From chemistry-request@server.ccl.net Tue Jan 16 05:10:12 2001
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To: chemistry@ccl.net
From: Francois Dupradeau <fyd@u-picardie.fr>
Subject: Gamess: orientation of molecules

        Dear all,

        I try to optimize a small structure using GAMESS (using Cartesian
coordinates and C1 symetry). I realized that "sometimes" GAMESS inverts (X
axis is inverted, I think...) the structure before to optimized it. The
problem is that it looks like that it depends on the coordinates of the
starting structure (the starting structure is always the same structure,
only the coordinates change...) provided in the GAMESS input.

        Is it possible to PREDICT if the axis inversion will take place or
not before to optimize this structure ? 
        (if yes, HOW ?)

        I think it important to calculate the electrostatic potential...

Thanks,
Best regards,
Francois
 --
F.-Y. Dupradeau            
http://www.u-picardie.fr/UPIC/UPJV/recherche/labos/bpd/fyd.htm


From chemistry-request@server.ccl.net Tue Jan 16 07:05:01 2001
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From: "T.Tsuru" <telkuni@venus.dti.ne.jp>
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Subject: MOPAC users group and consortium
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Hi all !

Is there any users group and consortium of MOPAC ?

If you know its web sites, please teach me the URL.

Sincerely,
Telkuni

---------------------------------------------------
         Telkuni Tsuru     telkuni@venus.dti.ne.jp

  Representative of Research Information Service
  of Molecular/with Knowledge Management
     Bunshi Gijyutu
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From chemistry-request@server.ccl.net Tue Jan 16 06:59:38 2001
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From: Knut Teigen <knut.teigen@pki.uib.no>
Subject: electrostatic potential surface
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Dear Computational Chemists,

I have a question regarding electrostatic potential surfaces that I hope 
you will be able to help me with:

I have a 30 atom structure of a organic compound.
I would like to calculate the difference in in the electrostatic surface 
potential of this structure and the reduced form of the same coumpound. 
Then I would like to visualize the difference in electrostatic surface 
potential between these two compounds as a colored surface on one of them.

Is there any software available out there that can do this for me?

Kind regards
Knut Teigen
_____________________________________________________

Knut Teigen                                telephone: +4755586328
Dept. of Biochemistry                  fax: +4755586400
Faculty of Medicine                     mobile: +4792428369
University of Bergen                    eMail: knut.teigen@pki.uib.no
Norway
_____________________________________________________



From chemistry-request@server.ccl.net Tue Jan 16 09:02:31 2001
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From: "Phung Quan" <quanph@hcmuns.edu.vn>
To: <chemistry@ccl.net>
Subject: Solvent in G98W
Date: Tue, 16 Jan 2001 21:03:27 +0700

Dear CCLers,
We are using G98W.
We'd like to calculate free energy (delta G) of an organic compound in
many kinds of solvents. However we could only do this in some solvents
which are available in Gaussian 98. In case we want to operate in other
solvent such as cyclopentanon, what should we do?
We really need your help!
Best regards

Phung Quan



From chemistry-request@server.ccl.net Tue Jan 16 10:21:46 2001
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Subject: Re: CCL:electrostatic potential surface
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Knut,

as I mentioned recently in the CCL, it is physically more reasonable to consider the COSMO surface charge density sigma as a
local measure of polarity on the surface than ESP. For examples see our homepage www.cosmologic.de. Our software COSMOtherm can
very well visualize sigma on the surface, and with a small change it will visualize the difference in sigma. 

Andreas


--------------------------------------------------------------------------------
Dr. Andreas Klamt
COSMOlogic GmbH&CoKG
Burscheider Str. 515
51381 Leverkusen, Germany

Tel.: 49-2171-73168-1  Fax: ...-9
e-mail: andreas.klamt@cosmologic.de
web:    www.cosmologic.de
--------------------------------------------------------------------------------
COSMOlogic
        Your Competent Partner for
        Computational Chemistry and Fluid Thermodynamics
--------------------------------------------------------------------------------

From chemistry-request@server.ccl.net Tue Jan 16 10:26:13 2001
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Phung,

this can be done with COSMOtherm. See our homepage www.cosmologic.de and reference therein. We can treat any solvent, even
mixtures at variable temperature. Presently this can be done only based on DMol3/COSMO or Turbomole/COSMO calculations, but
(hopefully) very soon, End of January?) the next Gaussian subrelease will work together with our COSMOtherm software as well. 

Andreas

 
--------------------------------------------------------------------------------
Dr. Andreas Klamt
COSMOlogic GmbH&CoKG
Burscheider Str. 515
51381 Leverkusen, Germany

Tel.: 49-2171-73168-1  Fax: ...-9
e-mail: andreas.klamt@cosmologic.de
web:    www.cosmologic.de
--------------------------------------------------------------------------------
COSMOlogic
        Your Competent Partner for
        Computational Chemistry and Fluid Thermodynamics
--------------------------------------------------------------------------------


From chemistry-request@server.ccl.net Tue Jan 16 10:42:54 2001
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Date: Tue, 16 Jan 2001 10:42:05 -0500
From: "Shobe, Dave" <dshobe@sud-chemieinc.com>
Subject: RE: electrostatic potential surface
To: "'Knut Teigen'" <knut.teigen@pki.uib.no>, chemistry@ccl.net
Message-id: 
 <157A51F55AAAD3119CD70008C7B1629DDAABE1@lvlxch01.unitedcatalysts.com>
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I'd be interested in the anwers to this but I also have a question.
Reducing the molecule, either by adding an electron or by adding hydrogen,
will cause the surface of the molecule (as defined by an
iso-electron-density surface) to move.  How does one normally handle that?

--David Shobe

-----Original Message-----
From: Knut Teigen [mailto:knut.teigen@pki.uib.no]
Sent: Tuesday, January 16, 2001 7:00 AM
To: chemistry@ccl.net
Subject: CCL:electrostatic potential surface


Dear Computational Chemists,

I have a question regarding electrostatic potential surfaces that I hope 
you will be able to help me with:

I have a 30 atom structure of a organic compound.
I would like to calculate the difference in in the electrostatic surface 
potential of this structure and the reduced form of the same coumpound. 
Then I would like to visualize the difference in electrostatic surface 
potential between these two compounds as a colored surface on one of them.

Is there any software available out there that can do this for me?

Kind regards
Knut Teigen
_____________________________________________________

Knut Teigen                                telephone: +4755586328
Dept. of Biochemistry                  fax: +4755586400
Faculty of Medicine                     mobile: +4792428369
University of Bergen                    eMail: knut.teigen@pki.uib.no
Norway
_____________________________________________________



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From chemistry-request@server.ccl.net Tue Jan 16 16:03:58 2001
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Schrodinger, Inc. announces that it is now shipping Jaguar 4.1, the latest 
version of the high-performance ab initio quantum chemistry package.  The new 
release of Jaguar introduces new features and includes improvements in 
performance over previous versions.  In addition, this version of Jaguar ships 
with Maestro 3.0, the latest release of Schrodinger's unified graphical user 
interface.  Among other new features, the combined Jaguar and Maestro package 
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* Allows molecular structure building and cleanup with a Universal Force Field,
* TIFF and JPEG image production,
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Jaguar and Maestro run on all common hardware platforms, including SGI, IBM, 
HP, Compaq, Sun and Linux.  For more information, please visit our website 
http://www.schrodinger.com.

From chemistry-request@server.ccl.net Tue Jan 16 12:45:46 2001
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Date: Tue, 16 Jan 2001 14:50:51 -0200
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    Dear Teigen/Shobe,
    I'm developing a fortran code to explore ESP surfaces, named AGOA
(http://www.dqf.ufpe.br/~zaldini/agoa.html).
    It reads a Gaussian CUBE file, identifying their maxima and minima
(for electrostatic potential values), and following, it writes a file
with the molecular geometry surrounded by these selected points, that
may be as much points as you need. This final file has a typical XYZ
format and can be read by several programs, like Rasmol, Chime, Re-view,
etc.
    In the case of you get interested, I can provide you the AGOA
executable for several plataforms (Windows, Linux, FreeBSD, Sun-Solaris,
IBM-Aix).
    Best Regards.


--
**************************************
Marcelo Zaldini Hernandes

PhD Student
Depart. de Quimica Fundamental
CCEN - UFPE - Recife - Pernambuco
Fone: 081 - 3271-8440 - ramal 45 ou 32
Fax: 081 - 3271-8442

http://www.dqf.ufpe.br/~zaldini
E-mail: zaldini@npd.ufpe.br
**************************************


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Dear Computational Chemists,

I have a question regarding electrostatic potential surfaces that I hope 
you will be able to help me with:

I have a 30 atom structure of a organic compound.
I would like to calculate the difference in in the electrostatic surface 
potential of this structure and the reduced form of the same coumpound. 
Then I would like to visualize the difference in electrostatic surface 
potential between these two compounds as a colored surface on one of them.

Is there any software available out there that can do this for me?

Kind regards
Knut Teigen
_____________________________________________________

Knut Teigen                                telephone: +4755586328
Dept. of Biochemistry                  fax: +4755586400
Faculty of Medicine                     mobile: +4792428369
University of Bergen                    eMail: knut.teigen@pki.uib.no
Norway
_____________________________________________________



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From chemistry-request@server.ccl.net Tue Jan 16 13:47:48 2001
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"Shobe, Dave" wrote:

> I'd be interested in the anwers to this but I also have a question.
> Reducing the molecule, either by adding an electron or by adding hydrogen,
> will cause the surface of the molecule (as defined by an
> iso-electron-density surface) to move.  How does one normally handle that?
>
> --David Shobe
>

For proteins, many people use a molecular surface and map the
potential (or difference potentials) to it using interpolation. You do need
to pick one surface or the other if there is a structural difference. You could
even calculate the potential on the surface in the first place, but this is
more difficult. Using empirical FF methods, I did this recently using OpenDX
to compare a couple similar proteins and successfully predict which
sidechains to mutate to functionally convert one to the other:
The experimental work is due to appear in J. Mol. Bio. shortly:

"Localization of the RAR Interaction Domain of Cellular Retinoic Acid Binding Protein-II"
Anuradha Budhu, Richard Gillilan and Noa Noy  (sorry, don't know the issue yet).

 A slightly earlier conference proceeding with more details on the computations and graphics is
still available online: http://w3.pppl.gov/vde2000/eproceedings.html
"What's Different in These Two Pictures? Structural Biology Using OpenDX", R. Gillilan


Another interesting approach would be to actually do isosurfaces of the
potential difference. This could be done quite easily with OpenDX and
probably a number of other progams (perhaps Grasp). I think the result
will be a bit more difficult to understand and visualize.


Richard Gillilan
MacCHESS
Cornell University



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Subject: Southeast Theoretical Chemistry Association Meeting at Auburn
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      Participate in the 2001 QM Odyssey 
(http://www.auburn.edu/~mckeeml/setca2001.html)
SETCA(Southeast Theoretical Chemistry Association)
             May 17-19, 2001
   Auburn University, Auburn, Alabama, USA


The 2001 SETCA will meet this year at Auburn University 
May 17-19, 2001.
The schedule will be:

Thursday(5/17)   evening reception, 
Friday(5/18)     full day; two oral sessions, poster session, banquet,
Saturday(5/19)   morning oral session, departure at lunchtime. 

This is an informal meeting where graduate students and 
postdocs are especially encouraged to attend.  For that 
reason, the registration fee is very low ($30/pp which 
includes the banquet).

Auburn is about 100 miles southwest Atlanta on I-85 with 
several economical hotels and motels within walking 
distance of campus.  Driving time from the airport is 
only 90 minutes with frequent shuttle service.

Best regards,

Michael L. McKee
Chairman of 2001 SETCA 

The following is a list of speakers who have accepted an 
invitation to make a presentation so far:

Dr. Wesley D. Allen, University of Georgia
Dr. Tom Cundari, University of Memphis 
Dr. Benjamin Gimarc, University of South Carolina 
Dr. Tracy Hamilton, University of Alabama at Birmingham
Dr. Jerzy Leszczynski, Jackson State University
Dr. Ming-Chang Lin, Emory University 
Dr. Peter Politzer, University of New Orleans
Dr. Paul v. R. Schleyer, University of Georgia 
Dr. Peter R. Schreiner, University of Georgia 
Dr. David Sherrill, Georgia Institute of Technology 
Dr. Thom Vreven, Gaussian, Inc.
Dr. Weitao Yang, Duke University

For more information contact:
--------------------------------------------------------- 
Dr. Michael L. McKee, Professor of Chemistry
Auburn Center for Molecular Modeling
Department of Chemistry
179 Chemistry Building
Auburn University
Auburn, Alabama 36849 U.S.A.
 
EMAIL: mckee@chem.auburn.edu
VOICE (334)844-6953) FAX (334)844-6959
http://www.auburn.edu/~mckeeml/setca2001.html
---------------------------------------------------------




