From owner-chemistry@ccl.net Wed Oct 12 01:28:00 2005
From: "Chas Simpson csimpson(0)hydrogen.cem.uct.ac.za" <owner-chemistry- -server.ccl.net>
To: CCL
Subject: CCL: W:Clarification: Test driven development/XP etc. in scientific ....
Message-Id: <-29554-051012012242-25722-FDAHXLtQDd1FvdKyLJQ18A- -server.ccl.net>
X-Original-From: "Chas  Simpson" <csimpson ~ hydrogen.cem.uct.ac.za>


Sent to CCL by: "Chas  Simpson" [csimpson . hydrogen.cem.uct.ac.za]
It appears either I made a type-o or that characters were stripped out of the email via the web interface. To clarify:

...A quick search on the Net revealed that the number and quality of software development tools available for Fortran and C++ were severely lacking in comparison with alternative languages such as Java or **C-SHARP**....

Apologies if this caused confusion.

Chas


From owner-chemistry@ccl.net Wed Oct 12 02:02:00 2005
From: "Per-Ola Norrby pon_._kemi.dtu.dk" <owner-chemistry..server.ccl.net>
To: CCL
Subject: CCL: constrained geometry optmisation of molecular complexes
Message-Id: <-29555-051012012320-25773-rXdqdtMnKkLZzJg9IdbP4A..server.ccl.net>
X-Original-From: Per-Ola Norrby <pon~~kemi.dtu.dk>
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Date: Wed, 12 Oct 2005 06:38:49 +0200
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Sent to CCL by: Per-Ola Norrby [pon:+:kemi.dtu.dk]
>I wish to perform geometry calculations on two of molecules, each 
>molecule contains rougly 20 heavy atoms. So far as I understand, HF 
>methods, semi-empirical methods and most DFT functionals will not 
>describe van-der-Waals forces (responsible for a good part of the 
>non-binding interaction?) correctly.

	You can get good non-bonding interactions out of 
well-parameterized empirical force fields.  And if you want to 
investigate which geometries are possible, no other methods are fast 
enough to give a reasonable sampling.  If you want to make an 
unbiased search, you probably have to go through thousands of 
possibilities, will full minimization of each, using either MD or 
some conformational search tool.

	Note that I said "well-parameterized".  There are several 
force fields around that give non-bonded interactions that are even 
worse than what you get out of HF or DFT.  So if you have an 
"unusual" molecule, no good force fields will be available. 
Developing one takes time, but it may well be the way to get the most 
accurate results.  And there are other possible pitfalls.  If your 
intermolecular interaction has a substantial contribution from charge 
transfer, for example, there are very few force fields that can 
handle it.

	And I would not use any constraints.  If you have to do that, 
it's a good sign your method is not accurate enough.  Calculating 
frequencies for a constrained geometry will always yield negative 
eigenvalues.

	/Per-Ola
-- 
Per-Ola Norrby, Assoc. Professor, http://organisk.kemi.dtu.dk/PON/
Technical University of Denmark, Department of Chemistry
Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark
Email: pon!^!kemi.dtu.dk  tel +45-45252123,  fax +45-45933968


From owner-chemistry@ccl.net Wed Oct 12 05:49:00 2005
From: "Noel O Boyle no228*cam.ac.uk" <owner-chemistry|-|server.ccl.net>
To: CCL
Subject: CCL: Re: Where can you publish articles on software?
Message-Id: <-29556-051012054305-11992-kTTB3WWR72C6rcqjbzfyug|-|server.ccl.net>
X-Original-From: "Noel O'Boyle" <no228]*[cam.ac.uk>
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Sent to CCL by: "Noel O'Boyle" [no228===cam.ac.uk]
On Tue, 2005-10-11 at 19:52 -0400, jle jle^^theworld.com wrote:
> Sent to CCL by: jle [jle-.-theworld.com]
> > This is why I would like to be able to publish an article on a
program.
> >
> Well, if what they want is done by a commercially available program,
> they can purchase and use it without concern (assuming most such
> programs, particularly in the QM field) are validated and tested well.

Except that they are restricted to the features available within that
program. For example, I used a well-known commercially-available package
during my PhD - I was very happy with its performance in general, but
when I wanted to do Morokuma decomposition I found that it wasn't
implemented. It *is* implemented in another freely-available package,
but that package wasn't able to converge the SCF. So what we have are
several different programs (some free and open-source, and some
commercially-available) which implement different subsets of useful
algorithms, and which are not interoperable.

> Otherwise, they can make the code available under the suitable open-
> source license or as a binary distribution on a website and post 
> pointers
> on places such as CCL.  We're still quite a small community, so if 
> something's
> good and available, it'll turn up, or be Google-able.

My point is that this doesn't happen - authors do *not* make the code
available, and so other scientists have to write it themselves (and not
all computational chemists can program).

> Writing the code's actually the smallest about of work.  Debugging it,
> validating it, maintaining it and possibly porting it are usually way 
> more
> work :-).
This is indeed true, and is part of the reason code is not released -
people aren't willing to support it, because of the work involved.

Regards,
Noel


From owner-chemistry@ccl.net Wed Oct 12 08:52:00 2005
From: "Bende Attila bende|s3.itim-cj.ro" <owner-chemistry{}server.ccl.net>
To: CCL
Subject: CCL: Frequency scaling factor!
Message-Id: <-29557-051012043038-6062-OuRVGla+UnjWOzBfzWcJqQ{}server.ccl.net>
X-Original-From: Bende Attila <bende]*[s3.itim-cj.ro>
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Date: Wed, 12 Oct 2005 10:52:17 +0000
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Sent to CCL by: Bende Attila [bende,;,s3.itim-cj.ro]
Hi everybody!

I would appreciate if you could give me some detailed lists or articles about 
vibrational frequency scaling factor values.
ex. Method (DFT, ab initio) / Basis set / Scaling factor.

In particularly, I'm interested in B3LYP/6-31G and B3LYP/6-31G** cases, but 
also for other case could come in useful for me.

Thanks in advance

-- 
Dr. Bende Attila (PhD)
Senior Researcher III 

***********************************************************************
National Institute of R&D of Izotopic and Molecular Tehnology
Str. Donath nr.71-103, P.O.Box 700
Cluj-Napoca, Ro-400293, Romania
Phone:+40-264-584037, int 216, Fax: +40-264-420042
e-mail: bende(~)s3.itim-cj.ro, AttlBende(~)yahoo.co.uk
web page: http://w3.itim-cj.ro/~bende
***********************************************************************


From owner-chemistry@ccl.net Wed Oct 12 09:48:00 2005
From: "Abrash, Samuel sabrash[]richmond.edu" <owner-chemistry(-)server.ccl.net>
To: CCL
Subject: CCL: Frequency scaling factor!
Message-Id: <-29558-051012094702-5105-tfxFq8rE3XUmyCeGZ/U2lw(-)server.ccl.net>
X-Original-From: "Abrash, Samuel" <sabrash/./richmond.edu>
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Sent to CCL by: "Abrash, Samuel" [sabrash*o*richmond.edu]
The best source for scaling factors is the NIST Computational Chemistry
Comparison and Benchmark Database.  The URL is:
http://srdata.nist.gov/cccbdb/

Click on the link for vibrations.

Best,
Samuel A. Abrash
Department of Chemistry
University of Richmond
Richmond, VA 23173
Phone:  804-289-8248
Fax:  804-297-1897
E-mail:  sabrash#%#richmond.edu
Web-page:  http://oncampus.richmond.edu/~sabrash
 
"Rabbi Yitzhak said:  At the time God created the world and desired to
reveal the depth of His being from out of the hidden, the light came
> from the darkness and they were joined together.  Because of this, out
of darkness came the light and out of the hidden came the revealed and
out of the good came evil and out of mercy came severe judgement, and
everything is intertwined  with everything else...the good inclination
and the evil inclination, the right and the left." - The Zohar

-----Original Message-----
> From: owner-chemistry#%#ccl.net [mailto:owner-chemistry#%#ccl.net] 
Sent: Wednesday, October 12, 2005 6:52 AM
To: Abrash, Samuel
Subject: CCL: Frequency scaling factor!


Sent to CCL by: Bende Attila [bende,;,s3.itim-cj.ro] Hi everybody!

I would appreciate if you could give me some detailed lists or articles
about vibrational frequency scaling factor values.
ex. Method (DFT, ab initio) / Basis set / Scaling factor.

In particularly, I'm interested in B3LYP/6-31G and B3LYP/6-31G** cases,
but also for other case could come in useful for me.

Thanks in advance

--
Dr. Bende Attila (PhD)
Senior Researcher III 

***********************************************************************
National Institute of R&D of Izotopic and Molecular Tehnology Str.
Donath nr.71-103, P.O.Box 700 Cluj-Napoca, Ro-400293, Romania
Phone:+40-264-584037, int 216, Fax: +40-264-420042
e-mail: bende:-:s3.itim-cj.ro, AttlBende:-:yahoo.co.uk web page:
http://w3.itim-cj.ro/~bende
***********************************************************************http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

From owner-chemistry@ccl.net Wed Oct 12 10:33:01 2005
From: "Nicolas Ferr nicolas.ferre.:.up.univ-mrs.fr" <owner-chemistry . server.ccl.net>
To: CCL
Subject: CCL: W:CCL: Frequency scaling factor!
Message-Id: <-29559-051012095534-16954-L5MbiNvLYfx2kp/G8NBI0Q . server.ccl.net>
X-Original-From: "Nicolas  Ferr" <nicolas.ferre*up.univ-mrs.fr>


Sent to CCL by: "Nicolas  Ferr" [nicolas.ferre(!)up.univ-mrs.fr]
> Sent to CCL by: Bende Attila [bende,;,s3.itim-cj.ro]
> Hi everybody!
>
> I would appreciate if you could give me some detailed lists or articles about vibrational frequency scaling factor values.
> ex. Method (DFT, ab initio) / Basis set / Scaling factor.
>
> In particularly, I'm interested in B3LYP/6-31G and B3LYP/6-31G** cases, but also for other case could come in useful for me.
>
> Thanks in advance
>

Maybe the latest paper ...

Irikura, K. K. and Johnson III, R. D. and N., Kacker R.
Uncertainties in Scaling Factors for ab Initio Vibrational Frequencies
J. Phys. Chem. A, 2005, 109, 8430-8437
See references therein. 

Hope this helps,

Nicolas


From owner-chemistry@ccl.net Wed Oct 12 11:07:01 2005
From: "Marcel Swart m.swart||few.vu.nl" <owner-chemistry-x-server.ccl.net>
To: CCL
Subject: CCL: Frequency scaling factor!
Message-Id: <-29560-051012101309-25943-IG5AUtvKmGvPVqouAsGBcw-x-server.ccl.net>
X-Original-From: Marcel Swart <m.swart%%few.vu.nl>
Content-Type: multipart/alternative; boundary=Apple-Mail-8-495268747
Date: Wed, 12 Oct 2005 16:12:04 +0200
Mime-Version: 1.0 (Apple Message framework v623)


Sent to CCL by: Marcel Swart [m.swart]*[few.vu.nl]

--Apple-Mail-8-495268747
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain;
	charset=WINDOWS-1252;
	format=flowed

On Oct 12, 2005, at 12:52 PM, Bende Attila bende|s3.itim-cj.ro wrote:

> Sent to CCL by: Bende Attila [bende,;,s3.itim-cj.ro]
> Hi everybody!
>
> I would appreciate if you could give me some detailed lists or=20
> articles about
> vibrational frequency scaling factor values.
> ex. Method (DFT, ab initio) / Basis set / Scaling factor.
>
> In particularly, I'm interested in B3LYP/6-31G and B3LYP/6-31G**=20
> cases, but
> also for other case could come in useful for me.

See:

R.S. Grev, C.L. Janssen, H.F. Schaefer III
J.Chem.Phys. 95 (1991) 5128

A.P. Scott, L. Radom
J.Phys.Chem. 100 (1996) 16502

=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=
=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96
dr. Marcel Swart

Theoretische Chemie
Vrije Universiteit Amsterdam
Faculteit der Exacte Wetenschappen

De Boelelaan 1083
1081 HV Amsterdam
The Netherlands

Tel		+31-(0)20-5987619
Fax		+31-(0)20-5987629
E-mail	m.swart(_)few.vu.nl
Web		http://www.few.vu.nl/~swart
=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=
=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96


--Apple-Mail-8-495268747
Content-Transfer-Encoding: quoted-printable
Content-Type: text/enriched;
	charset=WINDOWS-1252

On Oct 12, 2005, at 12:52 PM, Bende Attila bende|s3.itim-cj.ro wrote:


<excerpt>Sent to CCL by: Bende Attila [bende,;,s3.itim-cj.ro]

Hi everybody!


I would appreciate if you could give me some detailed lists or
articles about=20

vibrational frequency scaling factor values.

ex. Method (DFT, ab initio) / Basis set / Scaling factor.


In particularly, I'm interested in B3LYP/6-31G and B3LYP/6-31G**
cases, but=20

also for other case could come in useful for me.

</excerpt>

See:


R.S. Grev, C.L. Janssen, H.F. Schaefer III

J.Chem.Phys. 95 (1991) 5128


A.P. Scott, L. Radom

J.Phys.Chem. 100 (1996) 16502


=
<fontfamily><param>Helvetica</param><x-tad-smaller>=96=96=96=96=96=96=96=96=
=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=
=96=96=96=96=96=96=96=96=96=96=96

=
</x-tad-smaller></fontfamily><fontfamily><param>Papyrus</param><x-tad-bigg=
er>dr.
Marcel Swart

=
</x-tad-bigger></fontfamily><fontfamily><param>Papyrus</param><x-tad-small=
er>

=
</x-tad-smaller></fontfamily><fontfamily><param>Osaka</param><x-tad-smalle=
r>Theoretische
Chemie

Vrije Universiteit Amsterdam

Faculteit der Exacte Wetenschappen


De Boelelaan 1083

1081 HV Amsterdam

The Netherlands


Tel		+31-(0)20-5987619

Fax		+31-(0)20-5987629

E-mail	m.swart(_)few.vu.nl

Web		http://www.few.vu.nl/~swart

=
</x-tad-smaller></fontfamily><fontfamily><param>Helvetica</param><x-tad-sm=
aller>=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=
=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96

</x-tad-smaller></fontfamily>


--Apple-Mail-8-495268747--


From owner-chemistry@ccl.net Wed Oct 12 11:42:01 2005
From: "Colin L Weeks (cweeks(-)Princeton.EDU) cweeks(-)Princeton.EDU" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL: Frequency scaling factor!
Message-Id: <-29561-051012104153-1197-kH/abzyOUpTCWLbfc9pT2w^server.ccl.net>
X-Original-From: "Colin L Weeks (cweeks:_:Princeton.EDU)" <cweeks:_:Princeton.EDU>
Content-Disposition: inline
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Content-Transfer-Encoding: 7bit
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Date: Wed, 12 Oct 2005 09:59:15 -0400
MIME-Version: 1.0


Sent to CCL by: "Colin L Weeks (cweeks*Princeton.EDU)" [cweeks*Princeton.EDU]
Dear Bende,
  I suggest you have a look at the following paper:

A.P. Scott and L. Radom, Journal of Physical Chemistry, (1996) 100 p16502-16513

Regards, Colin

Dr Colin L. Weeks, Postdoctoral Research Associate
Department of Chemistry, Princeton University
Phone: +1 609-258-3908, Email: cweeks::princeton.edu

----- Original Message -----
> From: "Bende Attila bende|s3.itim-cj.ro" <owner-chemistry::ccl.net>
Date: Wednesday, October 12, 2005 6:52 am
Subject: CCL: Frequency scaling factor!

> 
> Sent to CCL by: Bende Attila [bende,;,s3.itim-cj.ro]
> Hi everybody!
> 
> I would appreciate if you could give me some detailed lists or 
> articles about 
> vibrational frequency scaling factor values.
> ex. Method (DFT, ab initio) / Basis set / Scaling factor.
> 
> In particularly, I'm interested in B3LYP/6-31G and B3LYP/6-31G** 
> cases, but 
> also for other case could come in useful for me.
> 
> Thanks in advance
> 
> -- 
> Dr. Bende Attila (PhD)
> Senior Researcher III 
> 
> ***********************************************************************
> National Institute of R&D of Izotopic and Molecular Tehnology
> Str. Donath nr.71-103, P.O.Box 700
> Cluj-Napoca, Ro-400293, Romania
> Phone:+40-264-584037, int 216, Fax: +40-264-420042
> e-mail: bende:-:s3.itim-cj.ro, AttlBende:-:yahoo.co.uk
> web page: http://w3.itim-cj.ro/~bende
> ***********************************************************************
> 
>


From owner-chemistry@ccl.net Wed Oct 12 12:17:00 2005
From: "Niels Hansen n.hansen[A]tuhh.de" <owner-chemistry,;,server.ccl.net>
To: CCL
Subject: CCL: Frequency scaling factor!
Message-Id: <-29562-051012104137-1076-AYvsoL/LYXZJFtwM9modyA,;,server.ccl.net>
X-Original-From: Niels Hansen <n.hansen#tuhh.de>
Content-Transfer-Encoding: 7bit
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Date: Wed, 12 Oct 2005 15:45:48 +0200
MIME-Version: 1.0


Sent to CCL by: Niels Hansen [n.hansen*|*tuhh.de]
Bende Attila bende|s3.itim-cj.ro wrote:

>Sent to CCL by: Bende Attila [bende,;,s3.itim-cj.ro]
>Hi everybody!
>
>I would appreciate if you could give me some detailed lists or articles about 
>vibrational frequency scaling factor values.
>ex. Method (DFT, ab initio) / Basis set / Scaling factor.
>
>In particularly, I'm interested in B3LYP/6-31G and B3LYP/6-31G** cases, but 
>also for other case could come in useful for me.
>
>Thanks in advance
>
>  
>
Try the "Database of Frequency Scaling Factors for Electronic Structure 
Methods" (http://comp.chem.umn.edu/database/freq_scale.htm)

Regards,
Niels


From owner-chemistry@ccl.net Wed Oct 12 12:52:00 2005
From: "Marcin Krol mykrol===cyf-kr.edu.pl" <owner-chemistry:-:server.ccl.net>
To: CCL
Subject: CCL: Frequency scaling factor!
Message-Id: <-29563-051012101516-26220-UNx87URgxW7cVfCZQnK2iA:-:server.ccl.net>
X-Original-From: Marcin Krol <mykrol * cyf-kr.edu.pl>
Content-Type: TEXT/PLAIN; charset=US-ASCII
Date: Wed, 12 Oct 2005 15:37:08 +0200 (METDST)
MIME-Version: 1.0


Sent to CCL by: Marcin Krol [mykrol,cyf-kr.edu.pl]
Hi,
Have a look at
http://comp.chem.umn.edu/database/freq_scale.htm
best
marcin


> I would appreciate if you could give me some detailed lists or articles about
> vibrational frequency scaling factor values.
> ex. Method (DFT, ab initio) / Basis set / Scaling factor.
>
> In particularly, I'm interested in B3LYP/6-31G and B3LYP/6-31G** cases, but
> also for other case could come in useful for me.
>
> Thanks in advance
>
> --
> Dr. Bende Attila (PhD)
> Senior Researcher III


From owner-chemistry@ccl.net Wed Oct 12 13:27:00 2005
From: "Perry E. Metzger perry*|*piermont.com" <owner-chemistry,;,server.ccl.net>
To: CCL
Subject: CCL: development environments...
Message-Id: <-29564-051012104509-2393-CJK+EtNldvZcZJUEIyt65Q,;,server.ccl.net>
X-Original-From: "Perry E. Metzger" <perry]![piermont.com>
Content-Type: text/plain; charset=us-ascii
Date: Wed, 12 Oct 2005 10:44:49 -0400
MIME-Version: 1.0


Sent to CCL by: "Perry E. Metzger" [perry===piermont.com]

"Chas Simpson" wrote:
> ..A quick search on the Net revealed that the number and quality of
> software development tools available for Fortran and C++ were
> severely lacking in comparison with alternative languages such as
> Java or C#.... 

FYI, I find I'm far far faster developing code just using emacs,
couple of debuggers and the command line than I am in an "integrated
development environment". For the most part, the best professional
programmers I know tend to feel the same way (though many of them use
other editors, such as vi.)

I think a good explanation of why this is can be found in Neil
Stephenson's interesting essay "In the beginning was the command
line", but suffice it to say, IDEs, like most graphical user interface
environments, are not themselves programmable, and thus it is
frequently difficult to get work done inside them efficiently. I like
GUIs for tasks like editing and visualizing molecules, but not for
tasks like writing software, because writing software is not
fundamentally a visual operation.

Stephenson makes another interesting argument -- that tools for
professionals and tools for non-professionals in most fields tend to
be pretty different. A professional chef uses kitchen equipment that
many people would find pretty ugly looking in their homes, and
possibly pretty dangerous -- he wants a stove that gets water boiling
very very fast and that gives him more control far more than he wants
nice enamel. Most of the best programmers I know feel similarly about
their tools.


Perry


From owner-chemistry@ccl.net Wed Oct 12 14:02:00 2005
From: "Vincent Xianlong Wang xloongw_-_yahoo.com" <owner-chemistry^^server.ccl.net>
To: CCL
Subject: CCL: Frequency scaling factor!
Message-Id: <-29565-051012112143-4264-sE6WzyCvqjwHI3qz0yvukw^^server.ccl.net>
X-Original-From: Vincent Xianlong Wang <xloongw : yahoo.com>
Content-Transfer-Encoding: 8bit
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Date: Wed, 12 Oct 2005 08:21:36 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: Vincent Xianlong Wang [xloongw:yahoo.com]


--- "Bende Attila bende|s3.itim-cj.ro"
<owner-chemistry++ccl.net> wrote:

> 
> Sent to CCL by: Bende Attila [bende,;,s3.itim-cj.ro]
> Hi everybody!
> 
> I would appreciate if you could give me some
> detailed lists or articles about 
> vibrational frequency scaling factor values.
> ex. Method (DFT, ab initio) / Basis set / Scaling
> factor.
> 
> In particularly, I'm interested in B3LYP/6-31G and
> B3LYP/6-31G** cases, but 
> also for other case could come in useful for me.

The scale factors are listed on Exploring Chemistry
with Electronic Structure Methods by Foresman, J. B.
and Frisch, A.
The frequency scale factor for the
B3LYP/6-31G(d)method is 0.9613 and the ZPE/thermal
scale factor is 0.9804.

> Thanks in advance
> 
> -- 
> Dr. Bende Attila (PhD)
> Senior Researcher III 
> 
>
***********************************************************************
> National Institute of R&D of Izotopic and Molecular
> Tehnology
> Str. Donath nr.71-103, P.O.Box 700
> Cluj-Napoca, Ro-400293, Romania
> Phone:+40-264-584037, int 216, Fax: +40-264-420042
> e-mail: bende:-:s3.itim-cj.ro,
> AttlBende:-:yahoo.co.uk
> web page: http://w3.itim-cj.ro/~bende
>
***********************************************************************
> 
> 
> 
> -= This is automatically added to each message by
> the mailing script =-
> To recover the email address of the author of the
> message, please change
> the strange characters on the top line to the ++
> sign. You can also
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From owner-chemistry@ccl.net Wed Oct 12 14:37:00 2005
From: "Russell D Johnson III russell.johnson-.-nist.gov" <owner-chemistry(~)server.ccl.net>
To: CCL
Subject: CCL: Frequency scaling factor
Message-Id: <-29566-051012105058-5167-R/vEVnk/eM/Gsob6F+Dz1Q(~)server.ccl.net>
X-Original-From: Russell D Johnson III <russell.johnson]|[nist.gov>
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Date: Wed, 12 Oct 2005 10:07:45 -0400
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Sent to CCL by: Russell D Johnson III [russell.johnson+/-nist.gov]
--=====================_2463062==.ALT
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Hello Dr. Attila,

        The NIST Computational Chemistry Comparison and Benchmark Database=
 (CCCBDB) has scaling factors for those methods/basis sets as well as many=
 others. See section III.B.4.a for scaling factors determined using=
 vibrational data in the CCCBDB. B3LYP/6-31G shows a scaling factor of 0.962=
 using 2730 vibrational frequencies from 271 molecules. The CCCBDB is online=
 at:
http://srdata.nist.gov/cccbdb/

        We also have a recent paper on the uncertainties of the scaling=
 factors:
J. Phys. Chem. A 2005, 109, 8430-8437.=20

The uncertainties in the scale factors, which can be used to provide=
 uncertainties for the predicted frequencies, are also available at the=
 CCCBDB.
For B3LYP/6-31G, the currently listed factor is=
 <http://srdata.nist.gov/cccbdb/vibscale2.asp?method=3D8&basis=3D9>0.962 =B1=
 0.041.
For B3LYP/6-31G**, the currently listed factor is=
 <http://srdata.nist.gov/cccbdb/vibscale2.asp?method=3D8&basis=3D3>0.961 =B1=
 0.045, although this uncertainty looks too large for a polarized basis set.=
=20

Best wishes,
Russ Johnson

At 06:52 2005-10-12, you wrote:

>Sent to CCL by: Bende Attila [bende,;,s3.itim-cj.ro]
>Hi everybody!
>
>I would appreciate if you could give me some detailed lists or articles=
 about=20
>vibrational frequency scaling factor values.
>ex. Method (DFT, ab initio) / Basis set / Scaling factor.
>
>In particularly, I'm interested in B3LYP/6-31G and B3LYP/6-31G** cases, but=
=20
>also for other case could come in useful for me.
>
>Thanks in advance
>
>--=20
>Dr. Bende Attila (PhD)
>Senior Researcher III=20
>
>***********************************************************************
>National Institute of R&D of Izotopic and Molecular Tehnology
>Str. Donath nr.71-103, P.O.Box 700
>Cluj-Napoca, Ro-400293, Romania
>Phone:+40-264-584037, int 216, Fax: +40-264-420042
>e-mail: bende:-:s3.itim-cj.ro, AttlBende:-:yahoo.co.uk
>web page: http://w3.itim-cj.ro/~bende
>***********************************************************************

Dr. Russell D. Johnson III
Research Chemist
National Institute of Standards and Technology
Computational Chemistry Group
100 Bureau Drive, Stop 8380
Gaithersburg, MD 20899-8380
voice: 301+975-2513 fax:301+869-4020
email: russell.johnson/./nist.gov=20
--=====================_2463062==.ALT
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<html>
<body>
Hello Dr. Attila,<br><br>
<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab>The NIST
Computational Chemistry Comparison and Benchmark Database (CCCBDB) has
scaling factors for those methods/basis sets as well as many others. See
section III.B.4.a for scaling factors determined using vibrational data
in the CCCBDB. B3LYP/6-31G shows a scaling factor of 0.962 using 2730
vibrational frequencies from 271 molecules. The CCCBDB is online at:<br>
<a href=3D"http://srdata.nist.gov/cccbdb/" eudora=3D"autourl">
http://srdata.nist.gov/cccbdb/</a><br><br>
<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab>We also
have a recent paper on the uncertainties of the scaling factors:<br>
<i>J. Phys. Chem. A</i> <b>2005</b>, <i>109</i>, 8430-8437. <br><br>
The uncertainties in the scale factors, which can be used to provide
uncertainties for the predicted frequencies, are also available at the
CCCBDB.<br>
For B3LYP/6-31G, the currently listed factor is
<a href=3D"http://srdata.nist.gov/cccbdb/vibscale2.asp?method=3D8&amp;basis=
=3D9">
0.962 =B1 0.041</a>.<br>
For B3LYP/6-31G**, the currently listed factor is
<a href=3D"http://srdata.nist.gov/cccbdb/vibscale2.asp?method=3D8&amp;basis=
=3D3">
0.961 =B1 0.045</a>, although this uncertainty looks too large for a
polarized basis set. <br><br>
Best wishes,<br>
Russ Johnson<br><br>
At 06:52 2005-10-12, you wrote:<br><br>
<blockquote type=3Dcite class=3Dcite cite=3D"">Sent to CCL by: Bende Attila
[bende,;,s3.itim-cj.ro]<br>
Hi everybody!<br><br>
I would appreciate if you could give me some detailed lists or articles
about <br>
vibrational frequency scaling factor values.<br>
ex. Method (DFT, ab initio) / Basis set / Scaling factor.<br><br>
In particularly, I'm interested in B3LYP/6-31G and B3LYP/6-31G** cases,
but <br>
also for other case could come in useful for me.<br><br>
Thanks in advance<br><br>
-- <br>
Dr. Bende Attila (PhD)<br>
Senior Researcher III <br><br>
***********************************************************************<br>
National Institute of R&amp;D of Izotopic and Molecular Tehnology<br>
Str. Donath nr.71-103, P.O.Box 700<br>
Cluj-Napoca, Ro-400293, Romania<br>
Phone:+40-264-584037, int 216, Fax: +40-264-420042<br>
e-mail: bende:-:s3.itim-cj.ro, AttlBende:-:yahoo.co.uk<br>
web page:
<a href=3D"http://w3.itim-cj.ro/~bende" eudora=3D"autourl">
http://w3.itim-cj.ro/~bende</a><br>
***********************************************************************<br>
</blockquote>
<x-sigsep><p></x-sigsep>
Dr. Russell D. Johnson III<br>
Research Chemist<br>
National Institute of Standards and Technology<br>
Computational Chemistry Group<br>
100 Bureau Drive, Stop 8380<br>
Gaithersburg, MD 20899-8380<br>
voice: 301+975-2513 fax:301+869-4020<br>
email: russell.johnson/./nist.gov</body>
</html>

--=====================_2463062==.ALT--


From owner-chemistry@ccl.net Wed Oct 12 15:12:01 2005
From: "Massimo Ottonelli massimo*_*chimica.unige.it" <owner-chemistry!=!server.ccl.net>
To: CCL
Subject: CCL: Frequency scaling factor!
Message-Id: <-29567-051012112954-5901-emnUJGym9/gfN1qaqCvh4w!=!server.ccl.net>
X-Original-From: Massimo Ottonelli <massimo__chimica.unige.it>
Content-Type: text/plain; charset="us-ascii"; format=flowed
Date: Wed, 12 Oct 2005 16:37:57 +0200
Mime-Version: 1.0


Sent to CCL by: Massimo Ottonelli [massimo+*+chimica.unige.it]

  Well I think that could be usefull the following link
                                                                        http://srdata.nist.gov/cccbdb/


At 10.52 12/10/2005 +0000, you wrote:

>Sent to CCL by: Bende Attila [bende,;,s3.itim-cj.ro]
>Hi everybody!
>
>I would appreciate if you could give me some detailed lists or articles about
>vibrational frequency scaling factor values.
>ex. Method (DFT, ab initio) / Basis set / Scaling factor.
>
>In particularly, I'm interested in B3LYP/6-31G and B3LYP/6-31G** cases, but
>also for other case could come in useful for me.
>
>Thanks in advance
>
>--
>Dr. Bende Attila (PhD)
>Senior Researcher III
>
>***********************************************************************
>National Institute of R&D of Izotopic and Molecular Tehnology
>Str. Donath nr.71-103, P.O.Box 700
>Cluj-Napoca, Ro-400293, Romania
>Phone:+40-264-584037, int 216, Fax: +40-264-420042
>e-mail: bende:-:s3.itim-cj.ro, AttlBende:-:yahoo.co.uk
>web page: http://w3.itim-cj.ro/~bende
>***********************************************************************

From owner-chemistry@ccl.net Wed Oct 12 15:47:01 2005
From: "David A. Case case]~[scripps.edu" <owner-chemistry---server.ccl.net>
To: CCL
Subject: CCL: PDB in Amber
Message-Id: <-29568-051012123029-25267-0AQh6FE/YKWOvV8XugobHA---server.ccl.net>
X-Original-From: "David A. Case" <case : scripps.edu>
Content-Disposition: inline
Content-Type: text/plain; charset=us-ascii
Date: Wed, 12 Oct 2005 08:45:33 -0700
Mime-Version: 1.0


Sent to CCL by: "David A. Case" [case[-]scripps.edu]
On Tue, Oct 11, 2005, DELIA SOTO sotodelia ~ hotmail.com wrote:

> I`m new in Amber and I have a question
> What I can do to read, in leap, a PDB file created in Chem3D?

I don't know why the usual "loadPdb" command should not work.  If it does not,
please post details about the error message, probably along with your pdb
file as well.  It's probably best to ask these questions to the amber mailing
list (see http://amber.scripps.edu for information on how to subscribe).

...good luck...dac


From owner-chemistry@ccl.net Wed Oct 12 16:22:01 2005
From: "Steve Williams willsd/./appstate.edu" <owner-chemistry|a|server.ccl.net>
To: CCL
Subject: CCL: Frequency scaling factor!
Message-Id: <-29569-051012113403-8313-I0K0chKeLNzqgwms3dArRQ|a|server.ccl.net>
X-Original-From: Steve Williams <willsd-x-appstate.edu>
Content-transfer-encoding: 7bit
Content-type: text/plain; format=flowed; charset=ISO-8859-1
Date: Wed, 12 Oct 2005 10:49:26 -0400
MIME-version: 1.0


Sent to CCL by: Steve Williams [willsd[*]appstate.edu]
Bende Attila bende|s3.itim-cj.ro wrote:

>Sent to CCL by: Bende Attila [bende,;,s3.itim-cj.ro]
>Hi everybody!
>
>I would appreciate if you could give me some detailed lists or articles about 
>vibrational frequency scaling factor values.
>ex. Method (DFT, ab initio) / Basis set / Scaling factor.
>
>In particularly, I'm interested in B3LYP/6-31G and B3LYP/6-31G** cases, but 
>also for other case could come in useful for me.
>
>Thanks in advance
>
>  
>
Try looking at http://srdata.nist.gov/cccbdb/vsf.asp
Steve Williams


From owner-chemistry@ccl.net Wed Oct 12 16:57:01 2005
From: "=?iso-8859-1?Q?BOUYER_Fr=E9d=E9ric_153746?= FB153746_+_ATIL.CEA.FR" <owner-chemistry[#]server.ccl.net>
To: CCL
Subject: CCL: Compilation troubles
Message-Id: <-29570-051012114759-15393-MP75m514V/P9o5vD86i6Lg[#]server.ccl.net>
X-Original-From: =?iso-8859-1?Q?BOUYER_Fr=E9d=E9ric_153746?= <FB153746^^ATIL.CEA.FR>
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Date: Wed, 12 Oct 2005 16:30:10 +0200
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Sent to CCL by: =?iso-8859-1?Q?BOUYER_Fr=E9d=E9ric_153746?= [FB153746]=[ATIL.CEA.FR]
This message is in MIME format. Since your mail reader does not understand
this format, some or all of this message may not be legible.

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Dear CCL users,
=20
Did anyone compile gaussian03 with g77 ? I have only the first =
executable,
but all the .exe are not build, because of some undefined references. I =
try
to compile the source code on a PC Xeon with redhat 9.
Many thanks in advance for any kind of hep and any tip that could help =
me
(makefile and flags to share).
=20
Regards,
=20
Fr=E9d=E9ric
=20

------_=_NextPart_001_01C5CF39.44F45178
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META HTTP-EQUIV=3D"Content-Type" CONTENT=3D"text/html; =
charset=3Diso-8859-1">
<TITLE>Message</TITLE>

<META content=3D"MSHTML 6.00.2800.1515" name=3DGENERATOR></HEAD>
<BODY>
<DIV>
<DIV><SPAN class=3D774140807-12102005><FONT face=3DArial size=3D2>Dear =
CCL=20
users,</FONT></SPAN></DIV>
<DIV><SPAN class=3D774140807-12102005><FONT face=3DArial=20
size=3D2></FONT></SPAN>&nbsp;</DIV>
<DIV><SPAN class=3D774140807-12102005><FONT face=3DArial size=3D2>Did =
anyone compile=20
gaussian03 with g77&nbsp;? I have only the first executable, but all =
the .exe=20
are not build, because of some undefined references. I try to compile =
the source=20
code on a PC Xeon with redhat 9.</FONT></SPAN></DIV>
<DIV><SPAN class=3D774140807-12102005><FONT face=3DArial><FONT =
size=3D2>Many thanks in=20
advance for any kind of hep and any tip that could help me<SPAN=20
class=3D455342814-12102005> (makefile and flags to=20
share).</SPAN></FONT></FONT></SPAN></DIV>
<DIV><SPAN class=3D774140807-12102005><FONT face=3DArial=20
size=3D2></FONT></SPAN>&nbsp;</DIV>
<DIV><SPAN class=3D774140807-12102005><FONT face=3DArial=20
size=3D2>Regards,</FONT></SPAN></DIV>
<DIV><SPAN class=3D774140807-12102005><FONT face=3DArial=20
size=3D2></FONT></SPAN>&nbsp;</DIV>
<DIV><SPAN class=3D774140807-12102005><FONT face=3DArial=20
size=3D2>Fr=E9d=E9ric</FONT></SPAN></DIV>
<DIV><SPAN style=3D"FONT-SIZE: 10pt; FONT-FAMILY: =
Arial"><?xml:namespace prefix =3D=20
o ns =3D "urn:schemas-microsoft-com:office:office" =
/><o:p>&nbsp;</o:p></SPAN><SPAN=20
style=3D"FONT-SIZE: 10pt; FONT-FAMILY: =
Arial"><o:p></DIV></DIV></o:p></SPAN></BODY></HTML>

------_=_NextPart_001_01C5CF39.44F45178--


From owner-chemistry@ccl.net Wed Oct 12 17:32:00 2005
From: "Shaji Chempath shaji]|[berkeley.edu" <owner-chemistry__server.ccl.net>
To: CCL
Subject: CCL: constrained geometry optmisation of molecular complexes
Message-Id: <-29571-051012140926-25819-nUxkbFmo0qo53BW4pJ/AZw__server.ccl.net>
X-Original-From: Shaji Chempath <shaji() berkeley.edu>
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Sent to CCL by: Shaji Chempath [shaji**berkeley.edu]
Dear Professor Norrby,
I had a look at your website and got some information about 
parametrizing intramolecular terms. Could you explain a bit more about 
the general strategies for developing non-bonded terms. Is it usually 
done by  parametrizing to match experimental values (of vapor pressure 
for example). Is it a good idea to parametrize against DFT. Are there 
any recent references which explains forcefield development strategies 
for nonbonded terms of "unusual" molecules?.
Thanks a lot
Shaji

>     Note that I said "well-parameterized".  There are several force 
> fields around that give non-bonded interactions that are even worse 
> than what you get out of HF or DFT.  So if you have an "unusual" 
> molecule, no good force fields will be available. Developing one takes 
> time, but it may well be the way to get the most accurate results.  
> And there are other possible pitfalls.  If your intermolecular 
> interaction has a substantial contribution from charge transfer, for 
> example, there are very few force fields that can handle it.


From owner-chemistry@ccl.net Wed Oct 12 18:07:00 2005
From: "Warren DeLano warren_-_delsci.com" <owner-chemistry{}server.ccl.net>
To: CCL
Subject: CCL: RE: Where can you publish articles on software?
Message-Id: <-29572-051012152247-13382-IG5AUtvKmGvPVqouAsGBcw{}server.ccl.net>
X-Original-From: "Warren DeLano" <warren-x-delsci.com>
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Date: Wed, 12 Oct 2005 12:23:06 -0700
MIME-Version: 1.0


Sent to CCL by: "Warren DeLano" [warren(~)delsci.com]

> Sent to CCL by: "Andy  Holder" [holdera%umkc.edu]

Ironically, JMGM editor Andy Holder offers compelling reasons for why
developer-scientists should shift their attention away from
closed-access journals like JMGM and toward peer-reviewed
open-access/open-source venues that better serve the overall needs of
the field.

> I am the editor of the Journal of Molecular Graphics and Modelling, 
> and we specifically EXCLUDE program announcements/descriptions from 
> our pages.  Programs are not original research, but may be 
> implementations of original research.

This fails to acknowledge the critical enabling role of software in
computational chemistry and conveys a shockingly dismissive view of the
original research aspects of computer programs!  To put it as politely
as I can, I most vehemently disagree.  Such comments insult and demean
the creative efforts of those who might have otherwise considered
publishing papers in JMGM.

> The data from JMGM indicate that our IF went DOWN 
> when we included these item and has been steadily increasing since we 
> eliminated them.

Effective running software is at least as impactful as algorithmic
descriptions, if not more so.  (We live in real buildings, not
architectural plans; we travel by plane, not via designs of planes).
"Impact Factor" (I.F.) in terms of follow-on citations has little
relevance as a measure of impact for scientific software and especially
so once usage becomes widespread (e.g. ChemDraw, RasMol, Excel, etc.).
Speaking from personal experience, recognizable PyMOL images are now
routinely found in Science, Nature, C&EN, and many other journals, but
such usage is rarely cited.  So what is PyMOL's impact factor?  Zero! It
has never been officially "published" per se, even though its source
code has been published continuously on the internet since early 2000.

> The algorithm is perhaps worthy of
> publication, and the program can certainly be mentioned, but is not in

> and of itself worthy of the valuable space in a research journal.

Such comments reflect little "editorial" sympathy for the
publish-or-perish plight faced by academic scientists who develop
practical algorithms in the form of working software programs instead of
abstract algorithms in the form of non-working descriptive publications.
Without such publications, the impact of developer-scientists is
invisible to tenure review committees and funding agencies.  That is
unfair to many scientists and damaging to the field as a whole since
better research software is very much needed.  Developer-scientists need
to be appropriately recognized and rewarded through career advancement,
and thus it is not by accident that so many talented scientific software
developers have chosen the private sector over the academic world.  The
system of academic credit is largely broken with respect to creation of
quality research software.

While JMCM may indeed have a fine "editorial" policy on this matter, it
is justified for the wrong reasons.  

Programs cannot truly be "published" in traditional journals because
they are too complex to describe precisely in such venues.  A standalone
print article does not deliver reproducibility and verifiability with
respect to research software.  Thus, journal articles describing
software do not meet fundamental requirements of the scientific method.

The only way to publish software in a scientifically robust manner is to
share source code, and that means publishing via the internet in an
open-access/open-source fashion.  Anything short of that amounts to
issuing unproven claims based on limited empirical tests regarding what
a given program allegedly does.  What is that called outside of science?
Advertising!  And as such, I agree that it does not belong in a
scientific journal.  Either you publish software with source code and
stand behind it, or you are blowing smoke and quite *literally* hiding
something -- no matter how noble your intent.

> Being a former member of the Dewar group, they certainly published a 
> large number of papers on semiempirical methods, but never published 
> any article on AMPAC itself.

Such comments confirm the notion that research software developers are
not recognized for the critical enabling contributions they make, and
reveal just how incapable the old closed-access, print-journal
publication system is of meeting current needs.

So, go live fellow research software developers, go live!  Bypass an
inadequate and obsolete system, and instead pursue internet-based
open-access/open-source publishing of your work.  If you lead, the world
will follow.

http://www.plos.org , http://www.doaj.org ,
http://pubchem.ncbi.nlm.nih.gov , http://www.blueobelisk.org ,
http://www.chmoogle.com , http://www.sf.net , etc.

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                     
Principal Scientist

. DeLano Scientific LLC  
. 400 Oyster Point Blvd., Suite 213           
. South San Francisco, CA 94080 USA   
. Biz:(650)-872-0942  Tech:(650)-872-0834     
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:warren-,-delsci.com      

> -----Original Message-----
> From: owner-chemistry-,-ccl.net [mailto:owner-chemistry-,-ccl.net]
> Sent: Tuesday, October 11, 2005 4:46 PM
> To: Warren DeLano
> Subject: CCL: W:CCL: Where can you publish articles on software?
> 
> 
> Sent to CCL by: "Andy  Holder" [holdera%umkc.edu] In reply to:
> 
> > This programme is surely useful, but the editors of
> research journals
> > would probably not accept it for publication. If this kind
> of article
> > is acceptable, I guess that many people would produce tons of 
> > technical programmes
> >>This is exactly what I think *should* be encouraged! If we look at 
> >>bioinformatics, the latest issue of "BMC Bioinformatics" has 7 
> >>software articles (this journal has an impact factor of 5.42); the 
> >>latest issue of "Bioinformatics" has 9 'Application Notes' (this 
> >>journal has an impact factor of 5.74). There is a real interest in 
> >>useful software that can make it easier to do science.
> 
> I am the editor of the Journal of Molecular Graphics and Modelling, 
> and we specifically EXCLUDE program announcements/descriptions from 
> our pages.  Programs are not original research, but may be 
> implementations of original research.
> 
> Being a former member of the Dewar group, they certainly published a 
> large number of papers on semiempirical methods, but never published 
> any article on AMPAC itself.  These programs were even run on just a 
> few examples of "suitable data of interest"!  The algorithm is perhaos

> worthy of publication, and the program can certainly be mentioned, but

> is not in and of itself worthy of the valuable space in a research 
> journal.
> 
> Comparison to various other journals with high impact factors is 
> anecdotal at best.  The data from JMGM indicate that our IF went DOWN 
> when we included these item and has been steadily increasing since we 
> eliminated them.  But that could also have been for a number of other 
> reasons.
> 
> My 0.02.
> 
> Regards, Andy Holder
> 
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- 
> JJJJJJJJ MMM   MMM   GGG   MMM   MMM |        ANDREW J. HOLDER
>    JJ     MM   MM   GG GG   MM   MM  |              Editor
>    JJ     MMM MMM  GG       MMM MMM  |J. of Molclr Grphcs & Modelling
>    JJ     MM M MM  GG GGGG  MM M MM  |        Dept. of Chemistry
> JJ JJ    MM  M  MM  GG GG  MM  M  MM |  Univ. of Missouri-Kansas City
>   JJ                 GGG             |      Kansas City, MO  64110
>                                      |        holdera-$-umkc.edu
>    Published by Elsevier Science     | (816)235-2293 * (816)235-6543F
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> 
> 
> 
>


From owner-chemistry@ccl.net Wed Oct 12 19:28:00 2005
From: "Evgeniy Gromov Evgeniy.Gromov##tc.pci.uni-heidelberg.de" <owner-chemistry[*]server.ccl.net>
To: CCL
Subject: CCL: Amber calculations with Gaussian
Message-Id: <-29573-051012130457-11527-Qj1WzHyQlW1gy+pdwTTiRg[*]server.ccl.net>
X-Original-From: Evgeniy Gromov <Evgeniy.Gromov-x-tc.pci.uni-heidelberg.de>
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Date: Wed, 12 Oct 2005 19:04:29 +0200
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Sent to CCL by: Evgeniy Gromov [Evgeniy.Gromov]|[tc.pci.uni-heidelberg.de]
Dear All,

I have a question concerning Amber type (molecular mechanics)
calculations using Gaussian03. Does anybody know some (free) soft
(except for GaussView) which allows one to specify automatically
all necessary for Amber input information (i.e. the type of
hybridization, partial charge etc. for all atoms) in the format
required by Gaussian. Thanks.

Best,
Evgeniy

-- 
_______________________________________
Dr. Evgeniy Gromov
Theoretische Chemie
Physikalisch-Chemisches Institut
Im Neuenheimer Feld 229
D-69120 Heidelberg
Germany

Telefon: +49/(0)6221/545263
Fax: +49/(0)6221/545221
E-mail: evgeniy(-)tc.pci.uni-heidelberg.de
_______________________________________


From owner-chemistry@ccl.net Wed Oct 12 20:03:00 2005
From: "Perry E. Metzger perry()piermont.com" <owner-chemistry#server.ccl.net>
To: CCL
Subject: CCL: Compilation troubles
Message-Id: <-29574-051012180140-21625-MenNq8NChWvvzYZvuLy7oQ#server.ccl.net>
X-Original-From: "Perry E. Metzger" <perry~~piermont.com>
Content-Type: text/plain; charset=us-ascii
Date: Wed, 12 Oct 2005 18:01:32 -0400
MIME-Version: 1.0


Sent to CCL by: "Perry E. Metzger" [perry++piermont.com]

> Did anyone compile gaussian03 with g77 ? I have only the first executable,
> but all the .exe are not build, because of some undefined references. I try
> to compile the source code on a PC Xeon with redhat 9.
> Many thanks in advance for any kind of hep and any tip that could help me
> (makefile and flags to share).

Hi!

In general, undefined references are caused by a failure in the link
command line to refer to all needed pieces of software, but without
the actual error information it is difficult to answer in your
specific case.

In order to make it easier to help with answering questions like this,
it is helpful if you post a transcript (or an edited transcript) of
the compile, and if you give us information on the versions of the
software you are trying to use.

To produce an accurate transcript, I suggest you either redirect both
stdout and stderr to a file, like this:

  make >make.out 2>&1

This will produce a full transcript of the compile, called "make.out"
(You can learn more about redirection commands in the man page for the
standard linux shell, via "man bash"). BTW, that works for any
command, not just "make".

Alternatively, you can use the "script" command ("man script" for
details). "script" is especially helpful if you are posting about
problems with an interactive command.

Versions of all the things you are using can, as I said, be
helpful. Most of the gcc based compile tools on Linux will tell you their
version numbers if you ask like this:

g77 --version

or

gcc --version

The version of the software you are compiling is also often quite
important, as well as how you set it up to compile.

By the way, on linux, you don't generally think of it as a ".EXE" file
since linux does not use the Microsoft .EXE convention. It is better
to call your .o files "object files" or ".o files", and your final
liked executable simply "the executable".

Perry


From owner-chemistry@ccl.net Wed Oct 12 20:38:00 2005
From: "David J Anick david.anick[a]rcn.com" <owner-chemistry||server.ccl.net>
To: CCL
Subject: CCL: Frequency scaling factor!
Message-Id: <-29575-051012141319-27540-GEcRoDcxk3esp/mdQRMMMQ||server.ccl.net>
X-Original-From: "David J Anick" <david.anick:-:rcn.com>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain;
	charset="iso-8859-1"
Date: Wed, 12 Oct 2005 12:17:33 -0400
MIME-Version: 1.0


Sent to CCL by: "David J Anick" [david.anick() rcn.com]
If you have not already done so, check out
http://srdata.nist.gov/cccbdb/
Click on Item XIII - Vibrations (left column) and then
you will see links for "C. Vibrational Frequency scaling factors".

Peace,
David Anick PhD MD
Harvard Medical School

----- Original Message ----- 
> From: "Bende Attila bende|s3.itim-cj.ro" <owner-chemistry-#-ccl.net>
To: "Anick, David " <david.anick-#-rcn.com>
Sent: Wednesday, October 12, 2005 6:52 AM
Subject: CCL: Frequency scaling factor!


>
> Sent to CCL by: Bende Attila [bende,;,s3.itim-cj.ro]
> Hi everybody!
>
> I would appreciate if you could give me some detailed lists or articles
about
> vibrational frequency scaling factor values.
> ex. Method (DFT, ab initio) / Basis set / Scaling factor.
>
> In particularly, I'm interested in B3LYP/6-31G and B3LYP/6-31G** cases,
but
> also for other case could come in useful for me.
>
> Thanks in advance
>
> -- 
> Dr. Bende Attila (PhD)
> Senior Researcher III
>
> ***********************************************************************
> National Institute of R&D of Izotopic and Molecular Tehnology
> Str. Donath nr.71-103, P.O.Box 700
> Cluj-Napoca, Ro-400293, Romania
> Phone:+40-264-584037, int 216, Fax: +40-264-420042
> e-mail: bende:-:s3.itim-cj.ro, AttlBende:-:yahoo.co.uk
> web page: http://w3.itim-cj.ro/~bende
> ***********************************************************************>


From owner-chemistry@ccl.net Wed Oct 12 21:34:00 2005
From: "Prashanth Athri athriprashanth++yahoo.com" <owner-chemistry##server.ccl.net>
To: CCL
Subject: CCL: Amber calculations with Gaussian
Message-Id: <-29576-051012212713-9393-DJo1GWZe79Xwe0xyo9VyTQ##server.ccl.net>
X-Original-From: Prashanth Athri <athriprashanth[A]yahoo.com>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=iso-8859-1
Date: Wed, 12 Oct 2005 18:27:04 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: Prashanth Athri [athriprashanth{:}yahoo.com]
I believe RED or XRED (w GUI) is free and does whats
needed.

http://www.u-picardie.fr/labo/lbpd/RED/

--- "Evgeniy Gromov
Evgeniy.Gromov##tc.pci.uni-heidelberg.de"
<owner-chemistry=-=ccl.net> wrote:

> 
> Sent to CCL by: Evgeniy Gromov
> [Evgeniy.Gromov]|[tc.pci.uni-heidelberg.de]
> Dear All,
> 
> I have a question concerning Amber type (molecular
> mechanics)
> calculations using Gaussian03. Does anybody know
> some (free) soft
> (except for GaussView) which allows one to specify
> automatically
> all necessary for Amber input information (i.e. the
> type of
> hybridization, partial charge etc. for all atoms) in
> the format
> required by Gaussian. Thanks.
> 
> Best,
> Evgeniy
> 
> -- 
> _______________________________________
> Dr. Evgeniy Gromov
> Theoretische Chemie
> Physikalisch-Chemisches Institut
> Im Neuenheimer Feld 229
> D-69120 Heidelberg
> Germany
> 
> Telefon: +49/(0)6221/545263
> Fax: +49/(0)6221/545221
> E-mail: evgeniy:_:tc.pci.uni-heidelberg.de
> _______________________________________
> 
> 
> 
> -= This is automatically added to each message by
> the mailing script =-
> To recover the email address of the author of the
> message, please change
> the strange characters on the top line to the =-=
> sign. You can also
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> header.> 
> E-mail to administrators: CHEMISTRY-REQUEST=-=ccl.net
> or use> 
> Before posting check wait time for next message at:
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> check:> 
> 
> 
> 



		
__________________________________ 
Start your day with Yahoo! - Make it your home page! 
http://www.yahoo.com/r/hs


From owner-chemistry@ccl.net Wed Oct 12 22:57:00 2005
From: "John McKelvey jmmckel*|*attglobal.net" <owner-chemistry---server.ccl.net>
To: CCL
Subject: CCL: RE: Where can you publish articles on software?
Message-Id: <-29577-051012201825-15805-LETqQT79bGkHW8V1k+WUMQ---server.ccl.net>
X-Original-From: John McKelvey <jmmckel*attglobal.net>
Content-Transfer-Encoding: 7bit
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Date: Wed, 12 Oct 2005 19:16:03 -0500
MIME-Version: 1.0


Sent to CCL by: John McKelvey [jmmckel]-[attglobal.net]
Folks,

Am I wrong on this: Didn't Tom Ziegler, or someone, publish a nice 
article on ADF a while ago?  Gave a lot of insight to  a very credible 
code!!!

Cheers,

John McKelvey


Warren DeLano warren_-_delsci.com wrote:

>Sent to CCL by: "Warren DeLano" [warren(~)delsci.com]
>
>  
>
>>Sent to CCL by: "Andy  Holder" [holdera%umkc.edu]
>>    
>>
>
>Ironically, JMGM editor Andy Holder offers compelling reasons for why
>developer-scientists should shift their attention away from
>closed-access journals like JMGM and toward peer-reviewed
>open-access/open-source venues that better serve the overall needs of
>the field.
>
>  
>
>>I am the editor of the Journal of Molecular Graphics and Modelling, 
>>and we specifically EXCLUDE program announcements/descriptions from 
>>our pages.  Programs are not original research, but may be 
>>implementations of original research.
>>    
>>
>
>This fails to acknowledge the critical enabling role of software in
>computational chemistry and conveys a shockingly dismissive view of the
>original research aspects of computer programs!  To put it as politely
>as I can, I most vehemently disagree.  Such comments insult and demean
>the creative efforts of those who might have otherwise considered
>publishing papers in JMGM.
>
>  
>
>>The data from JMGM indicate that our IF went DOWN 
>>when we included these item and has been steadily increasing since we 
>>eliminated them.
>>    
>>
>
>Effective running software is at least as impactful as algorithmic
>descriptions, if not more so.  (We live in real buildings, not
>architectural plans; we travel by plane, not via designs of planes).
>"Impact Factor" (I.F.) in terms of follow-on citations has little
>relevance as a measure of impact for scientific software and especially
>so once usage becomes widespread (e.g. ChemDraw, RasMol, Excel, etc.).
>Speaking from personal experience, recognizable PyMOL images are now
>routinely found in Science, Nature, C&EN, and many other journals, but
>such usage is rarely cited.  So what is PyMOL's impact factor?  Zero! It
>has never been officially "published" per se, even though its source
>code has been published continuously on the internet since early 2000.
>
>  
>
>>The algorithm is perhaps worthy of
>>publication, and the program can certainly be mentioned, but is not in
>>    
>>
>
>  
>
>>and of itself worthy of the valuable space in a research journal.
>>    
>>
>
>Such comments reflect little "editorial" sympathy for the
>publish-or-perish plight faced by academic scientists who develop
>practical algorithms in the form of working software programs instead of
>abstract algorithms in the form of non-working descriptive publications.
>Without such publications, the impact of developer-scientists is
>invisible to tenure review committees and funding agencies.  That is
>unfair to many scientists and damaging to the field as a whole since
>better research software is very much needed.  Developer-scientists need
>to be appropriately recognized and rewarded through career advancement,
>and thus it is not by accident that so many talented scientific software
>developers have chosen the private sector over the academic world.  The
>system of academic credit is largely broken with respect to creation of
>quality research software.
>
>While JMCM may indeed have a fine "editorial" policy on this matter, it
>is justified for the wrong reasons.  
>
>Programs cannot truly be "published" in traditional journals because
>they are too complex to describe precisely in such venues.  A standalone
>print article does not deliver reproducibility and verifiability with
>respect to research software.  Thus, journal articles describing
>software do not meet fundamental requirements of the scientific method.
>
>The only way to publish software in a scientifically robust manner is to
>share source code, and that means publishing via the internet in an
>open-access/open-source fashion.  Anything short of that amounts to
>issuing unproven claims based on limited empirical tests regarding what
>a given program allegedly does.  What is that called outside of science?
>Advertising!  And as such, I agree that it does not belong in a
>scientific journal.  Either you publish software with source code and
>stand behind it, or you are blowing smoke and quite *literally* hiding
>something -- no matter how noble your intent.
>
>  
>
>>Being a former member of the Dewar group, they certainly published a 
>>large number of papers on semiempirical methods, but never published 
>>any article on AMPAC itself.
>>    
>>
>
>Such comments confirm the notion that research software developers are
>not recognized for the critical enabling contributions they make, and
>reveal just how incapable the old closed-access, print-journal
>publication system is of meeting current needs.
>
>So, go live fellow research software developers, go live!  Bypass an
>inadequate and obsolete system, and instead pursue internet-based
>open-access/open-source publishing of your work.  If you lead, the world
>will follow.
>
>http://www.plos.org , http://www.doaj.org ,
>http://pubchem.ncbi.nlm.nih.gov , http://www.blueobelisk.org ,
>http://www.chmoogle.com , http://www.sf.net , etc.
>
>Cheers,
>Warren
>
>--
>Warren L. DeLano, Ph.D.                     
>Principal Scientist
>
>. DeLano Scientific LLC  
>. 400 Oyster Point Blvd., Suite 213           
>. South San Francisco, CA 94080 USA   
>. Biz:(650)-872-0942  Tech:(650)-872-0834     
>. Fax:(650)-872-0273  Cell:(650)-346-1154
>. mailto:warren%x%delsci.com      
>
>  
>
>>-----Original Message-----
>>From: owner-chemistry%x%ccl.net [mailto:owner-chemistry%x%ccl.net]
>>Sent: Tuesday, October 11, 2005 4:46 PM
>>To: Warren DeLano
>>Subject: CCL: W:CCL: Where can you publish articles on software?
>>
>>
>>Sent to CCL by: "Andy  Holder" [holdera%umkc.edu] In reply to:
>>
>>    
>>
>>>This programme is surely useful, but the editors of
>>>      
>>>
>>research journals
>>    
>>
>>>would probably not accept it for publication. If this kind
>>>      
>>>
>>of article
>>    
>>
>>>is acceptable, I guess that many people would produce tons of 
>>>technical programmes
>>>      
>>>
>>>>This is exactly what I think *should* be encouraged! If we look at 
>>>>bioinformatics, the latest issue of "BMC Bioinformatics" has 7 
>>>>software articles (this journal has an impact factor of 5.42); the 
>>>>latest issue of "Bioinformatics" has 9 'Application Notes' (this 
>>>>journal has an impact factor of 5.74). There is a real interest in 
>>>>useful software that can make it easier to do science.
>>>>        
>>>>
>>I am the editor of the Journal of Molecular Graphics and Modelling, 
>>and we specifically EXCLUDE program announcements/descriptions from 
>>our pages.  Programs are not original research, but may be 
>>implementations of original research.
>>
>>Being a former member of the Dewar group, they certainly published a 
>>large number of papers on semiempirical methods, but never published 
>>any article on AMPAC itself.  These programs were even run on just a 
>>few examples of "suitable data of interest"!  The algorithm is perhaos
>>    
>>
>
>  
>
>>worthy of publication, and the program can certainly be mentioned, but
>>    
>>
>
>  
>
>>is not in and of itself worthy of the valuable space in a research 
>>journal.
>>
>>Comparison to various other journals with high impact factors is 
>>anecdotal at best.  The data from JMGM indicate that our IF went DOWN 
>>when we included these item and has been steadily increasing since we 
>>eliminated them.  But that could also have been for a number of other 
>>reasons.
>>
>>My 0.02.
>>
>>Regards, Andy Holder
>>
>>-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- 
>>JJJJJJJJ MMM   MMM   GGG   MMM   MMM |        ANDREW J. HOLDER
>>   JJ     MM   MM   GG GG   MM   MM  |              Editor
>>   JJ     MMM MMM  GG       MMM MMM  |J. of Molclr Grphcs & Modelling
>>   JJ     MM M MM  GG GGGG  MM M MM  |        Dept. of Chemistry
>>JJ JJ    MM  M  MM  GG GG  MM  M  MM |  Univ. of Missouri-Kansas City
>>  JJ                 GGG             |      Kansas City, MO  64110
>>                                     |        holdera-$-umkc.edu
>>   Published by Elsevier Science     | (816)235-2293 * (816)235-6543F
>>-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
>>
>>
>>
>>-= This is automatically added to each message by the mailing script 
>>=- To recover the email address of the author of the message, please 
>>change the strange characters on the top line to the %x% sign. You can 
>>also> 
>>-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
>>-+-+-+-+-+>
>
>
>
>  
>


From owner-chemistry@ccl.net Wed Oct 12 23:32:01 2005
From: "Faisal Rahman s101alif ~~ mail.chem.itb.ac.id" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL: W:How to calculate the BSSE Correction
Message-Id: <-29578-051012231143-5593-MqiLeptf2pgZpabwFjDh6w+*+server.ccl.net>
X-Original-From: "Faisal  Rahman" <s101alif{=}mail.chem.itb.ac.id>


Sent to CCL by: "Faisal  Rahman" [s101alif ~ mail.chem.itb.ac.id]
Hi everybody ...

I'am a newbie here ...
I'am an undergraduate student of Chemistry Department of Bandung Institute of Technology. I'am doing my Final project, studying hydrogen bond between DNA Bases and HCl using DFT,MP2 and HF method using 6-31++G** basis set, using gaussian 03. I Have a problem with the BSSE correction. I don't know how to calculate it.
For example,  I get confused  to calculate the interaction energy that corrected with BSSE of complex adenine and HCl.So what should i do ... Could anyone tell me ... 
I ever read an article about BSSE, It tell that the correction of interaction energy can be done by calculate every singel molecule with the basis of other molecule. could anyone give the example of input file of gaussian to calculate the HCl energy on the basis of adenine or to calculate adenine on the basis of HCl?
Thank's before ...
I would very approciate it


Faisal Rahman
Chemistry Department of Bandung Institute of Technology