From chemistry-request@ccl.net Fri Apr 30 08:24:57 2004
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From: Ian Hovell <HOVELL<<at>>cetem.gov.br>
To: "'chemistry'" <chemistry<<at>>ccl.net>
Subject: CCL: imaginary frequencies
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Dear CCLers,
After carrying out a rather lengthy optimisation and frequency calculation
using G98w at the semiempirical level of AM1. I have found that I have a
single large negative frequency and six smaller near zero frequencies
indicating that I have a transition state. With out doing further
calculations what kind of error (percentage size) can I expect in the
calculated frequencies?
Ian Hovell 
e-mail hovell<<at>>cetem.gov.br <mailto:hovell<<at>>cetem.gov.br>  

From chemistry-request@ccl.net Fri Apr 30 11:37:10 2004
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Date: Fri, 30 Apr 2004 09:38:40 -0700 (PDT)
From: Vincent Xianlong Wang <xloongw..at..yahoo.com>
Subject: CCL: Segmentation fault with newzmat
To: chemistry..at..ccl.net
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Dear All,

We have Gaussian03 installed and running for about 3
months. The utility program 'newzmat' was running okay
at the beggining. But recently it doesn't work
anymore, only giving the error message, 'Segmentation
fault'. There was a power glitch before this if i'm
looking for an excuse, but other programs are running
okay. No helpful information was given after
contacting with the customer service from Gaussian
Inc.
Does anyone have the similar problem before? Or how 
should I try to solve this problem?
Thanks in advance for your suggestions.

Vincent

If it's helpful, the OS is Redhat Linux and the
hardware system is Dell Precision Workstation with
4-processors. And the following is the information
obtained from the gdb debugging program.   
 
gdb output message: 
 Starting program: /usr/local/g03/newzmat tmc000.chk
 [New Thread 1142446304 (LWP 17170)]

 Program received signal SIGSEGV, Segmentation fault.
 [Switching to Thread 1142446304 (LWP 17170)]
 0x0804b6c9 in mdcuto_ ()



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From chemistry-request@ccl.net Fri Apr 30 02:49:15 2004
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From: "Joerg K. Wegner" <wegnerj~at~informatik.uni-tuebingen.de>
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To: chemistry~at~ccl.net
Cc: Miguel Romero <mromcue~at~alumni.unav.es>
Subject: Re: CCL:FREE SOFTWARE
References: <40901E88.5060709~at~alumni.unav.es> <200404290948.29279.egonw~at~sci.kun.nl>
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Hi,

Overview:
http://zeus.polsl.gliwice.pl/~nikodem/linux4chemistry.html

Docking (academics):
Autodock (Linux only)
http://www.scripps.edu/pub/olson-web/doc/autodock/

Ghemical (includes Mopac) (+ OELib,OpenBabel, conformer generation !):
http://www.uku.fi/~thassine/ghemical/

QSAR:
JOELib
http://www-ra.informatik.uni-tuebingen.de/software/joelib/

Kind regards, Joerg

-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
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                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)



From chemistry-request@ccl.net Fri Apr 30 12:19:25 2004
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From: Vincent Xianlong Wang <xloongw~at~yahoo.com>
Subject: CCL: Segmentation fault with newzmat
To: CHEMISTRY~at~ccl.net
Cc: xloongw~at~yahoo.com
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Dear All,

We have Guassian03 package installed and running for
about three months. I have the problem with running
newzmat recently. It gives the error message of
'Segmentation fault'. It was running okay before.
There was a power glitch if i'm looking for an excuse.
But other programs are runing fine. 
Does anyone have met the similar problem before?
The system is 4-processor Dell Precision 650
workstation with Redhad Linux installed.
Debugging with gdb giving the information as follows,

 Starting program: /usr/local/g03/newzmat tmc000.chk
 [New Thread 1142446304 (LWP 17170)]

 Program received signal SIGSEGV, Segmentation fault.
 [Switching to Thread 1142446304 (LWP 17170)]
 0x0804b6c9 in mdcuto_ ()

Thanks for your suggestion.

Vincent


	
		
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From chemistry-request@ccl.net Fri Apr 30 10:13:27 2004
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From: "John McKelvey" <jmmckel{at}attglobal.net>
To: "Ian Hovell" <HOVELL{at}cetem.gov.br>, "'chemistry'" <chemistry{at}ccl.net>
References: <9E7055859B0BD811AE7B00105AD16BDF36B1AD{at}correio.cetem.gov.br>
Subject: Re: CCL:imaginary frequencies
Date: Fri, 30 Apr 2004 11:15:06 -0500
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Ian,

After finding out where the negative frequency came from, and redoing the
optimization, assuming that the most stable ground state is what you are
looking for, so that there are no negative frequencies then consider the
message i just received from Jimmy Stewart about the accuracy of vibrational
frequencies using the various MOPAC Hamiltonians,

"In general, they're all much the same.  Average errors are ~7%, except X-H
stretch, which is way too high.  With scaling, the error can be reduced to
~4%.
I published on this way back, but don't have reprints. See

1       Coolidge M. B., Marlin J. E., Stewart J. J. P., "Calculations of
Molecular Vibrational Frequencies Using Semiempirical Methods", J. Comp.
Chem. 12, 948-952 (1991). "



Regards,


John McKelvey



----- Original Message -----
From: "Ian Hovell" <HOVELL{at}cetem.gov.br>
To: "'chemistry'" <chemistry{at}ccl.net>
Sent: Friday, April 30, 2004 8:25 AM
Subject: CCL:imaginary frequencies


> Dear CCLers,
> After carrying out a rather lengthy optimisation and frequency calculation
> using G98w at the semiempirical level of AM1. I have found that I have a
> single large negative frequency and six smaller near zero frequencies
> indicating that I have a transition state. With out doing further
> calculations what kind of error (percentage size) can I expect in the
> calculated frequencies?
> Ian Hovell
> e-mail hovell{at}cetem.gov.br <mailto:hovell{at}cetem.gov.br>
>
> -= This is automatically added to each message by the mailing script =-
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>




From chemistry-request@ccl.net Thu Apr 29 14:42:41 2004
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From: "Warren DeLano" <warren_at_delanoscientific.com>
To: "'E.L. Willighagen'" <egonw_at_sci.kun.nl>,
   "'Miguel Romero'" <mromcue_at_alumni.unav.es>, <chemistry_at_ccl.net>
Cc: "'Miguel'" <miguel_at_jmol.org>
Subject: RE: FREE SOFTWARE
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	servernd.ccl.net

Well, I suppose I'd better "chime" in here too. 

PyMOL is another FREE option, and it has a complementary characteristics to
Jmol, which is good solid stuff too.  They're both worth a close look, as is
VMD.  As its name implies, PyMOL is heavily Python-oriented, in much the
same way as Jmol is Java oriented.

http://pymol.sf.net

Unlike Jmol, PyMOL isn't so much developed internationally, but there is
already a large international community (over 500 committed users, and
thousands of casuals users) who work together every day to help each other
make the most of the program.  

Though PyMOL is definitely a community-driven project, most PyMOL code
development is still performed under my direction via my small private
company.  However, PyMOL absolutely remains available as Python-license
open-source software, and our license is even less restrictive than Jmol's
LGPL.

The bottom line is that PyMOL can be used for FREE if you need a no cost
tool today.  We'd like you to pay for it, but the open-source license means
that we can't in any way compel you to do so.  

The key difference with PyMOL is that if at some point you are willing to
pay for it, then you will get additional value for your money: value such as
the formal accountability that large pharmaceutical companies often need.
Specifically, we'll work with your legal and IT departments to provide
compiled versions of PyMOL that satisfy their requirements as well as your
own.  If you become a PyMOL sponsor, then it is our job to make sure that
*your* specific needs for bug fixes, features, and support are met.  

Plus, DeLano Scientific will increasingly be offering a range of "incentive"
products on top of PyMOL which should always go a little bit beyond what you
can do with existing open-source code.  In other words, our commercial
approach doesn't involve directly competing with open-source, but rather
going beyond it.  Our vision is to ride the open-source wave, not to
obstruct it!

http://www.delanoscientific.com/about.html

Cheers,
Warren

--
mailto:warren_at_delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020
  

> -----Original Message-----
> From: Computational Chemistry List 
> [mailto:chemistry-request_at_ccl.net] On Behalf Of E.L. Willighagen
> Sent: Thursday, April 29, 2004 12:48 AM
> To: Miguel Romero; chemistry_at_ccl.net
> Cc: Miguel
> Subject: CCL:FREE SOFTWARE
> 
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
> 
> On Wednesday 28 April 2004 23:13, Miguel Romero wrote:
> > This is the first time I write to the CCL. I am starting a new 
> > molecular modeling project in a new research group. I've used 
> > comercial modeling software for many time but now I have to 
> switch to 
> > something else, preferably a FREE or reasonably priced software. I
> >
> > I am going to work with ligand-protein complexes and I need 
> > manipulation software, doking and molecular mechanics (geometry 
> > optimization and molecular dynamics) software. It can work 
> under linux or windows sistems.
> >
> > Can anybody help me.
> > thanks in advance for any help!
> 
> I'm not sure which programming language you plan to use (I 
> guess C, C++ or even fortran...), but for visualization I do 
> recommend Jmol
> (http://www.jmol.org) which is open source and has a very 
> good 3D visualization of proteins which is even being 
> improved every day by an international group of programmers and users.
> 
> And since Java can easily bind to C/C++ code, it is quite 
> straightforward to combine it with your code.
> 
> I hope this helps,
> 
> Egon
> 
> - --
> egonw_at_sci.kun.nl
> PhD on Molecular Representation in Chemometrics Nijmegen 
> University http://www.cac.sci.kun.nl/people/egonw/
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From chemistry-request@ccl.net Thu Apr 29 15:58:03 2004
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From: "Yevgeniy Podolyan" <podolyan:at:ccmsi.us>
To: <chemistry:at:ccl.net>
Subject: 04.11.12 13th Conference on Current Trends in Computational Chemistry, Jackson, MS, USA
Date: Thu, 29 Apr 2004 15:59:27 -0500
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Dear Colleagues:

We are pleased to announce and to invite you to attend the 13th Conference
on Current Trends in Computational Chemistry (CCTCC). This symposium,
organized by Jackson State University, covers all areas of computational
chemistry as well as quantum chemistry. This year the 13th CCTCC will be
held at the Jackson Hilton Hotel, Jackson, Mississippi on November 12-13,
2004. A banquet is scheduled for the Saturday evening and a dinner and
reception for Friday. 

The format consists of a series of (invited) plenary lectures and poster
presentations on Friday and Saturday covering applications as well as
theory. As suggested by Professor Pople, two years ago we inaugurated a new
tradition for the second decade of our conferences. Starting with the 11th
CCTCC each meeting is featuring a talk named after eminent computational
chemists. This year the third presentation in this series will be given by
Dr. Peter Pulay from the University of Arkansas. The 13th Conference will
also feature another talk given in the ancillary Noble Lecture Series. The
lectures in this series are presented in a relaxed, after-dinner atmosphere
by the noble speakers and are devoted to noble scientific events and people.
As such, it is an exceptional lecture to the conference and, contrary to the
regular talks, might not necessarily report any Current findings. This year
the talk will be delivered by Istvan Hargittai from Budapest University of
Technology and Economics, Hungary. 

We are planning to publish extended abstracts (up to four pages each) of all
invited talks and poster presentations. Original scientific contributions
will be published in a special issue of the International Journal of Quantum
Chemistry. Manuscripts for inclusion in the special issue should be
submitted in triplicate upon arrival at the registration desk. Submitted
papers will be subject to the journal's standard referee procedures.

This year, courtesy of Parallel Quantum Solutions, we will again award 3
monetary prizes for the best student posters.

For more information about the conference and to register visit our web site
at
http://cctcc.ccmsi.us

Jerzy Leszczynski
Chairman of the Organizing Committee




From chemistry-request@ccl.net Thu Apr 29 14:36:38 2004
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From: "Peter Gannett" <pgannett:at:hsc.wvu.edu>
To: <mromcue:at:alumni.unav.es>, <chemistry:at:ccl.net>, <egonw:at:sci.kun.nl>
Cc: <miguel:at:jmol.org>
Subject: Re: CCL:FREE SOFTWARE
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Miguel:

While not so good for manipulation and docking, the programs NAMD and
VMD are very good for MM/MD and visualization with some post MD run
processing.  Versions are available for Unix/Linux/Win.  

Pete Gannett

>>> "E.L. Willighagen" <egonw:at:sci.kun.nl> 4/29/2004 3:48:27 AM >>>
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

On Wednesday 28 April 2004 23:13, Miguel Romero wrote:
> This is the first time I write to the CCL. I am starting a new
molecular
> modeling project in a new research group. I've used comercial
modeling
> software for many time but now I have to switch to something else,
> preferably a FREE or reasonably priced software. I
>
> I am going to work with ligand-protein complexes and I need
manipulation
> software, doking and molecular mechanics (geometry optimization and
> molecular dynamics) software. It can work under linux or windows
sistems.
>
> Can anybody help me.
> thanks in advance for any help!

I'm not sure which programming language you plan to use (I guess C, C++
or 
even fortran...), but for visualization I do recommend Jmol 
(http://www.jmol.org) which is open source and has a very good 3D 
visualization of proteins which is even being improved every day by an

international group of programmers and users.

And since Java can easily bind to C/C++ code, it is quite
straightforward to 
combine it with your code.

I hope this helps,

Egon

- -- 
egonw:at:sci.kun.nl 
PhD on Molecular Representation in Chemometrics
Nijmegen University
http://www.cac.sci.kun.nl/people/egonw/ 
GPG: 1024D/D6336BA6

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Cc: chemistry$at$ccl.net
From: Konrad Hinsen <hinsen$at$cnrs-orleans.fr>
Subject: Re: CCL:FREE SOFTWARE
Date: Fri, 30 Apr 2004 10:38:46 +0200
To: Miguel Romero <mromcue$at$alumni.unav.es>
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On Apr 28, 2004, at 23:13, Miguel Romero wrote:

> This is the first time I write to the CCL. I am starting a new 
> molecular modeling project in a new research group. I've used 
> comercial modeling software for many time but now I have to switch to 
> something else, preferably a FREE or reasonably priced software. I
>
> I am going to work with ligand-protein complexes and I need 
> manipulation software, doking and molecular mechanics (geometry 
> optimization and molecular dynamics) software. It can work under linux 
> or windows sistems.

Have a look at

	http://dirac.cnrs-orleans.fr/MMTK/

You probably have to write some code yourself (docking for example), 
but that should be easy given that a lot of support code is there.
---------------------------------------------------------------------
Konrad Hinsen
Laboratoire Lion Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: hinsen$at$llb.saclay.cea.fr
---------------------------------------------------------------------




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From chemistry-request@ccl.net Fri Apr 30 12:54:07 2004
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Date: Fri, 30 Apr 2004 10:52:53 -0700
From: Douglas Sievers <dsievers^at^ucla.edu>
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To: chemistry^at^ccl.net
Subject: Question regarding Gaussian warnings and output file tags
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Dear CCLers,

As all users of Gaussian know, the output files are usually full of 
cryptic phrases, such as the following

********** Start **********

 EnCoef did     4 forward-backward iterations
 EnCoef did     4 forward-backward iterations
 EnCoef did     4 forward-backward iterations
 EnCoef did     1 forward-backward iterations
 EnCoef did     4 forward-backward iterations
 EnCoef did     6 forward-backward iterations
 Restarting incremental Fock formation.

 **** Warning!!: The largest alpha MO coefficient is  0.26465078D+02

   1 Symmetry operations used in ECPInt.
 ECPInt:  NShTT=   14878 NPrTT=   82700 LenC2=   13799 LenP2D=   52709.
 LDataN:  DoStor=F MaxTD1= 7 Len=  274
 LDataN:  DoStor=T MaxTD1= 7 Len=  274

********** End **********

Is there a resource which explains what these things mean? I can imagine 
the largest MO coefficient being very large (or greater than 1) would 
have some implications, but I'm not sure if this is something that the 
program is fixing on its own, or if this means my calculation result 
will be poor. Also, all of the flags, such as NShTT, DoStor, etc., are 
not explained in any of the manuals that I have. Does anyone know if the 
"Programmers manual" from Gaussian has more help on these details?

Thank you all!

Doug Sievers
dsievers^at^ucla.edu


From chemistry-request@ccl.net Fri Apr 30 14:18:04 2004
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From: "Dr. Daniel Glossman-Mitnik" <daniel.glossman=at=cimav.edu.mx>
To: <CHEMISTRY=at=ccl.net>, <help=at=gaussian.com>
Subject: CCL: questions about G03W functionalities
Date: Fri, 30 Apr 2004 13:19:26 -0700
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Dear netters !!!

=20

I have several questions regarding the functionalities in G03W:

=20

1)   The implementation of ONIOM within G03W allows the calculation

     of atomic charges according to some population analysis ?=20

     The results given by GaussViewW are those charges or it is=20

     necessary to do some additional algebraic operations ?

=20

2)   Is it possible to calculate polarizabilities with ONIOM in G03W ?

           How are they obtained ?

=20

3)   According to the Gaussian brochure, it should be possible to

     calculate  NMR shifts within ONIOM, but GaussViewW does not

      have this option ? How this can be circunvected ?

=20

4)   In the literature, a ONIOM-PCM has been described. Has it been

     Implemented in G03W ?

=20

5)   What about UV spectra with ONIOM ?

=20

6)   In G03W  there is an option for doing PBC calculations. Where can

           I find information (and examples) on how to construct the =
input
for

           that kind of calculations ? (i.e., how do you know the
translation

           vectors? )

=20

Thanks in advance.

=20

Best regards

=20

                                       Dr. Daniel Glossman-Mitnik=20

=20

*************************************************************************=
***
******************

             Dr. Daniel Glossman-Mitnik

=20

CIMAV - Centro de Investigaci=F3n en Materiales Avanzados, SC=20

QCyNAM - Grupo de Qu=EDmica Computacional y Nanotecnolog=EDa Molecular

Miguel de Cervantes 120 - Complejo Industrial Chihuahua

Chihuahua, Chih. 31109 - MEXICO

Tel=E9fono: (52) 614 4391151                FAX:       (52) 614 4391112

E-mail:    daniel.glossman=at=cimav.edu.mx

              dglossman=at=prodigy.net.mx

*************************************************************************=
***
*******************=20

=20


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<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:black'>Dear netters !!!</span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:black'>&nbsp;</span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Arial;color:black'>I have several =
questions
regarding the functionalities in G03W:</span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Arial;color:black'>&nbsp;</span></f=
ont></p>

<p class=3DMsoNormal =
style=3D'margin-left:36.0pt;text-indent:-18.0pt'><font size=3D2
color=3Dblack face=3DArial><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:
Arial;color:black'>1)<font size=3D1 face=3D"Times New Roman"><span
style=3D'font:7.0pt "Times New Roman"'>&nbsp; =
</span></font></span></font><font
size=3D2 color=3Dblack face=3DArial><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:Arial;color:black'>=A0The implementation of ONIOM within =
G03W allows
the calculation</span></font></p>

<p class=3DMsoNormal style=3D'margin-left:18.0pt'><font size=3D2 =
color=3Dblack
face=3DArial><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:Arial;
color:black'>=A0=A0=A0 =A0of atomic charges according to some population =
analysis ? </span></font></p>

<p class=3DMsoNormal style=3D'margin-left:18.0pt'><font size=3D2 =
color=3Dblack
face=3DArial><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:Arial;
color:black'>=A0=A0=A0 =A0The results given by GaussViewW are those =
charges or it is </span></font></p>

<p class=3DMsoNormal style=3D'margin-left:18.0pt'><font size=3D2 =
color=3Dblack
face=3DArial><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:Arial;
color:black'>=A0=A0=A0=A0 necessary to do some additional algebraic =
operations ?</span></font></p>

<p class=3DMsoNormal style=3D'margin-left:18.0pt'><font size=3D2 =
color=3Dblack
face=3DArial><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:Arial;
color:black'>&nbsp;</span></font></p>

<p class=3DMsoNormal =
style=3D'margin-left:36.0pt;text-indent:-18.0pt'><font size=3D2
color=3Dblack face=3DArial><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:
Arial;color:black'>2)<font size=3D1 face=3D"Times New Roman"><span
style=3D'font:7.0pt "Times New Roman"'>&nbsp; =
</span></font></span></font><font
size=3D2 color=3Dblack face=3DArial><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:Arial;color:black'>=A0Is it possible to calculate =
polarizabilities
with ONIOM in G03W ?</span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Arial;color:black'>=A0=A0=A0=A0=A0=A0=
=A0=A0=A0=A0 How are they obtained
?</span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Arial;color:black'>&nbsp;</span></f=
ont></p>

<p class=3DMsoNormal =
style=3D'margin-left:36.0pt;text-indent:-18.0pt'><font size=3D2
color=3Dblack face=3DArial><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:
Arial;color:black'>3)<font size=3D1 face=3D"Times New Roman"><span
style=3D'font:7.0pt "Times New Roman"'>&nbsp; =
</span></font></span></font><font
size=3D2 color=3Dblack face=3DArial><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:Arial;color:black'>=A0According to the Gaussian brochure, it =
should
be possible to</span></font></p>

<p class=3DMsoNormal style=3D'margin-left:18.0pt'><font size=3D2 =
color=3Dblack
face=3DArial><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:Arial;
color:black'>=A0=A0=A0 =A0calculate =A0NMR shifts within ONIOM, but =
GaussViewW does not</span></font></p>

<p class=3DMsoNormal style=3D'margin-left:18.0pt'><font size=3D2 =
color=3Dblack
face=3DArial><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:Arial;
color:black'>=A0=A0=A0=A0=A0 have this option ? How this can be =
circunvected ?</span></font></p>

<p class=3DMsoNormal style=3D'margin-left:18.0pt'><font size=3D2 =
color=3Dblack
face=3DArial><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:Arial;
color:black'>&nbsp;</span></font></p>

<p class=3DMsoNormal =
style=3D'margin-left:36.0pt;text-indent:-18.0pt'><font size=3D2
color=3Dblack face=3DArial><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:
Arial;color:black'>4)<font size=3D1 face=3D"Times New Roman"><span
style=3D'font:7.0pt "Times New Roman"'>&nbsp; =
</span></font></span></font><font
size=3D2 color=3Dblack face=3DArial><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:Arial;color:black'>=A0In the literature, a ONIOM-PCM has =
been
described. Has it been</span></font></p>

<p class=3DMsoNormal style=3D'margin-left:18.0pt'><font size=3D2 =
color=3Dblack
face=3DArial><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:Arial;
color:black'>=A0=A0=A0=A0 Implemented in G03W ?</span></font></p>

<p class=3DMsoNormal style=3D'margin-left:18.0pt'><font size=3D2 =
color=3Dblack
face=3DArial><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:Arial;
color:black'>&nbsp;</span></font></p>

<p class=3DMsoNormal =
style=3D'margin-left:36.0pt;text-indent:-18.0pt'><font size=3D2
color=3Dblack face=3DArial><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:
Arial;color:black'>5)<font size=3D1 face=3D"Times New Roman"><span
style=3D'font:7.0pt "Times New Roman"'>&nbsp; =
</span></font></span></font><font
size=3D2 color=3Dblack face=3DArial><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:Arial;color:black'>=A0What about UV spectra with ONIOM =
?</span></font></p>

<p class=3DMsoNormal style=3D'margin-left:18.0pt'><font size=3D2 =
color=3Dblack
face=3DArial><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:Arial;
color:black'>&nbsp;</span></font></p>

<p class=3DMsoNormal =
style=3D'margin-left:36.0pt;text-indent:-18.0pt'><font size=3D2
color=3Dblack face=3DArial><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:
Arial;color:black'>6)<font size=3D1 face=3D"Times New Roman"><span
style=3D'font:7.0pt "Times New Roman"'>&nbsp; =
</span></font></span></font><font
size=3D2 color=3Dblack face=3DArial><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:Arial;color:black'>=A0In G03W =A0there is an option for =
doing PBC
calculations. Where can</span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Arial;color:black'>=A0=A0=A0=A0=A0=A0=
=A0=A0=A0=A0 I find
information (and examples) on how to construct the input =
for</span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Arial;color:black'>=A0=A0=A0=A0=A0=A0=
=A0=A0=A0=A0 that kind of
calculations ? (i.e., how do you know the translation</span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Arial;color:black'>=A0=A0=A0=A0=A0=A0=
=A0=A0=A0=A0 vectors? )</span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Arial;color:black'>&nbsp;</span></f=
ont></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:black'>Thanks in =
advance.</span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:black'>&nbsp;</span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Arial;color:black'>Best =
regards</span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Arial;color:black'>&nbsp;</span></f=
ont></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Arial;color:black'>=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
Dr. Daniel Glossman-Mitnik </span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3D"Times New =
Roman"><span
lang=3DEN-US =
style=3D'font-size:12.0pt;color:black'>&nbsp;</span></font></p>

<div>

<div>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Arial;color:black'>****************=
*************************************************************************=
*****</span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Arial;color:black'>&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></font><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial;color:black'><img width=3D146 height=3D112
src=3D"cid:image002.jpg@01C42EB5.C282D950" border=3D0>&nbsp;&nbsp;&nbsp; =
</span></font><font
size=3D4 color=3Dblack face=3DArial><span =
style=3D'font-size:13.5pt;font-family:Arial;
color:black'>Dr. Daniel Glossman-Mitnik</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3D"Times New =
Roman"><span
style=3D'font-size:12.0pt;color:black'>&nbsp;</span></font></p>

<div>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:black'>CIMAV - Centro de Investigaci=F3n =
en
Materiales Avanzados, SC </span></font></p>

</div>

<div>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3D"Minya =
Nouvelle"><span
style=3D'font-size:12.0pt;font-family:"Minya =
Nouvelle";color:black'>QCyNAM</span></font><font
size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial;
color:black'> - Grupo de Qu=EDmica Computacional y Nanotecnolog=EDa =
Molecular</span></font></p>

</div>

<div>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:black'>Miguel de Cervantes 120 - Complejo
Industrial Chihuahua</span></font></p>

</div>

<div>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:black'>Chihuahua, Chih. 31109 - =
MEXICO</span></font></p>

</div>

<div>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:black'>Tel=E9fono: (52) 614
4391151&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;
FAX:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; (52) 614 =
4391112</span></font></p>

</div>

<div>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:black'>E-mail:&nbsp;&nbsp;&nbsp; <a
href=3D"mailto:daniel.glossman=at=cimav.edu.mx">daniel.glossman=at=cimav.edu.mx=
</a></span></font></p>

</div>

<div>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:black'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp=
;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a
href=3D"mailto:dglossman=at=prodigy.net.mx">dglossman=at=prodigy.net.mx</a></sp=
an></font></p>

</div>

<div>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:black'>***********************************=
************************************************************</span></font=
><font
size=3D2 color=3D"#0033cc" face=3DArial><span =
style=3D'font-size:10.0pt;font-family:
Arial;color:#0033CC'>&nbsp;</span></font></p>

</div>

</div>

</div>

<p><font size=3D2 color=3D"#0033cc" face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial;color:#0033CC'>&nbsp;</span></font></p>

</div>

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From chemistry-request@ccl.net Fri Apr 30 13:34:56 2004
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	Fri, 30 Apr 2004 14:36:23 -0400 (EDT)
Date: Fri, 30 Apr 2004 14:36:23 -0400
From: "Igor Filippov [Contr]" <igorf*at*helix.nih.gov>
To: Vincent Xianlong Wang <xloongw*at*yahoo.com>
cc: chemistry*at*ccl.net
Subject: Re: CCL:Segmentation fault with newzmat
In-Reply-To: <20040430163840.27307.qmail*at*web20211.mail.yahoo.com>
Message-ID: <Pine.SGI.4.58.0404301429200.1737433*at*helix.nih.gov>
References: <20040430163840.27307.qmail*at*web20211.mail.yahoo.com>
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Dear Vincent,

We've had the same problem as well. Didn't have the power glitch though :)
Our way out was to use old newzmat from g98 installation - you'll have to
write a small wrap-around script to be able to use g98 program in g03
environment, nothing too complex - I can send you our version, but
it'll have to be adapted to your environment anyway.
Moreover I've seen this problem with new newzmat even at the Gaussian
meeting in Boston last summer, I think it finally got to work there,
but on my local install we have to use g98 version of newzmat.

Best regards,

--------------------------------------------------------------------------
Igor Filippov
Contractor - SAIC-Frederick
National Cancer Institute


On Fri, 30 Apr 2004, Vincent Xianlong Wang wrote:

> Dear All,
>
> We have Gaussian03 installed and running for about 3
> months. The utility program 'newzmat' was running okay
> at the beggining. But recently it doesn't work
> anymore, only giving the error message, 'Segmentation
> fault'. There was a power glitch before this if i'm
> looking for an excuse, but other programs are running
> okay. No helpful information was given after
> contacting with the customer service from Gaussian
> Inc.
> Does anyone have the similar problem before? Or how
> should I try to solve this problem?
> Thanks in advance for your suggestions.
>
> Vincent
>
> If it's helpful, the OS is Redhat Linux and the
> hardware system is Dell Precision Workstation with
> 4-processors. And the following is the information
> obtained from the gdb debugging program.
>
> gdb output message:
>  Starting program: /usr/local/g03/newzmat tmc000.chk
>  [New Thread 1142446304 (LWP 17170)]
>
>  Program received signal SIGSEGV, Segmentation fault.
>  [Switching to Thread 1142446304 (LWP 17170)]
>  0x0804b6c9 in mdcuto_ ()
>
>
>
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