the Denver ACS meeting to include
the following:

_Standing Symposia_
- Bioinformatics
- Computational Analysis of Spectroscopic Analysis
- Drug Discovery (ADMETox, Ligand-based design, Methodology, and
Target-based design)
- Material Science
- Membranes
- Molecular Mechanics (Applications, Force Field Development,
Methodology, and Proteins)
- Quantum Chemistry (Applications, DFT, and Methodology)
- Water

_Awards_
- Chemical Computing Group Excellence Award
- Hewlett-Packard Outstanding Junior Faculty Award

_Special Topics_
- Challenges in Industrial Computational Methods (Cynthia Bancale & Jeff Grandy)
- Cheminformatics Aspects of High Throughput Screening: From Robots to
Models (Y Jane Tseng)
- Computational Modeling of Photo-catalysis and Photo-induced Charge
Transfer Dynamics on Surfaces (Dimitri Kilin & Ivan Mikhaylov)
- Emerging Technologies in Computational Chemistry (Curt Breneman)
- Mining Protein-Ligand Interaction Space (Veerabahu Shanmugasundaram
& Mehran Jalaie)
- Predicting and Disrupting Protein Interactions (Dmytro Kozakov,
Sandor Vajda, & Ilya Vakser)
- The Computational Chemistry Component of Battery Research (Bill Swope)

The COMP technical program for Denver with descriptions can be found
here: http://abstracts.acs.org/chem/242nm/meetingview.php?page=session&par_id=268



*Graduate Student and Post Doc Image Contest*
One of the most powerful aspects of computational chemistry,
biochemistry, and structural biology is the ability to create stunning
images of our work. Our images are able to explain complex ideas and
allow non-computational scientists the ability to understand our
research. To highlight this aspect of the computational science, the
COMP Division of ACS is pleased to announce the Graduate Student and
Post Doc Image Competition.

_Criteria and Prize_
The COMP Programming Board will select the winning image and award the
creator complimentary registration to that ACS National Meeting; a
$180 value for Graduate Students and a $355 value for Post Docs. The
image must be created and submitted by a Graduate Student or Post Doc
that is a member of the ACS and the COMP Division. Additionally, the
image must be original work and cannot have been used in a previous
publication (e.g., article image, Table of Contents image, or journal
cover image).

Images are due by 5pm Eastern Time on Tuesday, May 3rd, 2011. Please
email your image to Emilio Xavier Esposito ( emilio.esposito||gmail.com
). The image must be 3 inches wide by 4.5 inches tall, at least 300
dpi, and a PNG, EPS, JPEG, or PDF. Only one image per submitter. The
creator of the winning image will be notified by email no later than
Tuesday, May 25th, 2011.


* Organize a symposium within COMP in 2012*
The COMP Programming Board is always looking for individuals that want
to organize symposia and provides the framework and tools necessary to
organize a great symposium. If you are interested in organizing a
symposium for the 2012 national ACS meetings in San Diego (spring
2012) or Philadelphia (fall 2012) – or the 2013 national ACS meetings
– please contact Emilio Xavier Esposito ( emilio.esposito||gmail.com ).
This is an excellent opportunity for its members to organize symposia
that are of interest to the scientific community. We are excited to
receive your ideas for symposia.


From owner-chemistry@ccl.net Mon Mar 28 12:57:00 2011
From: "pascal boulet pascal.boulet::univ-provence.fr" <owner-chemistry::server.ccl.net>
To: CCL
Subject: CCL:G: PES scan without optimisation (Gaussian 09)
Message-Id: <-44231-110328120336-6853-YtojAK7F0qQud68CROfmnw::server.ccl.net>
X-Original-From: pascal boulet <pascal.boulet ~~ univ-provence.fr>
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Sent to CCL by: pascal boulet [pascal.boulet(-)univ-provence.fr]
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    Dear all,<br>
    <br>
    I am trying to do a PES scan with Gaussian 09, without optimizing
    the structure. I am starting with a simple test case (propanol) but
    it does not work.<br>
    <br>
    At some point of the output Gaussian says: <br>
    <font color="#3333ff">Scan the potential surface.<br>
      &nbsp;Variable&nbsp;&nbsp; Value&nbsp;&nbsp;&nbsp;&nbsp; No. Steps Step-Size<br>
      &nbsp;-------- ----------- --------- ---------<br>
      &nbsp;A total of&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1 points will be computed.</font><br>
    <br>
    Here is my input file, which, I thought, should compute 36 energies:<br>
    <br>
    <font color="#3333ff">%chk=propanol_scan.chk<br>
      #p hf/sto-3g scan<br>
      <br>
      propanol_01<br>
      <br>
      0 1<br>
      &nbsp;C&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>
      &nbsp;H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; B1<br>
      &nbsp;H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; B2&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; A1<br>
      &nbsp;H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; B3&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; A2&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
      D1&nbsp;&nbsp;&nbsp; 0<br>
      &nbsp;C&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; B4&nbsp;&nbsp;&nbsp; 4&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; A3&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
      D2&nbsp;&nbsp;&nbsp; 0<br>
      &nbsp;H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; B5&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; A4&nbsp;&nbsp;&nbsp; 4&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
      D3&nbsp;&nbsp;&nbsp; 0<br>
      &nbsp;H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; B6&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; A5&nbsp;&nbsp;&nbsp; 4&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
      D4&nbsp;&nbsp;&nbsp; 0<br>
      &nbsp;C&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; B7&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; A6&nbsp;&nbsp;&nbsp; 4&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
      D5&nbsp;&nbsp;&nbsp; 0<br>
      &nbsp;H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; B8&nbsp;&nbsp;&nbsp; 5&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; A7&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
      D6&nbsp;&nbsp;&nbsp; 0<br>
      &nbsp;H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; B9&nbsp;&nbsp;&nbsp; 5&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; A8&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
      D7&nbsp;&nbsp;&nbsp; 0<br>
      &nbsp;O&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; B10&nbsp;&nbsp;&nbsp; 5&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; A9&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
      D8&nbsp;&nbsp;&nbsp; 0<br>
      &nbsp;H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 11&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; B11&nbsp;&nbsp;&nbsp; 8&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; A10&nbsp;&nbsp;&nbsp; 5&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
      D9&nbsp;&nbsp;&nbsp; 0<br>
      <br>
      &nbsp;&nbsp; B1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1.09379995<br>
      &nbsp;&nbsp; B2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1.09380033<br>
      &nbsp;&nbsp; B3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1.09365548<br>
      &nbsp;&nbsp; B4&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1.55449843<br>
      &nbsp;&nbsp; B5&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1.09801752<br>
      &nbsp;&nbsp; B6&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1.09801742<br>
      &nbsp;&nbsp; B7&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1.53715727<br>
      &nbsp;&nbsp; B8&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1.09860057<br>
      &nbsp;&nbsp; B9&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1.09860097<br>
      &nbsp;&nbsp; B10&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1.43062911<br>
      &nbsp;&nbsp; B11&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.98873516<br>
      &nbsp;&nbsp; A1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 108.56516452<br>
      &nbsp;&nbsp; A2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 108.03000700<br>
      &nbsp;&nbsp; A3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 110.18781967<br>
      &nbsp;&nbsp; A4&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 110.90073191<br>
      &nbsp;&nbsp; A5&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 110.90068161<br>
      &nbsp;&nbsp; A6&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 112.00470629<br>
      &nbsp;&nbsp; A7&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 110.28798067<br>
      &nbsp;&nbsp; A8&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 110.28800781<br>
      &nbsp;&nbsp; A9&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 104.46660354<br>
      &nbsp;&nbsp; A10&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 109.60416683<br>
      &nbsp;&nbsp; D1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 116.91630157<br>
      &nbsp;&nbsp; D2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 121.36885060<br>
      &nbsp;&nbsp; D3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -59.09579569<br>
      &nbsp;&nbsp; D4&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 59.09571542<br>
      &nbsp;&nbsp; D5&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 180.00000000<br>
      &nbsp;&nbsp; D6&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 60.19216054<br>
      &nbsp;&nbsp; D7&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -60.19187035<br>
      &nbsp;&nbsp; D8&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -180.00000000<br>
      &nbsp;&nbsp; D9&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -180.00000000<br>
      <br>
      7 5 8 11 -57.5 S 20 0.5</font>&nbsp; <br>
    <br>
    <br>
    This input seems to look the same as what I found in examples of
    gaussian, but obviously there is something wrong. Could you please
    give me a hint?<br>
    <br>
    Thank you for your help,<br>
    Best regards<br>
    Pascal<br>
    <br>
    <br>
    <pre class="moz-signature" cols="72">-- 

!!!!WARNING: my phone number has CHANGED!!!!

Dr. pascal Boulet, computational chemist
University of Aix-Marseille I 
Laboratoire Chimie Provence, UMR 6264
Group of Theoretical Chemistry
Avenue Normandie-Niemen
13397 Marseille Cedex 20
France
**********
Tel. (+33) (0)413.55.18.10
Fax. (+33) (0)491.55.18.50
**********
<a class="moz-txt-link-freetext" href="http://www.lc-provence.fr">http://www.lc-provence.fr</a>
<a class="moz-txt-link-freetext" href="https://sites.google.com/a/univ-provence.fr/pb-comput-chem">https://sites.google.com/a/univ-provence.fr/pb-comput-chem</a>
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From owner-chemistry@ccl.net Mon Mar 28 14:55:01 2011
From: "Tobias Kraemer tobias.kraemer!=!chem.ox.ac.uk" <owner-chemistry.:.server.ccl.net>
To: CCL
Subject: CCL:G: PES scan without optimisation (Gaussian 09)
Message-Id: <-44232-110328140355-14764-g8iCIXxTg7Rsgm+9z/6hTg.:.server.ccl.net>
X-Original-From: Tobias Kraemer <tobias.kraemer[#]chem.ox.ac.uk>
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Sent to CCL by: Tobias Kraemer [tobias.kraemer^-^chem.ox.ac.uk]
Dear Pascal.....


The stepsize and number of steps should be in the same line as the 
variable, following the variable definition.
So, for example, from the Gaussian manual, R1 1.41 3 0.05 means, that R1 
should be scanned in three steps by 0.05.
It works for me....

I believe in your case the last line is ignored and Gaussian simply 
calculates the energy of the input structure.


Hope this helps


Tobi


From owner-chemistry@ccl.net Mon Mar 28 15:30:01 2011
From: "Nuno A. G. Bandeira nuno.bandeira~!~ist.utl.pt" <owner-chemistry_._server.ccl.net>
To: CCL
Subject: CCL: PES scan without optimisation (Gaussian 09)
Message-Id: <-44233-110328144424-21921-swZKIusWQsiwSs6K+Ci8+A_._server.ccl.net>
X-Original-From: "Nuno A. G. Bandeira" <nuno.bandeira||ist.utl.pt>
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Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira{:}ist.utl.pt]
This is a multi-part message in MIME format.
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Dear Pascal,

You have to define your dihedral in the variable section. Here's what it 
says in the G09 manual under the scan keyword:

/This calculation type keyword requests that a potential energy surface 
(PES) scan be done. A rigid PES scan is performed,which consists of 
single point energy evaluations over a rectangular grid involving 
selected internal coordinates. Themolecular structure must be defined 
using Z-matrix coordinates. The number of steps and step size for each 
variable arespecified on the variable definition lines, following the 
variable's initial value. For example:

R1 1.41 3 0.05A1 104.5 2 1.0A2 120.0

This input causes variable R1 to be stepped 3 times by 0.05. Thus, four 
R1 values (1.41, 1.46, 1.51 and 1.56) will be done foreach combination 
of other variables. Similarly, 3 values for A1 (104.5, 105.5 and 106.5) 
will be used, and A2 will be heldfixed at 120.0. All in all, a total of 
12 energy evaluations will be performed. Any number of variables can be 
stepped. Theunits of the step-sizes are controlled by the Units keyword 
and default to Angstroms and degrees./

Therefore in your input you should tamper with the variable D8.

-- 
Nuno A. G. Bandeira, AMRSC
Departamento de Química Física i Inorgánica
Despatx 207, N4 - Universitat Rovira i Virgili
Campus Sescelades, Carrer Marcel.lí Domingo
43007 Tarragona - SPAIN
--



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    Dear Pascal,<br>
    <br>
    You have to define your dihedral in the variable section. Here's
    what it says in the G09 manual under the scan keyword:<br>
    <br>
    <i>This calculation type keyword requests that a potential energy
      surface (PES) scan be done. A rigid PES scan is performed,which
      consists of single point energy evaluations over a rectangular
      grid involving selected internal coordinates. Themolecular
      structure must be defined using Z-matrix coordinates. The number
      of steps and step size for each variable arespecified on the
      variable definition lines, following the variable&#8217;s initial value.
      For example:<br>
      <br>
      R1 1.41 3 0.05A1 104.5 2 1.0A2 120.0<br>
      <br>
      This input causes variable R1 to be stepped 3 times by 0.05. Thus,
      four R1 values (1.41, 1.46, 1.51 and 1.56) will be done foreach
      combination of other variables. Similarly, 3 values for A1 (104.5,
      105.5 and 106.5) will be used, and A2 will be heldfixed at 120.0.
      All in all, a total of 12 energy evaluations will be performed.
      Any number of variables can be stepped. Theunits of the step-sizes
      are controlled by the Units keyword and default to Angstroms and
      degrees.</i><br>
    <br>
    Therefore in your input you should tamper with the variable D8.<br>
    <br>
    <pre class="moz-signature" cols="72">-- 
Nuno A. G. Bandeira, AMRSC  
Departamento de Qu&iacute;mica F&iacute;sica i Inorg&aacute;nica
Despatx 207, N4 - Universitat Rovira i Virgili
Campus Sescelades, Carrer Marcel.l&iacute; Domingo
43007 Tarragona - SPAIN
--

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From owner-chemistry@ccl.net Mon Mar 28 16:05:01 2011
From: "Eduardo edulsa()ufpr.br" <owner-chemistry##server.ccl.net>
To: CCL
Subject: CCL:G: About optical properties in gaussian
Message-Id: <-44234-110328145153-22584-cjurB8JNzss1Ykx9cqOyPg##server.ccl.net>
X-Original-From: Eduardo <edulsa*_*ufpr.br>
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Date: Mon, 28 Mar 2011 15:50:42 -0300
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Sent to CCL by: Eduardo [edulsa{=}ufpr.br]
Dear CCLers

I am performing some calculations (g03) aiming the optical rotation 
properties. My first test was a s-valinol molecule (CAS 2026-48-4). 
After a geometry optimization step (opt=tight), I got a value for 
Alpha-D equals to -158.98 deg. The experimental value is + 16.9 deg. I 
am get confuse because, unless I was strongly wrong, they are not the 
same despite -160 and +20 be complementary angles. So please, could 
anyone help me to explain and understand what is happening?

My best wishes

Eduardo

-- 
Eduardo Lemos de Sa
Associated Professor at Chemistry Department
Universidade Federal do Parana
Dep. Quimica, P. Box 19081, 81531-990 Curitiba PR / Brazil
phone: +55(41)33613300
fax  : +55(41)33613186


From owner-chemistry@ccl.net Mon Mar 28 16:40:01 2011
From: "Eduardo edulsa^_^ufpr.br" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL:G: About optical rotation calculation
Message-Id: <-44235-110328141914-19742-r3AiRm4MFdn8CpDTvPF7/Q-#-server.ccl.net>
X-Original-From: Eduardo <edulsa : ufpr.br>
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Date: Mon, 28 Mar 2011 15:18:20 -0300
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Sent to CCL by: Eduardo [edulsa|a|ufpr.br]
Dear CCLers

I am performing some calculations (g03) aiming the optical rotation 
properties. My first test was a s-valinol molecule (CAS 2026-48-4). 
After a geometry optimization step (opt=tight), I got a value for 
Alpha-D equals to -158.98 deg. The experimental value is + 16.9 deg. I 
am get confuse because, unless I was strongly wrong, they are not the 
same despite -160 and +20 be complementary angles. So please, could 
anyone help me to explain and understand what is happening?

My best wishes

Eduardo

-- 
Eduardo Lemos de Sa
Associated Professor at Chemistry Department
Universidade Federal do Parana
Dep. Quimica, P. Box 19081, 81531-990 Curitiba PR / Brazil
phone: +55(41)33613300
fax  : +55(41)33613186


From owner-chemistry@ccl.net Mon Mar 28 17:27:00 2011
From: "Prof. Curt M. Breneman brenec%rpi.edu" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL: Emerging Technologies in Computational Chemistry Competition Symposium - Sponsored by Schrodinger, Inc.
Message-Id: <-44236-110328154449-17842-ev2HMXo8REvZ2fFoe0GeTw+*+server.ccl.net>
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Call for Papers: 2010 Symposium on Emerging Technologies in Computational
Chemistry

American Chemical Society National Meeting, Denver, CO

Aug. 28- Sept 1, 2011

 

>>>> Note: The Deadline for COMP Abstracts for the Denver meeting is April
4th, 2011 <<<<

 

$1,000 prize to be awarded at the ACS national meeting, Denver, Colorado.

 

In cooperation with Schrodinger, Inc, the Computers in Chemistry Division
(COMP) of the ACS 

will hold the annual Symposium on Emerging Technologies in Computational
Chemistry at the

American Chemical Society National Meeting, Denver, Colorado, Aug. 21st -
Sept 1st 

2011. The objective of the symposium is to stimulate, reward, and publicize

methodological advances in computational chemistry.

 

The talks will be evaluated at the meeting by a panel of experts on the

quality of the presentation, and the impact that the research will have on

the future of computational chemistry and allied sciences. The symposium is

ideal for presenting your latest and best research on new techniques,

applications and software development.

 

Schrodinger, Inc., sponsors a $1,000 prize for the best talk at the

symposium.

 

All are invited to participate. To take part, it is necessary to submit a

regular short ACS abstract the PACS system. It is also necessary

to also email a longer (~1000-word) abstract to the organizer. The talks

must be original and not be repeats of talks at other ACS symposia. The long

abstracts will be evaluated, and those individuals selected for an oral

presentation at the symposium will be notified. Applications for the

Emerging Technologies Symposium that cannot be accepted will be rescheduled

in one of the other COMP sessions at the meeting.

 

Long abstracts must be sent by e-mail to:

 

Prof. Curt M. Breneman

Past Chair, ACS Division of Computers in Chemistry

Acting Head, RPI Department of Chemistry and Chemical Biology

brenec_at_rpi_dot_edu

 

 


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vlink=3Dpurple><div class=3DWordSection1><p class=3DMsoNormal><b>Call =
for Papers: 2010 Symposium on Emerging Technologies in Computational =
Chemistry<o:p></o:p></b></p><p class=3DMsoNormal>American Chemical =
Society National Meeting, Denver, CO<o:p></o:p></p><p =
class=3DMsoNormal>Aug. 28- Sept 1, 2011<o:p></o:p></p><p =
class=3DMsoNormal><o:p>&nbsp;</o:p></p><p =
class=3DMsoNormal><b>&gt;&gt;&gt;&gt; Note: The Deadline for COMP =
Abstracts for the Denver meeting is April 4<sup>th</sup>, 2011 =
&lt;&lt;&lt;&lt;<o:p></o:p></b></p><p =
class=3DMsoNormal><o:p>&nbsp;</o:p></p><p class=3DMsoNormal><b><i>$1,000 =
prize to be awarded at the ACS national meeting, Denver, =
Colorado.<o:p></o:p></i></b></p><p =
class=3DMsoNormal><o:p>&nbsp;</o:p></p><p class=3DMsoNormal>In =
cooperation with Schrodinger, Inc, the Computers in Chemistry Division =
(COMP) of the ACS <o:p></o:p></p><p class=3DMsoNormal>will hold the =
annual Symposium on Emerging Technologies in Computational Chemistry at =
the<o:p></o:p></p><p class=3DMsoNormal>American Chemical Society =
National Meeting, Denver, Colorado, Aug. 21<sup>st</sup> - Sept =
1<sup>st</sup> <o:p></o:p></p><p class=3DMsoNormal>2011. The objective =
of the symposium is to stimulate, reward, and publicize<o:p></o:p></p><p =
class=3DMsoNormal>methodological advances in computational =
chemistry.<o:p></o:p></p><p class=3DMsoNormal><o:p>&nbsp;</o:p></p><p =
class=3DMsoNormal>The talks will be evaluated at the meeting by a panel =
of experts on the<o:p></o:p></p><p class=3DMsoNormal>quality of the =
presentation, and the impact that the research will have =
on<o:p></o:p></p><p class=3DMsoNormal>the future of computational =
chemistry and allied sciences. The symposium is<o:p></o:p></p><p =
class=3DMsoNormal>ideal for presenting your latest and best research on =
new techniques,<o:p></o:p></p><p class=3DMsoNormal>applications and =
software development.<o:p></o:p></p><p =
class=3DMsoNormal><o:p>&nbsp;</o:p></p><p class=3DMsoNormal>Schrodinger, =
Inc., sponsors a $1,000 prize for the best talk at the<o:p></o:p></p><p =
class=3DMsoNormal>symposium.<o:p></o:p></p><p =
class=3DMsoNormal><o:p>&nbsp;</o:p></p><p class=3DMsoNormal>All are =
invited to participate. To take part, it is necessary to submit =
a<o:p></o:p></p><p class=3DMsoNormal>regular short ACS abstract the PACS =
system. It is also necessary<o:p></o:p></p><p class=3DMsoNormal>to also =
email a longer (~1000-word) abstract to the organizer. The =
talks<o:p></o:p></p><p class=3DMsoNormal>must be original and not be =
repeats of talks at other ACS symposia. The long<o:p></o:p></p><p =
class=3DMsoNormal>abstracts will be evaluated, and those individuals =
selected for an oral<o:p></o:p></p><p class=3DMsoNormal>presentation at =
the symposium will be notified. Applications for the<o:p></o:p></p><p =
class=3DMsoNormal>Emerging Technologies Symposium that cannot be =
accepted will be rescheduled<o:p></o:p></p><p class=3DMsoNormal>in one =
of the other COMP sessions at the meeting.<o:p></o:p></p><p =
class=3DMsoNormal><o:p>&nbsp;</o:p></p><p class=3DMsoNormal>Long =
abstracts must be sent by e-mail to:<o:p></o:p></p><p =
class=3DMsoNormal><o:p>&nbsp;</o:p></p><p class=3DMsoNormal>Prof. Curt =
M. Breneman<o:p></o:p></p><p class=3DMsoNormal>Past Chair, ACS Division =
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Head, RPI Department of Chemistry and Chemical Biology<o:p></o:p></p><p =
class=3DMsoNormal>brenec_at_rpi_dot_edu<o:p></o:p></p><p =
class=3DMsoNormal><o:p>&nbsp;</o:p></p><p =
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