From chemistry-request@ccl.net Mon Nov  8 09:47:31 2004
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From: Reynier Suardiaz del Rio <reynier_s:at:yahoo.com>
Subject: example for coupling constant calculation in G03
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Hi
Can anybody send me an example to calculate coupling constants for selected atoms rather than all at once, in G03 rev. C1 or C2?
I will apreciate any help
 Best
 
 RSR



 



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<DIV>Hi</DIV>
<DIV>Can anybody send me an example&nbsp;to calculate coupling constants for selected atoms rather than all at once, in G03 rev. C1 or C2?</DIV>
<DIV>I will apreciate any help<BR>&nbsp;Best<BR>&nbsp;<BR>&nbsp;RSR
<P><BR></P></DIV>
<DIV>&nbsp;</DIV><p><br><hr size=1><b>Do You Yahoo!?</b><br>
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From chemistry-request@ccl.net Sun Nov  7 23:19:03 2004
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Colleagues,

=20

When you carry out one experiment per week, you can store your results
on cards or in a paper notebook and analyze the numbers using a slide
rule.  When you run a thousand experiments per day, your requirements
change.  The results of your experiments are captured electronically and
the systems you used to query, browse and analyze your data better be
fast, organized and intelligent.

=20

At the American Chemical Society National Meeting next Spring in San
Diego (March 13-17, 2005) the Division of Chemical Information will
present a symposium on 'Informatics and High Throughput Experimentation'
and we are looking for speakers.

=20

Does your organization have a novel strategy for handling high
throughput experimental data?  Do you have an interesting application to
share?  An architecture you're working on?

=20

Please consider giving a talk at the symposium in San Diego!

=20

The best way to submit an abstract is online at http://oasys.acs.org/
The deadline for submissions in November 23, 2004.

=20

=20

If you have any questions or need help, please contact me at
mmiller/at/symyx.com or 801/569-1390.

=20

Thanks,

Mitch Miller

=20

=20

=20

Mitchell Miller, Ph.D.
Principal Software Engineer
Symyx Discovery Tools

Voice:      801 569-1390

 <mailto:mmiller/at/symyx.com> mmiller/at/symyx.com
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=20


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<p class=3DMsoNormal><font size=3D3 face=3DArial><span =
style=3D'font-size:12.0pt;
font-family:Arial'>Colleagues,</span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3DArial><span =
style=3D'font-size:12.0pt;
font-family:Arial'>&nbsp;</span></font></p>

<p class=3DMsoNormal style=3D'text-autospace:none'><font size=3D3 =
face=3DArial><span
style=3D'font-size:12.0pt;font-family:Arial'>When you carry out one =
experiment
per week, you can store your results on cards or in a paper notebook and
analyze the numbers using a slide rule.&nbsp; When you run a thousand
experiments per day, your requirements change.&nbsp; The results of your
experiments are captured electronically and the systems you used to =
query,
browse and analyze your data better be fast, organized and =
intelligent.</span></font></p>

<p class=3DMsoNormal style=3D'text-autospace:none'><font size=3D3 =
face=3DArial><span
style=3D'font-size:12.0pt;font-family:Arial'>&nbsp;</span></font></p>

<p class=3DMsoNormal style=3D'text-autospace:none'><font size=3D3 =
face=3DArial><span
style=3D'font-size:12.0pt;font-family:Arial'>At the American Chemical =
Society
National Meeting next Spring in </span></font><font face=3DArial><span
  style=3D'font-family:Arial'>San Diego</span></font><font =
face=3DArial><span
style=3D'font-family:Arial'> (</span></font><font
 face=3DArial><span style=3D'font-family:Arial'>March 13-17, =
2005</span></font><font
face=3DArial><span style=3D'font-family:Arial'>) the Division of =
Chemical
Information will present a symposium on &#8216;Informatics and High =
Throughput
Experimentation&#8217; and we are looking for =
speakers.</span></font></p>

<p class=3DMsoNormal style=3D'text-autospace:none'><font size=3D3 =
face=3DArial><span
style=3D'font-size:12.0pt;font-family:Arial'>&nbsp;</span></font></p>

<p class=3DMsoNormal style=3D'text-autospace:none'><font size=3D3 =
face=3DArial><span
style=3D'font-size:12.0pt;font-family:Arial'>Does your organization have =
a novel strategy
for handling high throughput experimental data?&nbsp; Do you have an
interesting application to share?&nbsp; An architecture you&#8217;re =
working
on?</span></font></p>

<p class=3DMsoNormal style=3D'text-autospace:none'><font size=3D3 =
face=3DArial><span
style=3D'font-size:12.0pt;font-family:Arial'>&nbsp;</span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3DArial><span =
style=3D'font-size:12.0pt;
font-family:Arial'>Please consider giving a talk at the symposium in =
</span></font><font
  face=3DArial><span style=3D'font-family:Arial'>San =
Diego</span></font><font
face=3DArial><span style=3D'font-family:Arial'>!</span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3DArial><span =
style=3D'font-size:12.0pt;
font-family:Arial'>&nbsp;</span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3DArial><span =
style=3D'font-size:12.0pt;
font-family:Arial'>The best way to submit an abstract is online at <a
href=3D"http://oasys.acs.org/">http://oasys.acs.org/</a>&nbsp; <b><span
style=3D'font-weight:bold'>The deadline for submissions in =
</span></b></span></font><b><font face=3DArial><span =
style=3D'font-family:Arial;font-weight:bold'>November 23, =
2004</span></font></b><b><font
face=3DArial><span =
style=3D'font-family:Arial;font-weight:bold'>.</span></font></b></p>

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

<p class=3DMsoNormal><font size=3D3 face=3DArial><span =
style=3D'font-size:12.0pt;
font-family:Arial'>&nbsp;</span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3DArial><span =
style=3D'font-size:12.0pt;
font-family:Arial'>If you have any questions or need help, please =
contact me at
<a href=3D"mailto:mmiller/at/symyx.com">mmiller/at/symyx.com</a> or =
801/569-1390.</span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3DArial><span =
style=3D'font-size:12.0pt;
font-family:Arial'>&nbsp;</span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3DArial><span =
style=3D'font-size:12.0pt;
font-family:Arial'>Thanks,</span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3DArial><span =
style=3D'font-size:12.0pt;
font-family:Arial'>Mitch Miller</span></font></p>

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

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

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

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Mitchell Miller, Ph.D.<br>
Principal Software Engineer<br>
Symyx Discovery Tools</span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Voice:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 801 =
569-1390</span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><a href=3D"mailto:mmiller/at/symyx.com"><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>mmiller/at/symyx.com</span></fo=
nt></a></span></font><font
size=3D2 face=3DArial><span =
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solely for
the intended recipient. If you are not the intended recipient, and have
received this message in error, please contact the sender immediately, =
permanently
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thereto.</span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
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From chemistry-request@ccl.net Mon Nov  8 03:24:47 2004
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Date: Mon, 8 Nov 2004 08:42:54 +0000
From: Phil Biggin <PHIL^at^biop.ox.ac.uk>
To: chemistry^at^ccl.net
CC: phil^at^biop.ox.ac.uk
Subject: conference announcement - membrane proteins
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            (vms).1041108084039.54405C-100000^at^fennel.biop.ox.ac.uk>
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Dear Colleagues,

I would like to draw your attention to a two-day conference organized
on behalf of the Molecular Graphics and Modelling Society:-

Membranes and Membrane Proteins
April 4-6th 2005
St Catz College, Oxford
http://indigo1.biop.ox.ac.uk/mgms2005/

Many thanks,

Phil Biggin


From chemistry-request@ccl.net Mon Nov  8 02:59:13 2004
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Date: Mon, 8 Nov 2004 09:12:08 +0100 (CET)
From: =?UTF-8?Q?Dirk_Cla=C3=9Fen-Houben?= <dirk.classen-houben^at^biovertis.com>
To: chemistry^at^ccl.net, sjm^at^le.ac.uk
Subject: Re: CCL:nmrcore/nmrclust
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Hi again,

meanwhile I've found the source code (for Linux) somewere, but I only
get error messages when I try to compile the program. Does anybody have
a running version on any linux system?

Regards, Dirk.

On Nov 05, 2004 09:23 AM, Dirk ClaC en-Houben
<dirk.classen-houben^at^biovertis.com> wrote:

> Hi everybody,
> 
> has anybody succesfully used nmrcore on a linux computer (redhat
> enterprise 3 WS). The program seems to be written for sgi irix and I
> get
> this error message:
> 
>     nmrcore: Exec format error. Wrong Architecture.
> 
> If anybody has a version running on linux please chare that one with
> me.
> 
> Thanks in advance for your help and kind regards, 
> 
> Dirk.
> 
> Dirk Classen-Houben
> BV Biotechnologies GmbH
> (Biovertis - information-driven drug design AG)
> Campus Vienna Biocenter 6
> 1030 Vienna, Austria
> 
> Phone +43-1-7989303-111
> Fax +43-1-7989303-400
> Email dirk.classen-houben^at^biovertis.com
> 
> 
> 
> 
> 
> 
> 
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> 
> 
> 
> 
Dirk Classen-Houben
BV Biotechnologies GmbH
(Biovertis - information-driven drug design AG)
Campus Vienna Biocenter 6
1030 Vienna, Austria

Phone +43-1-7989303-111
Fax +43-1-7989303-400
Email dirk.classen-houben^at^biovertis.com








From chemistry-request@ccl.net Mon Nov  8 13:55:25 2004
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Date: Mon, 8 Nov 2004 14:08:45 -0500 (EST)
From: "A. Boufarik" <aboufer2000.-at-.yahoo.ca>
Subject: Basis set quality metrics
To: "Comp. Chem. List" <chemistry.-at-.ccl.net>
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Hi all,
 
I am working on this project of a molecule subject to a static electric field and of course I use an extended basis set to allow for polarization. However, I would like to compare the suitability of 3 basis sets. Is there a set of quality metrics to check. For instance, I have read that for molecules under electric fields one such metrics is the polarizability. 
 
Are there other metrics since energy is no longer a good metric when using polarization orbitals.
 
Cheers
 
Boufarik 







---------------------------------
Post your free ad now! Yahoo! Canada Personals

--0-2067044528-1099940925=:14155
Content-Type: text/html; charset=us-ascii

<DIV>
<DIV>Hi all,</DIV>
<DIV>&nbsp;</DIV>
<DIV>I am working on this project of a molecule subject to a static electric field and of course I use an extended basis set to allow for polarization. However, I would like&nbsp;to&nbsp;compare the suitability of&nbsp;3 basis sets. Is there a set of&nbsp;quality&nbsp;metrics to check. For instance, I have read that for&nbsp;molecules under electric fields one such metrics is the polarizability.&nbsp;</DIV>
<DIV>&nbsp;</DIV>
<DIV>Are there other metrics since energy is no longer a good metric when using polarization orbitals.</DIV>
<DIV>&nbsp;</DIV>
<DIV>Cheers</DIV>
<DIV>&nbsp;</DIV>
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From chemistry-request@ccl.net Mon Nov  8 12:36:44 2004
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From: "Ross Walker" <ross[at]rosswalker.co.uk>
To: <chemistry[at]ccl.net>
Subject: RE: question about nitro groups in AMBER
Date: Mon, 8 Nov 2004 09:50:05 -0800
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Dear Ken,

> In AMBER each atom has a designated type which is defined to 
> set of parameters 
> in AMBER.  It appears that nitro groups are not able to be 
> characterized by 
> the existing atom type definitions.  Are NO2 groups able to 
> be studied with 
> AMBER?  

Yes, as long as you provide the missing parameters.

>Have the parameters for NO2 been determined 
> previously?  

I don't know if there are published parameters available, a literature
search may turn up some useful results. However, it should be fairly easy to
come up with your own parameters. Chapter 12 of the Amber 8 manual has a
section on parameter development. At a first guess you can simply calculate
equilibrium bond lengths and force constants from QM calculations. The same
with angles and dihedrals. As for charges this is a completely automated
method. See http://www.u-picardie.fr/labo/lbpd/RED/ for a program that will
do it for you.

You could also use the Generalised amber force field GAFF along with the
antechamber program that is provided with Amber8. The GAFF force field is
designed to study drug like molecules etc both in solution and in protein
environments. In this way you can do mixed simulations, e.g. using the FF99
amino acid force field for a protein and the GAFF force field for a
coenzyme...

>Is it 
> possible to define your own parameters manually and if so 
> how?  Is there a 
> systematic method to how parameters are defined in AMBER?  
> Any assistance 
> would be greatly appreciated.

You should check out the Amber tutorials
http://amber.scripps.edu/tutorial/index.html

You could also take a look at this 'provisional' tutorial which explains
how, once you have your parameters, you can use xleap to define non-standard
residues and build prmtop and inpcrd files for non-standard systems.
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four/index.htm

All the best
Ross

/\
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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross[at]rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |