From chemistry-request@ccl.net Fri Oct 24 06:12:11 2003
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From: Eugen Leitl <eugen[at]leitl.org>
To: chemistry[at]ccl.net
Subject: Re: CCL:Searchable Chemical Database - Substructures and Similarity
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On Thu, Oct 23, 2003 at 08:39:25AM +0200, Sorel.Muresan[at]astrazeneca.com wrote:
> Hi Don,
> 
> Try ChemNavigator at www.chemnavigator.com (you have to register).
> 
> You'll get access to more than 12 million chemical samples, a search
> interface, and all info to order compounds.
> 

Another commercial (free demo accounts) alternative which is somewhat
complementary to CAS is http://infochem.de 

SPRESIweb has 4.5 million organic and organo-metallic compounds,
searchable by structure, substructure and reaction; 3.5 million reactions
abstracted from 380000 references (including 98000 patents).

Disclaimer: I work for the company.

-- Eugen* Leitl <a href="http://leitl.org">leitl</a>
______________________________________________________________
ICBM: 48.07078, 11.61144 http://www.leitl.org
8B29F6BE: 099D 78BA 2FD3 B014 B08A  7779 75B0 2443 8B29 F6BE


From chemistry-request@ccl.net Fri Oct 24 04:18:15 2003
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From: =?UNKNOWN?Q?Rub=E9n?= Meana =?UNKNOWN?Q?Pa=F1eda?=
 <rubenmp~at~correo.uniovi.es>
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Dear CCLers,
I have technical problems with Molden and Linux. When I try changing 
value of z-matrix parameters on certain outputs of Gaussian I obtained 
this error:

X Error of failed request: BadWindow (invalid Window parameter)
  Major opcode of failed request:  2 (X_ChangeWindowAttributes)
  Resource id in failed request:  0x0
  Serial number of failed request:  2923
  Current serial number in output stream:  2924

Thanks in advanced











From chemistry-request@ccl.net Fri Oct 24 08:20:18 2003
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   =?iso-8859-1?Q?Chemistry_=28Correio_eletr=F4nico=29?= <chemistry{at}ccl.net>
Subject: CCL:RES: Help With Gaussian 98 Hindered Rotor Calculations
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Dear Jim,
Welcome to the club.
I too have had the same problem.
I am trying to do the same with propylbenzene radicals using HF and b3lyp
methods. In both cases where the radical center is on the end carbon or
middle carbon of the propyl chain G98 fails with the same message that you
are getting.
About a month ago I wrote to Douglas Fox at Gaussian

The answer was this:-

   Dr. Hovell,

   The option FREQ=ReadInfo is not implemented.  This functionality
is implemented as FREQ=ReadHindered or FREQ=ReadHind for short.  
The input is slightly different than the manual suggests,

VMAX 25.0
7 8 3 1 1

would set the barrier cutoff, between atoms 7 and 8, for a threefold
barrier with a symmetry number of 1 and only 1 well would be considered.
Repeat if further barriers need to be considered.

   I am doubtful that even getting this right will fix an error regarding
the number of degrees of freedom.  If problems persist please send
the input and the last 100 lines of the output file.
   
 Douglas J. Fox
  Technical Support
  Gaussian, Inc.
  help{at}gaussian.com

So I sent him a copy of my problem, I am still waiting for a reply. As far
as I know this is an old problem that has never been solved.
When I asked a similar question to the CCL group a while back. I received a
number of replies. Here there are, I have not yet tried all of their ideas
yet.


I have been running into similar problems with freq=hindered, in particular 
when there is a ring present.

I usually follow this procedure.
first look at the connectivity list (*.out) and check if there are no 
connection between next nearest neighbors. They have to be removed 
(geom=modred)
sometimes it is necessary to add some angles and dihedrals.
what helps for problems with ring structures is to "break" the ring 
structure using the connectivity list (remove a connection, angle, 
dihedral). Though this has no influence on the calculated properties (I 
guess so??) it does sometimes solve the problem with hindered rotors.

Just as a note: the hindered rotor method is not all that accurate-in some 
cases we found large deviations between a fully correct approach (using a 
calculated rotor PES and solving the corresponding 1D schrodinger equation 
for internal rotation) and the hindered rotor approach of gaussian.

For the more accurate approach you should look into the recent papers of 
Sumathy, Green et al. and Van Speybroeck, et al.
Some codes are available on the net, but you might want to contact the 
authors of the previous papers to obtain a version of their code.

Kind regards,
Mark Saeys
Laboratory for Petrochemical Engineering
Ghent University
Krijgslaan 281 (S5)
B9000 Gent
Belgium
tel: .32.(0)9.264.56.78
fax: .32.(0)9.264.49.99
http://lptnt01.rug.ac.be/chemical.engineering

	---------------------------------------

The only other things I can think of might be to use ub3lyp/6-31+G(d),
include nosymm keyword and maybe reduce the step size with IOp(1/8=n),
default is 30, use 5 maybe. I had some problems with some b3lyp optimsation
earlier this year. I got around the problem by performing scans with
HF/3-21G(d) and then capturing the coordinates and writing XYZ files for the
two minima and the highest point on the scan. Then I wrote a QST3 file with
b3lyp keyword and the calculation then behaved! 

Have you tried a opt=stable calculation to check that you have a sensible
wavefunction? You could maybe constrain some geometries, as in fix the
aromatic ring ( fix dihedrals to zero around the carbons in the aromatic
ring ) to be flat and then run the optimisation again. 

These are just ideas and you might think I am mad.

James Robinson [prsjjr{at}bath.ac.uk]

	 ------------------------------------------

 I don't know if this would work, but maybe adding nosymm would help?  

	--Shobe, Dave [dshobe{at}sud-chemieinc.com]  
	 ----------------------------------- 

try ub3lyp/6-31+G(d) single point to see if that convergences.

	James Robinson [prsjjr{at}bath.ac.uk]

	----------------------------------
Hello,

I don't know just what causes your problem, but I have heard that diffuse
(+)
functions can sometimes be a pain. Plus functions are probably not needed
for
propylbenzene (it is not an anion), and also, for DFT (unlike ab initio)
going
beyond 6-31G* tends to give little or no improvement:
J Phys Chem A, 1997, 101, 208
J Phys Chem 1994, 98, 11623

elewars [elewars{at}trentu.ca]

---------------------------------

The experimentally determined sixfold "barrier" for the 'hindered' rotation
in toluene is 5 cm^-1 (0.014 kcal/mol!!!) in the s0 state - not really a
barrier at all! It is 25 cm^-1 in the S1 electronically excited state.
[J. Mol. Spect. 97 (1983) 186]

I doubt that it is possible to calculate a barrier accurately which ist as
low as these numbers are. But perhaps you can try just to calculate the
barrier height from two single points at the min and max value, take the
internal methyl rotor rotational constant from the vibrational analysis and
calculate the contribution to the partition function from the internal
rotor quantum mechanical problem.

Regards
Wolfgang Roth [Wolfgang.Roth1{at}epost.de]


-------------------------------------

Thanks for forcing me to produce this short summary. Even if it is
inconclusive at the moment. If you find a solution to this problem please
let me know.

 
Ian Hovell - Ph.D. 
NUCLEO DE MODELAGEM MOLECULAR-NMM 
Centro de Tecnologia Mineral - CETEM 
Ministerio da Cijncia e da Tecnologia- MCT 
Avenida Ipj, No 900 - Cidade Universitaria 
Ilha do Fundco Rio de Janeiro RJ Brasil 
CEP 21941-590 
tel 00 55 (xx) 3865 7344 ou 3865 - 7216 
Fax 00 55 (xx) 22602837 ou 2290-4286 
e-mail hovell{at}cetem.gov.br 




From chemistry-request@ccl.net Fri Oct 24 12:37:46 2003
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From: "Phil Hultin" <hultin[at]cc.UManitoba.CA>
To: "Computational Chemistry List" <chemistry[at]ccl.net>
Subject: Advertising
Date: Fri, 24 Oct 2003 11:37:10 -0500
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Is it just me, or do others agree that commercial advertising such as recent
postings from David Gallagher have no place on CCL?

I have observed an increase in the number of commercial advertisements (as
distinct from comments suggesting that one program/product does a particular
task better or worse than another, coming from persons with no direct
connection to the products in question) over the last year or so, and I
think this has no place on this discussion list.

I may be way off base on this, so what do others think?
Dr. Philip G. Hultin
Associate Department Head and
Associate Professor of Chemistry
University of Manitoba
Winnipeg, MB, Canada R3T 2N2
(vox) 204-474-9814
(fax) 204-474-7608
mailto:hultin[at]cc.umanitoba.ca
http://www.umanitoba.ca/chemistry/


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<BODY>
<DIV><FONT face=3DArial size=3D2><SPAN class=3D437383416-24102003>Is it =
just me, or do=20
others agree that commercial advertising such as recent postings from =
David=20
Gallagher have no place on CCL?</SPAN></FONT></DIV>
<DIV><FONT face=3DArial size=3D2><SPAN=20
class=3D437383416-24102003></SPAN></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2><SPAN class=3D437383416-24102003>I have =
observed an=20
increase in the number of commercial advertisements (as distinct from =
comments=20
suggesting that one program/product does a particular task better or =
worse than=20
another, coming from persons with no direct connection to the products =
in=20
question) over the last year or so, and I think this has no place on =
this=20
discussion list.</SPAN></FONT></DIV>
<DIV><FONT face=3DArial size=3D2><SPAN=20
class=3D437383416-24102003></SPAN></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2><SPAN class=3D437383416-24102003>I may =
be way off=20
base on this, so what do others think?</SPAN></FONT></DIV>
<P><FONT size=3D2>Dr. Philip G. Hultin<BR>Associate Department Head=20
and<BR>Associate Professor of Chemistry<BR>University of =
Manitoba<BR>Winnipeg,=20
MB, Canada R3T 2N2<BR>(vox) 204-474-9814<BR>(fax) 204-474-7608<BR><A=20
href=3D"mailto:hultin[at]cc.umanitoba.ca">mailto:hultin[at]cc.umanitoba.ca</A><=
BR><A=20
href=3D"http://www.umanitoba.ca/chemistry/"=20
target=3D_blank>http://www.umanitoba.ca/chemistry/</A> </FONT></P>
<DIV>&nbsp;</DIV></BODY></HTML>

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From chemistry-request@ccl.net Fri Oct 24 12:12:10 2003
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Date: Fri, 24 Oct 2003 17:11:36 +0100 (BST)
From: Val Gillet <V.Gillet~at~sheffield.ac.uk>
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To: chemistry~at~ccl.net
Subject: CCL: REMINDER: Call for papers: Chemoinformatics Sheffield 2004
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Closing date 31st October, 2003.

                       Call For Papers

The Chemical Structure Association Trust and the Molecular Graphics and 
Modelling Society announce their Third Joint Sheffield Conference 
on Chemoinformatics.  The conference will be held in The Octagon Centre 
and Tapton Hall of Residence, University of Sheffield, UK,
> from 21st to 23rd April 2004. Offers of papers are welcomed in all 
aspects of chemoinformatics. Possible topics include (but are not limited
to): 

* High-Throughput Screening including: assay QC and its influence on data 
	mining; design of screening collections; systems based design

* Virtual Screening including: docking and pharmacophore analysis;
	similarity methods; clustering

* Computational Methods for Lead Identification and Optimisation
	including: structure-activity methods; structure-based design

* New Algorithms and Technologies including: machine learning algorithms; 
	data handling and visualisation

* Case histories incorporating any of the above

Authors wishing to submit a paper for consideration should 
send a title and abstract to Val Gillet (v.gillet~at~sheffield.ac.uk) 
by 31st October 2003. Submissions will be selected as either oral
contributions or posters by the Organising Committee. In selecting
papers for oral presentation we will seek to achieve a balance between
new methodologies and successful applications of methods. 
Further details of the conference and registration information will follow
later in the year and will be posted at cisrg.shef.ac.uk/shef2004.












From chemistry-request@ccl.net Fri Oct 24 10:10:53 2003
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Date: Fri, 24 Oct 2003 11:10:17 -0300
From: Joey Harriman <s808o~at~unb.ca>
To: CCL posting <chemistry~at~ccl.net>
Subject: Implicit MD simulations in AMBER
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Hi everyone,

I am currently in the process of running some implicit MD simulations in Amber7.  As far
as I can tell the only flags that need to be included in the MD input file are:
gbsa=1
igb=1
extdiel=***

Can anyone confirm this?  In addition, I am trying to do a MD simulation on a ligand in
Toluene (extdiel=2.4)...are there any suggestions to make this calculation faster?  I
am currently usine SHAKE 2 for the calculations.

Thanks in advance for your response,
Joey Harriman
----------------------------------
Joey Harriman
MSc Computational Chemistry
University of New Brunswick
Room 228
Toole Hall
s808o~at~unb.ca
476-6543
----------------------------------


From chemistry-request@ccl.net Fri Oct 24 14:26:56 2003
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Date: Fri, 24 Oct 2003 14:25:45 -0400 (EDT)
From: "Dr. Jan K Labanowski" <jkl-.at.-ccl.net>
To: chemistry-.at.-ccl.net
cc: "Dr. Jan K Labanowski" <jkl-.at.-ccl.net>, hultin-.at.-cc.UManitoba.CA
Subject: Re: Advertising
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> Is it just me, or do others agree that commercial advertising such as recent
> postings from David Gallagher have no place on CCL?

The rules of CCL commercial advertizing are as follows:
-----------------------------
http://www.ccl.net/chemistry/aboutccl/rules/index.shtml

Commercial Announcements

 If you wish to submit a commercial announcement to the list, please respect
 the following rules:

  Be brief -- Short (25 lines or less) commercial postings are allowed of
  they are relevant to CCL community.

  Be straightforward -- The subject line should be straightforward.

  No reposting -- Reposts of software announcements are not permitted
  unless new features/releases become available.

  No "vaporware" -- Announcements of "vaporware" (software that is
  not yet working/available), and invitations to expositions and trade
                      shows at meetings are not allowed.

  No job advertisements (to list)
-----------------------------

The rules (as many other things in life) are a compromise at which
we arrived early in the list operation.
My personal thinking is that commercial software is commonly used
by computational chemists, and some important announcements should
reach the CCL. Availability of new products and a short summary of their
capabilities should be welcome. At the same time, I would not like to see
price incentives discussed on CCL.

Jan

Jan K. Labanowski         |  phone: 614-292-9279,  FAX: 614-292-7168
Ohio Supercomputer Center |  E-mail: jkl-.at.-ccl.net
1224 Kinnear Rd,          |  http://www.ccl.net/~jkl
Columbus, OH 43212-1163   |  http://www.ccl.net/    http://asdn.net/