From chemistry-request@ccl.net Wed Aug  4 19:56:46 2004
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From: john <jmmckel<<at>>attglobal.net>
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To: Tapas Kar <tapaskar<<at>>cc.usu.edu>
CC: CCL <chemistry<<at>>ccl.net>
Subject: Re: CCL:SCF Convergence problem in G03
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There may be several issues/approaches, IMHO

First, look at the initial gues around the homo-lumo gap..  Are there
unfilled orbitals that are essentially degenerate with orbitals to be
filled?  If so a single determinate solution may not work.... and bad
convergence would not be a surprise

Second, if the above is not the case, then start off using a lower level
of theory and/or basis sets, and see if that will converge...  SCF
convergence can be more art than science..

Roothan did not guarantee us SCF convergence, only the right to try.

:-)  Regards,

John McKelvey


Tapas Kar wrote:

> Hi experts,
>
> I am getting SCF convergence problem with single-point calculations on
> large C200-O3 to C260-O3 systems using B3LYP/6-31G* basis in G03. I
> tried vshift=300, SCF=QC  and different guess with no luck. Also tried
> anion(-2) and cation (+2)of the same.  Energy is highly oscillating >
> from one step to other, even +/- 20au. Is there any option in G03 to
> get my job done. Gamess looks don t allow more than certain number of
> basis functions.
>
> Thanks
>
> Tapas
>
>
> -------------------------------------------------------------------------------
>
> "We owe a lot to the Indians, who taught us how to count, without
> which no worthwhile scientific discovery could have been made."
>                                            - Albert Einstein -
>
> -------------------------------------------------------------------------------
>
> Tapas Kar, Ph. D
> Department of Chemistry & Biochemistry
> UtahStateUniversity
> Logan, UT84322-0300
> Tel: 435-797-7230
>
> Fax: 435-797-3390
> Email: tapaskar<<at>>cc.usu.edu
> Web: http://www.chem>.usu.edu/faculty/Tapas/index.html
>          http://www.chem.usu>.edu/~tapaskar/index.html
>



From chemistry-request@ccl.net Thu Aug  5 03:33:26 2004
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From: Wai-To Chan <chan{at}curl.gkcl.yorku.ca>
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Subject: SCF Convergence problem in G03
To: chemistry{at}ccl.net
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<<<<<<
I am getting SCF convergence problem with single-point calculations on large
C200-O3 to C260-O3 systems using B3LYP/6-31G* basis in G03. I tried
vshift=300, SCF=QC  and different guess with no luck. Also tried anion(-2)
and cation (+2)of the same.  Energy is highly oscillating from one step to
other, even +/- 20au. Is there any option in G03 to get my job done. Gamess
looks don't allow more than certain number of basis functions.
>>>>>

   If the cause of the convergence problem is small spacing 
between the LUMO and HOMO you may instead of using 
VSHIFT try using the Hartree-Fock method 
which tend to give larger HOMO-LUMO gap first. If HF 
works you can use the HF orbitals as the initial guess for a BHandHLYP 
single point job followed by B3LYP. There are different variations 
you can try like starting with 6-31G and then enlarge it to 
6-31G*. 

  As for GAMESS not being able to handle the size of your system 
is it just some parameter to reset to increase the basis size limit?
My experience is that GAMESS has more power SCF convergence 
accelerator but you have to be patient with extensive experimentation. 
For an oscillating SCF problem I will first try the damping
method with DIIS deactivated. 
 

  It looks like your system may be vulnerable to spin-symmetry
breaking if the O3 group is a diradical. In that case I can imagine 
how difficult SCF convergence can be for a system of such size. 

Wai-To Chan 


From chemistry-request@ccl.net Thu Aug  5 05:42:40 2004
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From: "Peter Gannett" <pgannett:at:hsc.wvu.edu>
To: <chemistry:at:ccl.net>, <JPandey:at:chla.usc.edu>
Subject: Re: CCL:Download of libraries
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Jaya:

Several can be found at:

http://dtpws4.ncifcrf.gov/docs/3d_database/dis3d.html 

There are about 400,000 compounds in the database.  

Pete Gannett

>>> "Pandey, Jaya" <JPandey:at:chla.usc.edu> 8/4/2004 1:58:35 PM >>>
Dear All,

Can someone tell me a source of downloading libraires for screening
with the
docking tools?

Thanks,

Jaya




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From chemistry-request@ccl.net Thu Aug  5 02:48:54 2004
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Subject: G03: LANL2DZ basis set for Se Te...
To: chemistry/at/ccl.net
Date: Thu, 5 Aug 2004 03:53:14 -0400 (EDT)
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<<<<<<<<<<<
Hello CCLers

I get the following warning while using LANL2DZ basis set for Se or
(Te) atom  in Gaussian 03.

" Warning!  Se atom    1 may be hypervalent but has no d functions."

In the Gaussian book (Exploring Chemistry.. Foresman and Frisch) I saw
something about  adding diffuse functions manually with a file called
"plus.gbn"

do I have to add  d functions manually?  or is the LANL2DZ basis set
good enough. I am mainly interested in the structure of molecules like
(H2SeO4)

I saw a thread titled "generating or augmenting basis sets" from last
year on ccl.net but could not find the answer. Thanks a lot for your
help
>>>>>>>>>>>>>

  I've used ECP basis sets like lanl2dz and SDD for transition metal
and main group elements. I don't recall ever seeing messages
like this. I guess the warning is caused by the unsually large number
atoms linked to the Se atom.  

  I've read reports of lanl2dz calculations involving augmentation
of the ECP basis with polararization and diffuse function. But 
I can't think of a source of the additional basis functions to
use. Gaussian has full-electron basis set like 6-31+G(d,p) 
for Se but I don't know if transferring the d function to 
lanl2dz is a good idea.

In case that is what you want the way 
to do this is simply using the option "extrabasis" to 
add the extra basis functions to the specified 
atom. The older versions of gaussian come in with 
a basis set library which you can easily look up for the 
exponents of the polarization and diffuse functions.
With the recent versions you have to extract the basis
set information manually. 

  As an illustraction if I want to augment Se with 
the d function from 6-311G** I will first run a job like 

rhf/6-311G(d,p) gfinput (or gfprint) 

on the above molecule. The gfinput option will
print out the basis set details in a convenient 
format.  I will then run a job like 

rhf/lanl2dz extrabasis 

  This extrabasis option requires you to append the
basis function details to the end of your input file. 

  Without any augmentation lanl2dz and SDD will use the 
D95 basis set for the light atoms. So you may consider 
the use of polarization functions
> from D95** instead of 6-31+G* or 6-311+G*. My experience
is that augmentation of the light atoms alone with polarization 
functions from D95** generally results in significant improvement
of the performance of the ECP basis for geometry optimization 
particularly on the bond distance between the heavy
atom and the ligand. But I don't know what the appropriate approach
is for the augmentation of the heavy atom. 

Wai-To Chan


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The Nanotech Hub presents over the Internet the Program from the Pacific 
Rim Conference in Nanoscience, Broome, Australia to be held 7-12 September 
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From chemistry-request@ccl.net Thu Aug  5 15:29:03 2004
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From: Eric Hu <yhu_2003|at|yahoo.com>
Subject: peptide conformational search
To: chemistry|at|ccl.net
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Hi, I have a synthesized 21-mer polypeptide. There is
a confirmed disulfide bond at the C-terminus and could
be a beta turn somewhere. To my best understanding,
Monte Carlo search would be a good starting point. Are
there any more systematical approaches and softwares
to predict possible conformation or at least provide
several resonable guesses? Thanks.

Eric

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From chemistry-request@ccl.net Thu Aug  5 16:01:49 2004
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Reply-To: <mark|at|arguslab.com>
From: "Mark Thompson" <mark|at|arguslab.com>
To: <chemistry|at|ccl.net>
Subject: ArgusLab updated licenses
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We have updated the license date in the latest ArgusLab 4.0 beta installer
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Take care,
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*********************************
Mark Thompson
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From chemistry-request@ccl.net Thu Aug  5 10:23:29 2004
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Subject: RI-BLYP vs B3LYP
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Hello..

Has anyone benchmarked RI-BLYP vs B3LYP?  There is some evidence that
RI-BLYP is significantly faster than B3LYP using cc-TVZ.  My
observations for 6-31G*/5D so far is only slightly better that a factor
of two...  All runs have been done on a single Xeon processor.

Any thoughts on this?

Thanks!

John McKelvey



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CHEMAXON ANNOUNCES FREE SOFTWARE FOR THE ACADEMIC COMMUNITY VIA THE 
JCHEM AND MARVIN ACADEMIC PACAKGE

Budapest, Hungary: ChemAxon, a software solutions provider for life 
sciences today announced free licenses for Marvin and JChem toolkits for 
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Academic Package program.

ChemAxon's Academic Package is a community driven effort to enable 
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educational institutions, with some restrictions, successful applicants 
will receive free licenses to all ChemAxon's toolkits. The program aims 
to give schools and universities the basic tools to develop interactive 
chemistry teaching resources and advanced tools to enable students and 
staff to perform original research from within a single powerful platform.

ChemAxon's Java based Cheminformatics toolkits include: Marvin for 
editing and viewing chemical structures, reactions and queries, 
Calculator Plugins for prediction of various properties based on 
structure, JChem Base for structure and reaction searching and database 
handling, JChem Cartridge for Oracle. database integration, Reactor for 
structure transformations and virtual synthesis, Screen for 
pharmacophore and structure based screening and other tools for the 
exploration of drug design.

"We believe there will be 2 main areas of interest; with Marvin and 
JChem Base to deliver cheminformatics platforms for online, offline 
campus wide chemistry teaching and our more focused toolkits to support 
original research" Ferenc Csizmadia, CEO of ChemAxon said, and added, 
"Our toolkits have benefited greatly from the relationships ChemAxon has 
enjoyed with educators and researchers since the beginning and this is a 
way to giving something back."


About ChemAxon
ChemAxon is a leader in providing Java based chemical software 
development platforms for the biotechnology and pharmaceutical 
industries. With core capabilities including; structure visualization 
and management, property predictions, virtual synthesis, screening and 
drug design, ChemAxon focuses upon active interaction with users and 
core portability to create powerful, cost effective cross platform 
solutions and programming interfaces to power modern cheminformatics and 
chemical communication.

For further information please visit www.chemaxon.com or contact: Alex 
Allardyce, Director of Communications on: +361 453 2660 or aa:at:chemaxon.com.

For link to this story please visit: 
http://www.prnewswire.com/cgi-bin/stories.pl?ACCT=104&STORY=/www/story/07-27-2004/0002219110&EDATE=

-- 
Alex Allardyce
Communications Director


Chemaxon Ltd
Maramaros kvz 3/a
Budapest, 1037 Hungary
Tel.: +361 4532658
Fax.: +361 4532659

e-mail: aa:at:chemaxon.com



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