From chemistry-request@ccl.net Thu Feb 12 00:32:01 2004
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Date: Thu, 12 Feb 2004 00:32:11 -0500
Subject: Re: CCL:J.Comp.Chem. Style File Needed
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Cc: chemistry|at|ccl.net
To: "Taras V. Pogorelov" <pogorelo|at|uiuc.edu>
From: Richard Gillilan <reg8|at|cornell.edu>
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In an earlier message I offered to make available a modified version of 
a bst
style file for Latex that does J. Comp. Chem. format. Now that I 
examine the
copyright header (achemso.bst), I see that I may not distribute the 
modified
form.  Sorry to those who have asked.  I may contact the copyright 
holder to
ask permission or have the changes included in the official 
distribution.

  Richard


From chemistry-request@ccl.net Wed Feb 11 20:58:08 2004
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Date: Wed, 11 Feb 2004 17:58:17 -0800
Subject: Conference Announcement/ Philosophy of Chemistry & Biochemistry
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International Society for the Philosophy of Chemistry
8th Summer Symposium
Hatfield College
University of Durham
Sunday 15th - Wednesday 18th August 2004

Call for Papers

Previous summer symposia of the International Society for the
Philosophy of Chemistry have provided a forum for philosophers and
chemists to present papers on metaphysical, epistemological,
methodological, semantic, logical and historical issues raised by
thinking about the subject matter and science of chemistry. The 8th
Summer Symposium will continue this tradition. Papers are therefore
invited on any topic in the philosophy of chemistry.

If you would like to present a paper, please send a title and
abstract (of around 300 words) to Robin Hendry, as an email
attachment in Word or RTF formats, or (preferably) in the body of an
email message. You should also give your postal and email address,
and academic affiliation. I will notify you as soon as possible
whether your abstract has been accepted. The deadline for submitting
an abstract is Saturday 1 May 2004. The deadline for registration for
the conference is Thursday 1 July.

For further details see

http://www.dur.ac.uk/philosophy.department/general/events/ISPC.html


Please contact:

Dr RF Hendry
Department of Philosophy
University of Durham
50 Old Elvet
Durham
DH1 3HN UK

email: r.f.hendry=at=durham.ac.uk

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


Dr. Eric Scerri,
Department of Chemistry & Biochemistry,
UCLA,
Los Angeles,
CA 90095.

E-mail   scerri=at=chem.ucla.edu
Phone  310 576 0031

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

UCLA Web page
http://www.chem.ucla.edu/dept/Faculty/scerri/index.html


Editor of Foundations of Chemistry
http://www.kluweronline.com/issn/1386-4238


International Society for the Philosophy of Chemistry
http://www.georgetown.edu/faculty/earleyj/ISPC.html




--B_3159367101_26940113
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<HTML>
<HEAD>
<TITLE>Conference Announcement/ Philosophy of Chemistry &amp; Biochemistry<=
/TITLE>
</HEAD>
<BODY>
<FONT COLOR=3D"#0000FF"><FONT SIZE=3D"5"><FONT FACE=3D"Papyrus"><SPAN STYLE=3D'font=
-size:24.0px'><BR>
International Society for the Philosophy of Chemistry<BR>
8th Summer Symposium<BR>
Hatfield College<BR>
University of Durham<BR>
Sunday 15th - Wednesday 18th August 2004<BR>
<BR>
Call for Papers<BR>
</SPAN></FONT></FONT></FONT><FONT FACE=3D"Papyrus"><SPAN STYLE=3D'font-size:14.=
0px'><BR>
Previous summer symposia of the International Society for the<BR>
Philosophy of Chemistry have provided a forum for philosophers and<BR>
chemists to present papers on metaphysical, epistemological,<BR>
methodological, semantic, logical and historical issues raised by<BR>
thinking about the subject matter and science of chemistry. The 8th<BR>
Summer Symposium will continue this tradition. Papers are therefore<BR>
invited on any topic in the philosophy of chemistry.<BR>
<BR>
If you would like to present a paper, please send a title and<BR>
abstract (of around 300 words) to Robin Hendry, as an email<BR>
attachment in Word or RTF formats, or (preferably) in the body of an<BR>
email message. You should also give your postal and email address,<BR>
and academic affiliation. I will notify you as soon as possible<BR>
whether your abstract has been accepted. The deadline for submitting<BR>
an abstract is Saturday 1 May 2004. The deadline for registration for<BR>
the conference is Thursday 1 July.<BR>
<BR>
For further details see<BR>
<BR>
<a href=3D"http://www.dur.ac.uk/philosophy.department/general/events/ISPC.htm=
l">http://www.dur.ac.uk/philosophy.department/general/events/ISPC.html</a><B=
R>
<BR>
<BR>
Please contact:<BR>
<BR>
Dr RF Hendry<BR>
Department of Philosophy<BR>
University of Durham<BR>
50 Old Elvet<BR>
Durham<BR>
DH1 3HN UK<BR>
<BR>
email: r.f.hendry=at=durham.ac.uk<BR>
<BR>
------------------<BR>
</SPAN></FONT><SPAN STYLE=3D'font-size:14.0px'><FONT FACE=3D"Verdana"><BR>
<BR>
Dr. Eric Scerri,<BR>
Department of Chemistry &amp; Biochemistry,<BR>
UCLA,<BR>
Los Angeles,<BR>
CA 90095.<BR>
<BR>
E-mail &nbsp;&nbsp;scerri=at=chem.ucla.edu<BR>
Phone &nbsp;310 576 0031<BR>
<BR>
--------------------------------------------------------<BR>
<BR>
UCLA Web page<BR>
<a href=3D"http://www.chem.ucla.edu/dept/Faculty/scerri/index.html">http://ww=
w.chem.ucla.edu/dept/Faculty/scerri/index.html</a><BR>
<BR>
<BR>
Editor of Foundations of Chemistry<BR>
<a href=3D"http://www.kluweronline.com/issn/1386-4238">http://www.kluweronlin=
e.com/issn/1386-4238</a><BR>
<BR>
<BR>
International Society for the Philosophy of Chemistry<BR>
<a href=3D"http://www.georgetown.edu/faculty/earleyj/ISPC.html">http://www.ge=
orgetown.edu/faculty/earleyj/ISPC.html</a><BR>
<BR>
</FONT><FONT FACE=3D"Papyrus"><BR>
</FONT></SPAN>
</BODY>
</HTML>


--B_3159367101_26940113--



From chemistry-request@ccl.net Thu Feb 12 06:40:47 2004
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	Thu, 12 Feb 2004 12:40:57 +0100
Date: Thu, 12 Feb 2004 12:40:57 +0100 (CET)
From: Carlos Silva Lopez <csilval|at|uvigo.es>
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To: <csilval|at|uvigo.es>
cc: <chemistry|at|ccl.net>
Subject: Linda & G98
In-Reply-To: <1076441699.25582.112.camel|at|dhcp-539-820.geop.uc.edu>
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Hello CCLers!
I am setting up a cluster with dual processor nodes. I want to paralellize
 g98 jobs through tcp/ip. I have succeded parallelizing on the two
on-Mother Board processors, but Linda fails to parallelize through the
network. I can do rlogin and rsh with no passwd to every node on my
cluster. In my first attemp to run a g98 job a got several error messages,
something like:
"Wrong message from Linda on node X"
And the next attempts usually break with either this:
"ntsnet: worker on node host2 exited abnormally"
or this:
"ntsnet: too many workers exited to continue"
"ntsnet: needed: 1, started: 1, died: 1"

Could anybody shed some light on this issue?
Thanks a lot!

_-_-_-_-_-_-_-_-_-_-_-_-

   Carlos Silva Lspez
 Dept. Qummica Organica
  Universidade de Vigo
  Phone:(34) 986813721
-_-_-_-_-_-_-_-_-_-_-_-_





From chemistry-request@ccl.net Thu Feb 12 12:16:09 2004
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Subject: 17.th International mass pectromety conference Prague 2006
Date: Thu, 12 Feb 2004 18:16:12 +0100
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Prague/Czech Republic, Aug 27 - Sept 1, 2006

-------------------------------------------------------------------------=
-------

Invitation
We cordially invite you to attend the 17th International Mass =
Spectrometry Conference, to be held at the end of summer 2006 in Prague. =
The conference is attended by cca 1400 scientists from all around the =
world and will traditionaly cover different aspects (experimental and =
theoretical) of gas phase ion chemistry, biochemistry, and physics. =
Please visit the conference WEB page www.imsc2006.org -  for more =
details


-------------------------------------------------------------------------=
-------


RNDr. Jan H R U S A K, CSc.
Member of the Academy Council=20
Academy of Sciences of the Czech Republic
Narodni 3, 110 00 Pregue 1, Czech Republic
http://www.cas.cz/en/Academy.council.html
hrusak_at_kav.cas.cz
_________________________________________________________________________=
___________________________


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<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>
<DIV id=3Denvelopehome0>
<DIV id=3Denvelopehome>
<DIV id=3Dheader>
<P id=3Dwebname><IMG height=3D66=20
alt=3D"17th International Mass Spectrometry Conference"=20
src=3D"cid:002a01c3f18b$e9bfb8b0$9b3de793_at_it.kav.cas.cz" =
width=3D454></P>
<H2>Prague/Czech Republic, Aug 27 &#8211; Sept 1, 2006</H2></DIV>
<HR class=3Dcsshide>

<DIV class=3Darticle0>
<DIV class=3Darticle>
<H3 class=3Dfirst>Invitation</H3>
<P>We cordially invite you to attend the&nbsp;17th&nbsp;International =
Mass=20
Spectrometry Conference, to be held at the end of summer 2006 =
in&nbsp;Prague.=20
The conference is attended by cca 1400 scientists from all around the =
world and=20
will traditionaly cover different aspects (experimental and theoretical) =
of gas=20
phase ion chemistry, biochemistry, and&nbsp;physics. Please visit the =
conference=20
WEB page <A=20
href=3D"http://www.imsc2006.org"><STRONG>www.imsc2006.org</STRONG></A><ST=
RONG>=20
-&nbsp; </STRONG><FONT size=3D2>for more details</FONT></P>
<DIV class=3Dhomecontents>
<HR class=3Dcsshide>
</DIV></DIV></DIV>
<DIV class=3Darticle0wide>
<DIV class=3Dfooter></FONT><FONT face=3DArial =
size=3D2></FONT>&nbsp;</DIV>
<DIV class=3Dfooter><FONT face=3DArial size=3D2>RNDr. Jan H R U S A K, =
CSc.<BR>Member=20
of the Academy Council <BR>Academy of Sciences of the Czech =
Republic<BR>Narodni=20
3, 110 00 Pregue 1, Czech Republic<BR><A=20
href=3D"http://www.cas.cz/en/Academy.council.html">http://www.cas.cz/en/A=
cademy.council.html</A><BR><A=20
href=3D"mailto:hrusak_at_kav.cas.cz">hrusak_at_kav.cas.cz</A></FONT></DIV></DIV=
></DIV></DIV></DIV>
<DIV><FONT face=3DArial=20
size=3D2>________________________________________________________________=
____________________________________</FONT></DIV>
<DIV>&nbsp;</DIV>
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Date: Thu, 12 Feb 2004 13:15:54 +0100
To: chemistry:at:ccl.net
From: Jesus Rodriguez-Otero <qftjesus:at:usc.es>
Subject: problems with SCRF=PCM
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Dear CCLers,

I have a problem with PCM.
I want to use ethylene glycol as solvent (dielectric=37.7)
In the keywords I put: scrf=(pcm,read) and at the end of the file EPS=37.7
These are the manual instructions.
But in the output says:  Solvent: WATER  and the results are the water ones
Which is the problem??

Jesus Rodriguez-Otero



From chemistry-request@ccl.net Thu Feb 12 03:18:46 2004
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Please note that 2 complete issues of the journal
Foundations of Chemistry
for the year 2003
can be viewed on-line at

http://www.kluweronline.com/issn/1386-4238

Then go to link for,

journal contents.






--============_-1135548573==_ma============
Content-Type: text/html; charset="us-ascii"

<!doctype html public "-//W3C//DTD W3 HTML//EN">
<html><head><style type="text/css"><!--
blockquote, dl, ul, ol, li { margin-top: 0 ; margin-bottom: 0 }
 --></style><title>Foundations of Chemistry</title></head><body>
<div><br></div>
<div>Please note that 2 complete issues of the journal</div>
<div><font size="+1" color="#663300"><u><b>Foundations of
Chemistry</b></u></font></div>
<div>for the year 2003<br>
can be viewed on-line at</div>
<div><br>
http://www.kluweronline.com/issn/1386-423<span
></span>8<br>
<br>
Then go to link for,<br>
</div>
<div>journal contents.</div>
<div><br></div>
<div><br></div>
<div><br></div>
<div><br>
<br>
<br>
</div>
</body>
</html>
--============_-1135548573==_ma============--


From chemistry-request@ccl.net Thu Feb 12 09:45:04 2004
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Date: Thu, 12 Feb 2004 09:45:22 -0500
Subject: Re: CCL:J.Comp.Chem. Style File Needed
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To: Richard Gillilan <reg8$at$cornell.edu>
From: Richard Gillilan <reg8$at$cornell.edu>
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Ok, now that I look at the WHOLE license file for the achemso package 
which is a
separate file, it appears to be ok to copy any amount of the code and 
give it a
new file name as long as proper credit for the used code is given to 
Mats Dahlgren,
and it is clear in the header that I'm the one who should handle 
complaints and code
fixes etc, rather than Mats. I can't really be responsible at this 
time, however, the
changes are simple, here is my hack (use at your own risk):

% REG:    { "\textit{" swap$ * "}" * }

FUNCTION {emphasize}
{ duplicate$ empty$
     { pop$ "" }
     { "" swap$ * "" * }
   if$
}

%    { "\textsl{" swap$ * ",}" * }
FUNCTION {slantc}
{ duplicate$ empty$
     { pop$ "" }
     { "" swap$ * "," * }
   if$
}

%    { "\textbf{" swap$ * ",}" * }

FUNCTION {emboldenc}
{ duplicate$ empty$
     { pop$ "" }
     { "" swap$ * "," * }
   if$
}


The official achemso can be found here: 
(http://www.homenet.se/matsd/latex/).


Richard

On Thursday, February 12, 2004, at 12:32 AM, Richard Gillilan wrote:

> In an earlier message I offered to make available a modified version 
> of a bst
> style file for Latex that does J. Comp. Chem. format. Now that I 
> examine the
> copyright header (achemso.bst), I see that I may not distribute the 
> modified
> form.  Sorry to those who have asked.  I may contact the copyright 
> holder to
> ask permission or have the changes included in the official 
> distribution.
>
>  Richard
>



From chemistry-request@ccl.net Thu Feb 12 04:16:31 2004
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Date: Thu, 12 Feb 2004 10:21:36 +0100 (CET)
From: Tom Kuppens <tom$at$hartree4.UGent.be>
To: CHEMISTRY$at$ccl.net
Subject: SUM: G03 with Linda
Message-ID: <Pine.LNX.4.44.0402121009390.16122-100000$at$hartree4.UGent.be>
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Hi there,
I managed to get linda working.
Here is a little summary:


Marcel Swart
]did you try putting 
]%NprocL=2
]instead of
]%NPROCLINDA=2



Christoph Steinbeck
]First of all, my jobs contain the statement %nprocl=8. But your longer 
]and uppercased statement might well be due to a newer version (I have 
]G98 and linda).
]Secondly, there was a way of making linda insert debug statements into 
]the gaussian log. That was very helpful to find the reason for not 
]aquiring any workers.
]Thirdly, the compile script used to make a two version, one was g98 and 
]g98l (for linda-enabled). If you mistake these, you'll never use Linda.


]Igor Filippov
]
]- use tcpdump to listen on the wire if gaussian/linda is actually
]trying to comminicate to other nodes


Fernando D. Vila
]- Add the following lines to your .tsnet.config:
]Tsnet.Node.lindarsharg: ssh
]Tsnet.Node.lindarcparg: scp
]This makes linda use the secure versions. (Obviously, you have to have 
]everythhing setup without a password).
]
]- For some reason I haven't discovered yet, 
]parts of the directives you put in the .tsnet.config don't get passed to 
]the Gaussian execution. Reading the Linda manual and checking some 
]webpages, I found that you can pass the linda option to Gaussian using the 
]GAUSS_LFLAGS env variable. Right now I have it setup as follows:
]
]setenv GAUSS_LFLAGS "-maxprocspernode 2 -wait 30"
]
]maxprocspernode was one of the directives that I couldn't get transmited
]to Gaussian. With this env variable Gaussian finds it.


Jenn Sturm
]
]-the initial revisions of g03, at least in binary  
]form, came with a bug where it only checked a user's primary group  
]membership. So, for instance, my groups are:
]
]hamilton users staff
]
]and g03 was owned by group users. Since my primary group is hamilton,  
]it wouldn't let me run *only* the linda binaries.
]
]To solve the problem, I had to run the following explicitly as root:
]
]chmod -R o+rX /usr/local/g98
]
]to give the executables other-group execution privileges.
]
]If this is no help, have you tried to explicity request verbose  
]reporting from Linda? To do so, I believe the command (tcsh) is
]
]setenv GAUSS_LFLAGS -vv
]
]and then run g03l


I also found out that you have to set your environment on the workernode. 
I did it with the ssh ~/.ssh/environment settings. If there are other ways, 
let me know.

Thanks for the help! 

Tom Kuppens


Research group Quantumchemistry
Department of Inorganic and Physical Chemistry WE06V
Ghent University
Krijgslaan 281 - S3, 9000 Ghent, Belgium
Tel  +32(0)9 264 4444
Fax  +32(0)9 264 4983
-- 
http://allserv.UGent.be/~tkuppens
----
 Yesterday I was a dog.  Today I'm a dog.  Tomorrow I'll probably still
 be a dog. Sigh!  There's so little hope for advancement.
    -- Snoopy



From chemistry-request@ccl.net Thu Feb 12 10:54:01 2004
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Date: Thu, 12 Feb 2004 11:53:18 -0400
From: Katie Doucet <kgdct)at(mta.ca>
To: CCL <chemistry)at(ccl.net>
Subject: Playing Frequencies in PowerPoint?
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I was wondering if anyone knows of a way (either a program or a simple trick) 
to play frequencies in a Microsoft PowerPoint presentation without having to 
close out of the presentation.

Thanks
-K.Doucet


From chemistry-request@ccl.net Thu Feb 12 03:25:39 2004
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From: Nicolas =?iso-8859-1?q?Ferr=E9?= <Nicolas.Ferre!at!up.univ-mrs.fr>
Organization: LCTMM
To: chemistry!at!ccl.net
Subject: Re: CCL:J.Comp.Chem. Style File Needed
Date: Thu, 12 Feb 2004 09:25:11 +0100
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--Boundary-00=_nhzKAjV0VHh/s86
Content-Type: text/plain;
  charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable
Content-Disposition: inline

Le Mercredi 11 F=E9vrier 2004 19:50, Antitsa Stoycheva a =E9crit :
> Continuing the discussion:

Here is the jcc.bst file I generated three years ago with makebst (see CTAN=
=20
archive).

Hope this helps,
=2D-=20
 Dr. Nicolas Ferr=E9
 Laboratoire de Chimie Th=E9orique et de Mod=E9lisation Mol=E9culaire
 UMR 6517 - CNRS Universit=E9 de Provence
 Case 521 - Facult=E9 de Saint-J=E9r=F4me
 Av. Esc. Normandie Niemen
 13397 MARSEILLE Cedex 20 (FRANCE)
 Tel : (+33)4.91.28.27.33              Fax : (+33)4.91.28.87.58

--Boundary-00=_nhzKAjV0VHh/s86
Content-Type: text/x-diff;
  charset="iso-8859-1";
  name="jcc.bst"
Content-Transfer-Encoding: quoted-printable
Content-Disposition: attachment;
	filename="jcc.bst"

%% Nicolas Ferr=E9, Universit=E9 de Provence, generated with makebst
%%
%% This is file `jcc.bst',
%% generated with the docstrip utility.
%%
%% The original source files were:
%%
%% merlin.mbs  (with options: `annote,seq-no,nm-rev,ed-rev,jnrlst,dt-jnl,xm=
th,jtit-x,jxper,jttl-rm,vnum-x,volp-com,jpg-1,num-xser,jnm-x,btit-rm,bt-rm,=
pre-pub,edby,edbyy,blk-com,com-blank,pp,ed,abr,xedn,jabr,xand')
%% ----------------------------------------
%% *** Journal of Computational Chemistry ***
%%=20
%% Copyright 1994-2000 Patrick W Daly
 % =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
 % IMPORTANT NOTICE:
 % This bibliographic style (bst) file has been generated from one or
 % more master bibliographic style (mbs) files, listed above.
 %
 % This generated file can be redistributed and/or modified under the terms
 % of the LaTeX Project Public License Distributed from CTAN
 % archives in directory macros/latex/base/lppl.txt; either
 % version 1 of the License, or any later version.
 % =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
 % Name and version information of the main mbs file:
 % \ProvidesFile{merlin.mbs}[2000/05/04 4.01 (PWD, AO, DPC)]
 %   For use with BibTeX version 0.99a or later
 %-------------------------------------------------------------------
 % This bibliography style file is intended for texts in ENGLISH
 % This is a numerical citation style, and as such is standard LaTeX.
 % It requires no extra package to interface to the main text.
 % The form of the \bibitem entries is
 %   \bibitem{key}...
 % Usage of \cite is as follows:
 %   \cite{key} =3D=3D>>          [#]
 %   \cite[chap. 2]{key} =3D=3D>> [#, chap. 2]
 % where # is a number determined by the ordering in the reference list.
 % The order in the reference list is that by which the works were original=
ly
 %   cited in the text, or that in the database.
 %---------------------------------------------------------------------

ENTRY
  { address
    annote
    author
    booktitle
    chapter
    edition
    editor
    howpublished
    institution
    journal
    key
    month
    note
    number
    organization
    pages
    publisher
    school
    series
    title
    type
    volume
    year
  }
  {}
  { label }
INTEGERS { output.state before.all mid.sentence after.sentence after.block }
=46UNCTION {init.state.consts}
{ #0 'before.all :=3D
  #1 'mid.sentence :=3D
  #2 'after.sentence :=3D
  #3 'after.block :=3D
}
STRINGS { s t}
=46UNCTION {output.nonnull}
{ 's :=3D
  output.state mid.sentence =3D
    { " " * write$ }
    { output.state after.block =3D
        { add.period$ write$
          newline$
          "\newblock " write$
        }
        { output.state before.all =3D
            'write$
            { add.period$ " " * write$ }
          if$
        }
      if$
      mid.sentence 'output.state :=3D
    }
  if$
  s
}
=46UNCTION {output}
{ duplicate$ empty$
    'pop$
    'output.nonnull
  if$
}
=46UNCTION {output.check}
{ 't :=3D
  duplicate$ empty$
    { pop$ "empty " t * " in " * cite$ * warning$ }
    'output.nonnull
  if$
}
=46UNCTION {fin.entry}
{ add.period$
  write$
  newline$
  annote missing$
    { "\bibAnnoteFile{" cite$ * "}" * write$ newline$ }
    { "\bibAnnote{" cite$ * "}{" * annote * "}" * write$ newline$
    }
  if$
}

=46UNCTION {new.block}
{ output.state before.all =3D
    'skip$
    { after.block 'output.state :=3D }
  if$
}
=46UNCTION {new.sentence}
{ output.state after.block =3D
    'skip$
    { output.state before.all =3D
        'skip$
        { after.sentence 'output.state :=3D }
      if$
    }
  if$
}
=46UNCTION {add.blank}
{  " " * before.all 'output.state :=3D
}

=46UNCTION {date.block}
{
   ", " * before.all 'output.state :=3D
%  skip$
}

=46UNCTION {not}
{   { #0 }
    { #1 }
  if$
}
=46UNCTION {and}
{   'skip$
    { pop$ #0 }
  if$
}
=46UNCTION {or}
{   { pop$ #1 }
    'skip$
  if$
}
STRINGS {z}
=46UNCTION {remove.dots}
{ 'z :=3D
  ""
  { z empty$ not }
  { z #1 #1 substring$
    z #2 global.max$ substring$ 'z :=3D
    duplicate$ "." =3D 'pop$
      { * }
    if$
  }
  while$
}
=46UNCTION {new.block.checka}
{ empty$
    'skip$
    'new.block
  if$
}
=46UNCTION {new.block.checkb}
{ empty$
  swap$ empty$
  and
    'skip$
    'new.block
  if$
}
=46UNCTION {new.sentence.checka}
{ empty$
    'skip$
    'new.sentence
  if$
}
=46UNCTION {new.sentence.checkb}
{ empty$
  swap$ empty$
  and
    'skip$
    'new.sentence
  if$
}
=46UNCTION {field.or.null}
{ duplicate$ empty$
    { pop$ "" }
    'skip$
  if$
}
=46UNCTION {emphasize}
{ duplicate$ empty$
    { pop$ "" }
    { "{\em " swap$ * "\/}" * }
  if$
}
=46UNCTION {tie.or.space.prefix}
{ duplicate$ text.length$ #3 <
    { "~" }
    { " " }
  if$
  swap$
}

=46UNCTION {capitalize}
{ "u" change.case$ "t" change.case$ }

=46UNCTION {space.word}
{ " " swap$ * " " * }
 % Here are the language-specific definitions for explicit words.
 % Each function has a name bbl.xxx where xxx is the English word.
 % The language selected here is ENGLISH
=46UNCTION {bbl.and}
{ "and"}

=46UNCTION {bbl.etal}
{ "et~al." }

=46UNCTION {bbl.editors}
{ "Eds." }

=46UNCTION {bbl.editor}
{ "ed." }

=46UNCTION {bbl.edby}
{ "edited by" }

=46UNCTION {bbl.edition}
{ "edn." }

=46UNCTION {bbl.volume}
{ "vol." }

=46UNCTION {bbl.of}
{ "of" }

=46UNCTION {bbl.number}
{ "no." }

=46UNCTION {bbl.nr}
{ "no." }

=46UNCTION {bbl.in}
{ "in" }

=46UNCTION {bbl.inn}
{ "In" }

=46UNCTION {bbl.pages}
{ "pp." }

=46UNCTION {bbl.page}
{ "p." }

=46UNCTION {bbl.chapter}
{ "Chapter" }

=46UNCTION {bbl.techrep}
{ "Tech. Rep." }

=46UNCTION {bbl.mthesis}
{ "Master's thesis" }

=46UNCTION {bbl.phdthesis}
{ "Ph.D. thesis" }

MACRO {jan} {"Jan."}

MACRO {feb} {"Feb."}

MACRO {mar} {"Mar."}

MACRO {apr} {"Apr."}

MACRO {may} {"May"}

MACRO {jun} {"Jun."}

MACRO {jul} {"Jul."}

MACRO {aug} {"Aug."}

MACRO {sep} {"Sep."}

MACRO {oct} {"Oct."}

MACRO {nov} {"Nov."}

MACRO {dec} {"Dec."}

MACRO {acmcs} {"ACM Comput. Surv."}

MACRO {acta} {"Acta Inf."}

MACRO {cacm} {"Commun. ACM"}

MACRO {ibmjrd} {"IBM J. Res. Dev."}

MACRO {ibmsj} {"IBM Syst.~J."}

MACRO {ieeese} {"IEEE Trans. Software Eng."}

MACRO {ieeetc} {"IEEE Trans. Comput."}

MACRO {ieeetcad}
 {"IEEE Trans. Comput. Aid. Des."}

MACRO {ipl} {"Inf. Process. Lett."}

MACRO {jacm} {"J.~ACM"}

MACRO {jcss} {"J.~Comput. Syst. Sci."}

MACRO {scp} {"Sci. Comput. Program."}

MACRO {sicomp} {"SIAM J. Comput."}

MACRO {tocs} {"ACM Trans. Comput. Syst."}

MACRO {tods} {"ACM Trans. Database Syst."}

MACRO {tog} {"ACM Trans. Graphic."}

MACRO {toms} {"ACM Trans. Math. Software"}

MACRO {toois} {"ACM Trans. Office Inf. Syst."}

MACRO {toplas} {"ACM Trans. Progr. Lang. Syst."}

MACRO {tcs} {"Theor. Comput. Sci."}

=46UNCTION {bibinfo.check}
{ swap$
  duplicate$ missing$
    {
      pop$ pop$
      ""
    }
    { duplicate$ empty$
        {
          swap$ pop$
        }
        { swap$
          pop$
        }
      if$
    }
  if$
}
=46UNCTION {bibinfo.warn}
{ swap$
  duplicate$ missing$
    {
      swap$ "missing " swap$ * " in " * cite$ * warning$ pop$
      ""
    }
    { duplicate$ empty$
        {
          swap$ "empty " swap$ * " in " * cite$ * warning$
        }
        { swap$
          pop$
        }
      if$
    }
  if$
}
STRINGS  { bibinfo}
INTEGERS { nameptr namesleft numnames }

=46UNCTION {format.names}
{ 'bibinfo :=3D
  duplicate$ empty$ 'skip$ {
  's :=3D
  "" 't :=3D
  #1 'nameptr :=3D
  s num.names$ 'numnames :=3D
  numnames 'namesleft :=3D
    { namesleft #0 > }
    { s nameptr
      "{vv~}{ll}{, f.}{, jj}"
      format.name$
      bibinfo bibinfo.check
      't :=3D
      nameptr #1 >
        {
          namesleft #1 >
            { ", " * t * }
            {
              "," *
              s nameptr "{ll}" format.name$ duplicate$ "others" =3D
                { 't :=3D }
                { pop$ }
              if$
              t "others" =3D
                {
                  " " * bbl.etal *
                }
                { " " * t * }
              if$
            }
          if$
        }
        't
      if$
      nameptr #1 + 'nameptr :=3D
      namesleft #1 - 'namesleft :=3D
    }
  while$
  } if$
}
=46UNCTION {format.names.ed}
{
  format.names
}
=46UNCTION {format.authors}
{ author "author" format.names
}
=46UNCTION {get.bbl.editor}
{ editor num.names$ #1 > 'bbl.editors 'bbl.editor if$ }

=46UNCTION {format.editors}
{ editor "editor" format.names duplicate$ empty$ 'skip$
    {
      "," *
      " " *
      get.bbl.editor
      *
    }
  if$
}
=46UNCTION {format.note}
{
 note empty$
    { "" }
    { note #1 #1 substring$
      duplicate$ "{" =3D
        'skip$
        { output.state mid.sentence =3D
          { "l" }
          { "u" }
        if$
        change.case$
        }
      if$
      note #2 global.max$ substring$ * "note" bibinfo.check
    }
  if$
}

=46UNCTION {format.title}
{ title
  duplicate$ empty$ 'skip$
    { "t" change.case$ }
  if$
  "title" bibinfo.check
}
=46UNCTION {output.bibitem}
{ newline$
  "\bibitem{" write$
  cite$ write$
  "}" write$
  newline$
  ""
  before.all 'output.state :=3D
}

=46UNCTION {n.dashify}
{
  't :=3D
  ""
    { t empty$ not }
    { t #1 #1 substring$ "-" =3D
        { t #1 #2 substring$ "--" =3D not
            { "--" *
              t #2 global.max$ substring$ 't :=3D
            }
            {   { t #1 #1 substring$ "-" =3D }
                { "-" *
                  t #2 global.max$ substring$ 't :=3D
                }
              while$
            }
          if$
        }
        { t #1 #1 substring$ *
          t #2 global.max$ substring$ 't :=3D
        }
      if$
    }
  while$
}

=46UNCTION {word.in}
{ bbl.in
  " " * }

=46UNCTION {format.date}
{
  ""
  duplicate$ empty$
  year  "year"  bibinfo.check duplicate$ empty$
    { swap$ 'skip$
        { "there's a month but no year in " cite$ * warning$ }
      if$
      *
    }
    { swap$ 'skip$
        {
          swap$
	  " " * swap$
        }
      if$
      *
    }
  if$
}
=46UNCTION {format.btitle}
{ title "title" bibinfo.check
  duplicate$ empty$ 'skip$
    {
    }
  if$
}
=46UNCTION {either.or.check}
{ empty$
    'pop$
    { "can't use both " swap$ * " fields in " * cite$ * warning$ }
  if$
}
=46UNCTION {format.bvolume}
{ volume empty$
    { "" }
    { ", " *
      bbl.volume volume tie.or.space.prefix
      "volume" bibinfo.check * *
      series "series" bibinfo.check
      duplicate$ empty$ 'pop$
        { swap$ bbl.of space.word * swap$
          emphasize * }
      if$
      "volume and number" number either.or.check
    }
  if$
}
=46UNCTION {format.number.series}
{ volume empty$
    { number empty$
        { series field.or.null }
        { series empty$
            { number "number" bibinfo.check }
        { output.state mid.sentence =3D
            { bbl.number }
            { bbl.number capitalize }
          if$
          number tie.or.space.prefix "number" bibinfo.check * *
          bbl.in space.word *
          series "series" bibinfo.check *
        }
      if$
    }
      if$
    }
    { "" }
  if$
}

=46UNCTION {format.edition}
{ edition duplicate$ empty$ 'skip$
    {
      output.state mid.sentence =3D
        { "l" }
        { "t" }
      if$ change.case$
      "edition" bibinfo.check
      " " * bbl.edition *
    }
  if$
}
INTEGERS { multiresult }
=46UNCTION {multi.page.check}
{ 't :=3D
  #0 'multiresult :=3D
    { multiresult not
      t empty$ not
      and
    }
    { t #1 #1 substring$
      duplicate$ "-" =3D
      swap$ duplicate$ "," =3D
      swap$ "+" =3D
      or or
        { #1 'multiresult :=3D }
        { t #2 global.max$ substring$ 't :=3D }
      if$
    }
  while$
  multiresult
}
=46UNCTION {format.pages}
{ pages duplicate$ empty$ 'skip$
    { duplicate$ multi.page.check
        {
	  bbl.page swap$
          n.dashify
        }
        {
          bbl.page swap$
        }
      if$
      tie.or.space.prefix
      "pages" bibinfo.check
      * *
    }
  if$
}
=46UNCTION {first.page}
{ 't :=3D
  ""
    {  t empty$ not t #1 #1 substring$ "-" =3D not and }
    { t #1 #1 substring$ *
      t #2 global.max$ substring$ 't :=3D
    }
  while$
}

=46UNCTION {format.journal.pages}
{ pages duplicate$ empty$ 'pop$
    { swap$ duplicate$ empty$
        { pop$ pop$ format.pages }
        {
          ", " *
          swap$
          first.page
          "pages" bibinfo.check
          *
        }
      if$
    }
  if$
}
=46UNCTION {format.vol.num.pages}
{ volume field.or.null
  duplicate$ empty$ 'skip$
    {
      "volume" bibinfo.check
    }
  if$
  format.journal.pages
}

=46UNCTION {format.chapter.pages}
{ chapter empty$
    'format.pages
    { type empty$
        { bbl.chapter }
        { type "l" change.case$
          "type" bibinfo.check
        }
      if$
      chapter tie.or.space.prefix
      "chapter" bibinfo.check
      * *
      pages empty$
        'skip$
        { ", " * format.pages * }
      if$
    }
  if$
}

=46UNCTION {format.booktitle}
{
  booktitle "booktitle" bibinfo.check
}
=46UNCTION {format.in.ed.booktitle}
{ format.booktitle duplicate$ empty$ 'skip$
    {
      editor "editor" format.names.ed duplicate$ empty$ 'pop$
        {
          get.bbl.editor
          swap$ "," *
          " " * swap$ *
          swap$
          "," *
          " " * swap$
          * }
      if$
      word.in swap$ *
    }
  if$
}
=46UNCTION {empty.misc.check}
{ author empty$ title empty$ howpublished empty$
  month empty$ year empty$ note empty$
  and and and and and
    { "all relevant fields are empty in " cite$ * warning$ }
    'skip$
  if$
}
=46UNCTION {format.thesis.type}
{ type duplicate$ empty$
    'pop$
    { swap$ pop$
      "t" change.case$ "type" bibinfo.check
    }
  if$
}
=46UNCTION {format.tr.number}
{ number "number" bibinfo.check
  type duplicate$ empty$
    { pop$ bbl.techrep }
    'skip$
  if$
  "type" bibinfo.check
  swap$ duplicate$ empty$
    { pop$ "t" change.case$ }
    { tie.or.space.prefix * * }
  if$
}
=46UNCTION {format.article.crossref}
{
  key duplicate$ empty$
    { pop$
      journal duplicate$ empty$
        { "need key or journal for " cite$ * " to crossref " * crossref * w=
arning$ }
        { "journal" bibinfo.check emphasize word.in swap$ * }
      if$
    }
    { word.in swap$ * " " *}
  if$
  " \cite{" * crossref * "}" *
}
=46UNCTION {format.crossref.editor}
{ editor #1 "{vv~}{ll}" format.name$
  "editor" bibinfo.check
  editor num.names$ duplicate$
  #2 >
    { pop$
      "editor" bibinfo.check
      " " * bbl.etal
      *
    }
    { #2 <
        'skip$
        { editor #2 "{ff }{vv }{ll}{ jj}" format.name$ "others" =3D
            {
              "editor" bibinfo.check
              " " * bbl.etal
              *
            }
            {
             bbl.and space.word
              * editor #2 "{vv~}{ll}" format.name$
              "editor" bibinfo.check
              *
            }
          if$
        }
      if$
    }
  if$
}
=46UNCTION {format.book.crossref}
{ volume duplicate$ empty$
    { "empty volume in " cite$ * "'s crossref of " * crossref * warning$
      pop$ word.in
    }
    { bbl.volume
      swap$ tie.or.space.prefix "volume" bibinfo.check * * bbl.of space.wor=
d *
    }
  if$
  editor empty$
  editor field.or.null author field.or.null =3D
  or
    { key empty$
        { series empty$
            { "need editor, key, or series for " cite$ * " to crossref " *
              crossref * warning$
              "" *
            }
            { series emphasize * }
          if$
        }
        { key * }
      if$
    }
    { format.crossref.editor * }
  if$
  " \cite{" * crossref * "}" *
}
=46UNCTION {format.incoll.inproc.crossref}
{
  editor empty$
  editor field.or.null author field.or.null =3D
  or
    { key empty$
        { format.booktitle duplicate$ empty$
            { "need editor, key, or booktitle for " cite$ * " to crossref "=
 *
              crossref * warning$
            }
            { word.in swap$ * }
          if$
        }
        { word.in key * " " *}
      if$
    }
    { word.in format.crossref.editor * " " *}
  if$
  " \cite{" * crossref * "}" *
}
=46UNCTION {format.org.or.pub}
{ 't :=3D
  ""
  address empty$ t empty$ and
    'skip$
    {
      t empty$
        { address "address" bibinfo.check *
        }
        { t *
          address empty$
            'skip$
	    { ": " * address "address" bibinfo.check * }
          if$
        }
      if$
    }
  if$
}
=46UNCTION {format.publisher.address}
{ publisher "publisher" bibinfo.warn format.org.or.pub
}

=46UNCTION {format.organization.address}
{ organization "organization" bibinfo.check format.org.or.pub
}

=46UNCTION {article}
{ output.bibitem
  format.authors "author" output.check
  crossref missing$
    {
      journal
      remove.dots
      "journal" bibinfo.check
      "journal" output.check
      add.blank
      format.date "year" output.check
      date.block
      format.vol.num.pages output
    }
    { format.article.crossref output.nonnull
      format.pages output
    }
  if$
  format.note output
  fin.entry
}
=46UNCTION {book}
{ output.bibitem
  author empty$
    { format.editors "author and editor" output.check
    }
    { format.authors output.nonnull
      crossref missing$
        { "author and editor" editor either.or.check }
        'skip$
      if$
    }
  if$
  format.btitle "title" output.check
  crossref missing$
    { format.bvolume output
      format.number.series output
      format.publisher.address output
    }
    {
      format.book.crossref output.nonnull
    }
  if$
  format.edition output
  ", " *
  format.date "year" output.check
  format.note output
  fin.entry
}
=46UNCTION {booklet}
{ output.bibitem
  format.authors output
  format.title "title" output.check
  howpublished "howpublished" bibinfo.check output
  address "address" bibinfo.check output
  format.date output
  format.note output
  fin.entry
}

=46UNCTION {inbook}
{ output.bibitem
  author empty$
    { format.editors "author and editor" output.check
    }
    { format.authors output.nonnull
      crossref missing$
        { "author and editor" editor either.or.check }
        'skip$
      if$
    }
  if$
  bbl.inn space.word *
  format.btitle "title" output.check
  crossref missing$
    {
      format.publisher.address output
    }
    {
      format.book.crossref output.nonnull
    }
  if$
  format.edition output
  ", " *
  format.date "year" output.check
  date.block
  add.blank
  format.pages "pages" output.check
  format.bvolume output
  format.number.series output
  format.note output
  fin.entry
}

=46UNCTION {incollection}
{ output.bibitem
  format.authors "author" output.check
  crossref missing$
    { format.in.ed.booktitle "booktitle" output.check
      format.publisher.address output
      format.bvolume output
      format.number.series output
      format.edition output
    }
    { format.incoll.inproc.crossref output.nonnull
    }
  if$
  format.date "year" output.check
  date.block
  add.blank
  format.pages "pages" output.check
  format.note output
  fin.entry
}
=46UNCTION {inproceedings}
{ output.bibitem
  format.authors "author" output.check
  crossref missing$
    { format.in.ed.booktitle "booktitle" output.check
      publisher empty$
        { format.organization.address output }
        { organization "organization" bibinfo.check output
          format.publisher.address output
        }
      if$
      format.bvolume output
      format.number.series output
      format.pages output
    }
    { format.incoll.inproc.crossref output.nonnull
      format.pages output
    }
  if$
  format.date "year" output.check
  date.block
  add.blank
  format.pages "pages" output.check
  format.note output
  fin.entry
}
=46UNCTION {conference} { inproceedings }
=46UNCTION {manual}
{ output.bibitem
  author empty$
    { organization "organization" bibinfo.check
      duplicate$ empty$ 'pop$
        { output
          address "address" bibinfo.check output
        }
      if$
    }
    { format.authors output.nonnull }
  if$
  format.btitle "title" output.check
  author empty$
    { organization empty$
        {
          address "address" bibinfo.check output
        }
        'skip$
      if$
    }
    {
      organization "organization" bibinfo.check output
      address "address" bibinfo.check output
    }
  if$
  format.edition output
  format.date output
  format.note output
  fin.entry
}

=46UNCTION {mastersthesis}
{ output.bibitem
  format.authors "author" output.check
  format.btitle
  "title" output.check
  bbl.mthesis format.thesis.type output.nonnull
  school "school" bibinfo.warn output
  address "address" bibinfo.check output
  format.date "year" output.check
  format.note output
  fin.entry
}

=46UNCTION {misc}
{ output.bibitem
  format.authors output
  format.title output
  howpublished "howpublished" bibinfo.check output
  format.date output
  format.note output
  fin.entry
  empty.misc.check
}
=46UNCTION {phdthesis}
{ output.bibitem
  format.authors "author" output.check
  format.btitle
  "title" output.check
  bbl.phdthesis format.thesis.type output.nonnull
  school "school" bibinfo.warn output
  address "address" bibinfo.check output
  format.date "year" output.check
  format.note output
  fin.entry
}

=46UNCTION {proceedings}
{ output.bibitem
  editor empty$
    { organization "organization" bibinfo.check output
    }
    { format.editors output.nonnull }
  if$
  format.btitle "title" output.check
  format.bvolume output
  format.number.series output
  editor empty$
    { publisher empty$
        'skip$
        {
          format.publisher.address output
        }
      if$
    }
    { publisher empty$
        {
          format.organization.address output }
        {
          organization "organization" bibinfo.check output
          format.publisher.address output
        }
      if$
     }
  if$
      format.date "year" output.check
  format.note output
  fin.entry
}

=46UNCTION {techreport}
{ output.bibitem
  format.authors "author" output.check
  format.title
  "title" output.check
  format.tr.number output.nonnull
  institution "institution" bibinfo.warn output
  address "address" bibinfo.check output
  format.date "year" output.check
  format.note output
  fin.entry
}

=46UNCTION {unpublished}
{ output.bibitem
  format.authors "author" output.check
  format.title "title" output.check
  format.date output
  format.note "note" output.check
  fin.entry
}

=46UNCTION {default.type} { misc }
READ
STRINGS { longest.label }
INTEGERS { number.label longest.label.width }
=46UNCTION {initialize.longest.label}
{ "" 'longest.label :=3D
  #1 'number.label :=3D
  #0 'longest.label.width :=3D
}
=46UNCTION {longest.label.pass}
{ number.label int.to.str$ 'label :=3D
  number.label #1 + 'number.label :=3D
  label width$ longest.label.width >
    { label 'longest.label :=3D
      label width$ 'longest.label.width :=3D
    }
    'skip$
  if$
}
EXECUTE {initialize.longest.label}
ITERATE {longest.label.pass}
=46UNCTION {begin.bib}
{ preamble$ empty$
    'skip$
    { preamble$ write$ newline$ }
  if$
  "\begin{thebibliography}{"  longest.label  * "}" *
  write$ newline$
  "\providecommand{\bibAnnoteFile}[1]{%"
  write$ newline$
  "  \IfFileExists{#1}{\begin{quotation}\noindent\textsc{Key:} #1\\"
  write$ newline$
  "  \textsc{Annotation:}\ \input{#1}\end{quotation}}{}}"
  write$ newline$
  "\providecommand{\bibAnnote}[2]{%"
  write$ newline$
  "  \begin{quotation}\noindent\textsc{Key:} #1\\"
  write$ newline$
  "  \textsc{Annotation:}\ #2\end{quotation}}"
  write$ newline$
}
EXECUTE {begin.bib}
EXECUTE {init.state.consts}
ITERATE {call.type$}
=46UNCTION {end.bib}
{ newline$
  "\end{thebibliography}" write$ newline$
}
EXECUTE {end.bib}
%% End of customized bst file
%%
%% End of file `jcc.bst'.



--Boundary-00=_nhzKAjV0VHh/s86--



From chemistry-request@ccl.net Thu Feb 12 02:58:31 2004
Received: from server.theo.chemie.tu-muenchen.de (server.theo.chemie.tu-muenchen.de [129.187.122.133])
	by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1C7wUU6002883
	for <CHEMISTRY!at!ccl.net>; Thu, 12 Feb 2004 02:58:31 -0500
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	id BF28CBAC2; Thu, 12 Feb 2004 08:58:44 +0100 (CET)
Date: Thu, 12 Feb 2004 08:58:44 +0100 (CET)
From: Mehdi Bounouar <mehdi.bounouar..at..ch.tum.de>
To: Olga Dmitrenko <odmitr..at..UDel.Edu>
Cc: CHEMISTRY..at..ccl.net
Subject: Re: CCL:Z-matrix input for Gamess-US wanted
In-Reply-To: <200402112055.i1BKtJ8L016696..at..copland.udel.edu>
Message-ID: <Pine.LNX.4.44.0402120847340.24012-100000..at..crease.theo.chemie.tu-muenchen.de>
MIME-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII
X-Spam-Status: No, hits=0.3 required=7.0 tests=UPPERCASE_25_50 autolearn=no 
	version=2.61
X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on 
	servernd.ccl.net

Hi,

If you coordinates are Z-mat you should put NZVAR = 3, which is equal to
3N-6 and not 0.

Mehdi


> Dear all,
>
> I would much appreciate if somebody of you will kindly send me an example of
> the Gamess-US
> input with the Z-matrix which really works for GAMESS VERSION = 20 JUN 2002
> (R2).
> Somehow... I have troubles to run simple example on methylene molecule (I
> copied it
> > from
> http://www.npaci.edu/Resources/SciComp/Applications/GAMESS/gamess_sect3.html
> :
>
> $CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE COORD=ZMT NZVAR=0 $END
> $SYSTEM TIMLIM=2 MEMORY=100000 $END
> $STATPT OPTTOL=1.0E-5  $END
> $BASIS  GBASIS=STO NGAUSS=2 $END
> $GUESS  GUESS=HUCKEL $END
> $DATA
> Methylene...1-A-1 state...RHF/STO-2G
> Cnv  2
>
> C
> H  1 rCH
> H  1 rCH  2 aHCH
>
> rCH=1.09
> aHCH=110.0
> $END
>
> I am getting "**** ERROR, NO  $DATA   GROUP WAS FOUND".
>
>
> -= This is automatically added to each message by the mailing script =-
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>
>
>
>
>



From chemistry-request@ccl.net Wed Feb 11 23:33:41 2004
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Date: Thu, 12 Feb 2004 10:06:04 +0530 (IST)
From: "Dr.Tapan K.Ghanty" <tapang<<at>>apsara.barc.ernet.in>
To: Olga Dmitrenko <odmitr<<at>>UDel.Edu>
Cc: CHEMISTRY<<at>>ccl.net
Subject: Re: CCL:Z-matrix input for Gamess-US wanted
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Hi,

I am sure, you don't have the problem with Z-matrix,
but rather your input file format is not proper. All
the input cards (e.g. $CONTRL etc etc) should start
> from the 2nd column in the input file, not from the
first column. And that is why your input was not working.
Here is the correct input file with the same z-mtrix
as used by you:

----------------- begin of input -----------------------
 $CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE COORD=ZMT NZVAR=0 $END
 $SYSTEM TIMLIM=2 MEMORY=100000 $END
 $STATPT OPTTOL=1.0E-5  $END
 $BASIS  GBASIS=STO NGAUSS=2 $END
 $GUESS  GUESS=HUCKEL $END
 $DATA
Methylene...1-A-1 state...RHF/STO-2G
Cnv  2

C
H  1 rCH
H  1 rCH  2 aHCH

rCH=1.09
aHCH=110.0
 $END
---------------end of input --------------------

With all the best,

Tapan Ghanty

-----------------------------------
Dr. Tapan Ghanty
Theoretical Chemistry Section
RC & CD Division, Chemistry Group,
Bhabha Atomic Resaerch Centre,
Mumbai 400 085, INDIA
------------------------------------

On Wed, 11 Feb 2004, Olga Dmitrenko wrote:

> Dear all,
>
> I would much appreciate if somebody of you will kindly send me an example of
> the Gamess-US
> input with the Z-matrix which really works for GAMESS VERSION = 20 JUN 2002
> (R2).
> Somehow... I have troubles to run simple example on methylene molecule (I
> copied it
> > from
> http://www.npaci.edu/Resources/SciComp/Applications/GAMESS/gamess_sect3.html
> :
>
> $CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE COORD=ZMT NZVAR=0 $END
> $SYSTEM TIMLIM=2 MEMORY=100000 $END
> $STATPT OPTTOL=1.0E-5  $END
> $BASIS  GBASIS=STO NGAUSS=2 $END
> $GUESS  GUESS=HUCKEL $END
> $DATA
> Methylene...1-A-1 state...RHF/STO-2G
> Cnv  2
>
> C
> H  1 rCH
> H  1 rCH  2 aHCH
>
> rCH=1.09
> aHCH=110.0
> $END
>
> I am getting "**** ERROR, NO  $DATA   GROUP WAS FOUND".
>
>
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>



From chemistry-request@ccl.net Thu Feb 12 15:42:16 2004
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Subject: undergraduate computational chemistry conference
Date: Thu, 12 Feb 2004 15:42:19 -0500
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Thread-Topic: undergraduate computational chemistry conference
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From: "Parish, Carol" <parish_at_hws.edu>
To: <chemistry_at_ccl.net>
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We are pleased to announce the third national conference devoted solely to undergraduate computational chemistry, to be held atHamilton College in Clinton, NY, from July 29 - 31.  This conference is a great opportunity for undergraduates to learn about the breadth of research in computational chemistry and to discuss their work with other undergraduate computational chemists as well as some leaders in the field.  We have assembled an excellent group of speakers, all of whom will be available to speak with undergraduates about their work and on career opportunities in the field of computational chemistry.  Our confirmed speakers are:

 

                        Wendy Cornell (Novartis)

Jimmie Doll (Brown University)

                        Sharon Hammes-Schiffer (Pennsylvania State University)

Rig Hernandez (Georgia Institute of Technology)

Jurgen Schnitker (Wavefunction)

                        Mark Tuckerman (New York University)

                        Veronica Vaida (University of Colorado)

 

Registration is $200 per faculty member, $100 per faculty guest, and $100 per undergraduate, and includes:

                        Two nights accommodation in recently-renovated college housing

                        All meals, including a barbecue dinner on Thursday, July 29

                        Social activities on Thursday and Friday nights.

Costs for the conference are being kept low due to generous financial assistance from Hamilton College and SGI.  Registration materials are due by July 5th, and the deadline for poster abstract submission is July 14th.  Undergraduates are strongly encouraged to submit posters.  Additional details about accommodations and poster submission, including registration forms, can be found on the web site http://mars.chem.hamilton.edu/conference <http://mars.chem.hamilton.edu/conference> .

  

Sincerely,

 

George C. Shields                   Carol Parish

Hamilton College                    Hobart & William Smith Colleges

 

Jeffery Greathouse                  Maria Gomez              

St. Lawrence University          Mt. Holyoke College   

 

Marc Zimmer                          Ramona Taylor

Connecticut College                College of the Holy Cross




From chemistry-request@ccl.net Thu Feb 12 14:30:47 2004
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Subject: Summary: One question about protein-ligand binding
From: Baoqiang Cao <caobg:at:email.uc.edu>
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Dear All,

I was asked to summarize this question replies. After got some responses
> from very nice person, it is time to share what I got. Please see below
if you like.

1,(Michel Petitjean)
"If you have the atom-pairs (e.g. H bonds, vdw bonds), a simple
criterion
is the variance:
M.Petitjean, Internet Electron J. Mol. Des., 2002,1[4],185-192.
http://www.biochempress.com
Note: a rigorous definition of what is a cavity is difficult. The ALVIS
software offer a simple approach, but it is parametrized by the
radius of the probe."
And Michel also suggested one freeware:

"The freeware DOG
http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#DOG"

2,(Hide the author's name, required by the author)
"You can you Autodock3.0 or Cerius2 to calculate it quantitatively."


Have a nice weekend.

Best,
 Cao

> >Dear all,
> >
> >Are there any ways to quantitatively describe how well a ligand fits a
> >protein cavity? Any clues will be welcome!
> >Thanks.
> >
> >Best,
> > Cao
> 
> If you have the atom-pairs (e.g. H bonds, vdw bonds), a simple criterion
> is the variance:
> M.Petitjean, Internet Electron J. Mol. Des., 2002,1[4],185-192.
> http://www.biochempress.com
> 
> Note: a rigorous definition of what is a cavity is difficult. The ALVIS
> software offer a simple approach, but it is parametrized by the
> radius of the probe.
> 
> Michel Petitjean,                     Email: petitjean:at:itodys.jussieu.fr
> ITODYS (CNRS, UMR 7086)                      ptitjean:at:ccr.jussieu.fr
> http://petitjeanmichel.free.fr/itoweb.petitjean.html
> http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html
> 
> -= This is automatically added to each message by the mailing script =-
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> 
> 
> 
> 



From chemistry-request@ccl.net Thu Feb 12 18:09:08 2004
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Date: Thu, 12 Feb 2004 15:09:07 -0800 (PST)
From: John Bushnell <bushnell-.at.-chem.ucsb.edu>
To: Katie Doucet <kgdct-.at.-mta.ca>
Cc: CCL <chemistry-.at.-ccl.net>
Subject: Re: CCL:Playing Frequencies in PowerPoint?
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	servernd.ccl.net

I think the trick is to somehow make your animation into an animated
gif.  Then you can just stick it into your presentation and it will play
automatically.  There are probably a variety of ways/programs to do
this.  Alternatively, you can make a jpeg movie, though I'm told that
you then have to include the movie files along with the presentation.

  Sorry not to be more specific  -  John

On Thu, 12 Feb 2004, Katie Doucet wrote:

> 
> I was wondering if anyone knows of a way (either a program or a simple trick) 
> to play frequencies in a Microsoft PowerPoint presentation without having to 
> close out of the presentation.
> 
> Thanks
> -K.Doucet
> 
> 
> -= This is automatically added to each message by the mailing script =-
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> 
> 
> 
> 
> 


