From owner-chemistry@ccl.net Thu Jul 15 03:36:00 2010
From: "Haibin Scopus lihb734[A]yahoo.com" <owner-chemistry:+:server.ccl.net>
To: CCL
Subject: CCL:G: G03: How to generate a beta spin-orbital cube file using cubegen?
Message-Id: <-42280-100715033306-29882-yYkV2SNAfK89jSw11g4Tog:+:server.ccl.net>
X-Original-From: Haibin Scopus <lihb734,+,yahoo.com>
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Sent to CCL by: Haibin Scopus [lihb734=yahoo.com]
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Dear Sir,
=C2=A0=C2=A0=C2=A0 Maybe, you can try the following keyword
in a script:
=C2=A0 #! /bin/sh
=C2=A0 cubegen 512mb BMO=3D1 fchfile.chk cubefile.cub -2 h
=C2=A0 cubegen 512mb BMO=3D2 fchfile.chk cubefile.cub -2 h
=C2=A0 =E2=80=A6=E2=80=A6
=C2=A0 cubegen 512mb BMO=3Dn fchfile.chk cubefile.cube -2 h=C2=A0 (n is the=
 number your MO want to be output)
=C2=A0=20


=C2=A0








Haibin Li

Institute of Functional Material Chemistry, Faculty of Chemistry
Northeast Normal University=20
changchun, Jilin, 130024 PR CHINA

E-mail: lihb734-$-nenu.edu.cn; lihb734-$-yahoo.com
http://www.nenu.edu.cn

--- On Thu, 7/15/10, Will James McDonald mcdonald*_*chemistry.ucsc.edu <own=
er-chemistry-$-ccl.net> wrote:


> From: Will James McDonald mcdonald*_*chemistry.ucsc.edu <owner-chemistry-$-cc=
l.net>
Subject: CCL: G03: How to generate a beta spin-orbital cube file using cube=
gen?
To: "Li, Hai-Bin " <lihb734-$-yahoo.com>
Date: Thursday, July 15, 2010, 12:28 AM



Sent to CCL by: "Will James McDonald" [mcdonald.:.chemistry.ucsc.edu]
Dear all,

I have a spin-unrestricted PBE0 density and I would like to visualize a few=
 of the beta spin-orbitals. However, if I use the cubegen utility and the M=
O=3Dn keyword, only the n-th alpha spin-orbital is generated. Am I missing =
something obvious? How can one generate a cube file for a beta spin orbital=
 without generating files for all beta spin-orbitals using the OccB keyword=
 (there are 100 occupied beta orbitals)?
Your help is greatly appreciated.

Will McDonald
mcdonald::chemistry.ucsc.edu
Dept. Chem. and Biochem.
University of CA, Santa Cruz



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<table cellspacing=3D"0" cellpadding=3D"0" border=3D"0" ><tr><td valign=3D"=
top" style=3D"font: inherit;"><DIV>Dear Sir,</DIV>
<DIV>&nbsp;&nbsp;&nbsp; Maybe, you can try the following keyword</DIV>
<DIV>in a script:</DIV>
<DIV>&nbsp; #! /bin/sh</DIV>
<DIV>&nbsp; cubegen 512mb BMO=3D1 fchfile.chk cubefile.cub -2 h</DIV>
<DIV>&nbsp; cubegen 512mb BMO=3D2 fchfile.chk cubefile.cub -2 h</DIV>
<DIV>&nbsp; =E2=80=A6=E2=80=A6</DIV>
<DIV>&nbsp; cubegen 512mb BMO=3Dn fchfile.chk cubefile.cube -2 h&nbsp; (n i=
s the number your MO want to be output)</DIV>
<DIV>&nbsp; <BR><BR></DIV>
<DIV>&nbsp;</DIV>
<DIV>
<HR>

<DIV></DIV>
<DIV>
<HR>

<DIV></DIV>
<DIV><STRONG>Haibin Li</STRONG><BR></DIV>
<DIV>Institute of Functional Material Chemistry, Faculty of Chemistry<BR><S=
TRONG>Northeast Normal University</STRONG> <BR>changchun, Jilin, 130024 PR =
CHINA<BR><BR>E-mail: lihb734-$-nenu.edu.cn; lihb734-$-yahoo.com<BR>http://www.n=
enu.edu.cn</DIV><BR><BR>--- On <B>Thu, 7/15/10, Will James McDonald mcdonal=
d*_*chemistry.ucsc.edu <I>&lt;owner-chemistry-$-ccl.net&gt;</I></B> wrote:<BR=
>
<BLOCKQUOTE style=3D"BORDER-LEFT: rgb(16,16,255) 2px solid; PADDING-LEFT: 5=
px; MARGIN-LEFT: 5px"><BR>From: Will James McDonald mcdonald*_*chemistry.uc=
sc.edu &lt;owner-chemistry-$-ccl.net&gt;<BR>Subject: CCL: G03: How to generat=
e a beta spin-orbital cube file using cubegen?<BR>To: "Li, Hai-Bin =
" &lt;lihb734-$-yahoo.com&gt;<BR>Date: Thursday, July 15, 2010, 12:28 AM<BR><=
BR>
<DIV class=3DplainMail><BR>Sent to CCL by: "Will James McDonald" [mcdonald.=
:.chemistry.ucsc.edu]<BR>Dear all,<BR><BR>I have a spin-unrestricted PBE0 d=
ensity and I would like to visualize a few of the beta spin-orbitals. Howev=
er, if I use the cubegen utility and the MO=3Dn keyword, only the n-th alph=
a spin-orbital is generated. Am I missing something obvious? How can one ge=
nerate a cube file for a beta spin orbital without generating files for all=
 beta spin-orbitals using the OccB keyword (there are 100 occupied beta orb=
itals)?<BR>Your help is greatly appreciated.<BR><BR>Will McDonald<BR>mcdona=
ld::chemistry.ucsc.edu<BR>Dept. Chem. and Biochem.<BR>University of CA, San=
ta Cruz<BR><BR><BR><BR>-=3D This is automatically added to each message by =
the mailing script =3D-<BR>To recover the email address of the author of th=
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From owner-chemistry@ccl.net Thu Jul 15 08:20:01 2010
From: "Liang Xinghua chemknight###hotmail.com" <owner-chemistry:-:server.ccl.net>
To: CCL
Subject: CCL:G: =?gb2312?B?tPC4tDogRzAzOiBIb3cgdG8gZ2VuZXJhdGUgYSBiZXRhIHNwaW4tbw==?= =?gb2312?B?cmJpdGFsIGN1YmUgZmlsZSB1c2luZyBjdWJlZ2VuPw==?=
Message-Id: <-42281-100714234441-23216-KIOz1CjwtzHKBtg7Z07rEw:-:server.ccl.net>
X-Original-From: "Liang Xinghua" <chemknight#,#hotmail.com>
Content-Transfer-Encoding: 8bit
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Date: Thu, 15 Jul 2010 11:44:31 +0800
MIME-Version: 1.0


Sent to CCL by: "Liang Xinghua" [chemknight**hotmail.com]
If you have total N alpha spin and N beta spin orbitals, you can use mo=n to
generate n-th alpha spin orbital and mo=N+n to generate n-th beta spin
orbital.

Best regards


Xinghua
----------------------------------------------------------------------------
-------------------------------------------------------
#################################################
Xinghua Liang, Ph.D candidate
State Key Lab for Phys. Chem. of Solid Surf. 
& Dept. of Chem.
Xiamen University, Xiamen 361005, CHINA
Email: chemknight[#]hotmail.com
       xhliang[#]xmu.edu.cn
################################################# 
 
-----ÓʼþÔ­¼þ-----
·¢¼þÈË: owner-chemistry+chemknight==hotmail.com[#]ccl.net
[mailto:owner-chemistry+chemknight==hotmail.com[#]ccl.net] ´ú±í Will James
McDonald mcdonald*_*chemistry.ucsc.edu
·¢ËÍʱ¼ä: 2010Äê7ÔÂ15ÈÕ 8:28
ÊÕ¼þÈË: Liang, Hua Xing 
Ö÷Ìâ: CCL: G03: How to generate a beta spin-orbital cube file using cubegen?


Sent to CCL by: "Will James McDonald" [mcdonald.:.chemistry.ucsc.edu]
Dear all,

I have a spin-unrestricted PBE0 density and I would like to visualize a few
of the beta spin-orbitals. However, if I use the cubegen utility and the
MO=n keyword, only the n-th alpha spin-orbital is generated. Am I missing
something obvious? How can one generate a cube file for a beta spin orbital
without generating files for all beta spin-orbitals using the OccB keyword
(there are 100 occupied beta orbitals)?
Your help is greatly appreciated.

Will McDonald
mcdonald::chemistry.ucsc.edu
Dept. Chem. and Biochem.
University of CA, Santa Cruzhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

From owner-chemistry@ccl.net Thu Jul 15 08:55:00 2010
From: "sobereva sobjubao{=}yahoo.com.cn" <owner-chemistry###server.ccl.net>
To: CCL
Subject: CCL:G: G03: How to generate a beta spin-orbital cube file using cubegen?
Message-Id: <-42282-100715070421-14001-2g8a8rY52gpcT/ARnjvdQg###server.ccl.net>
X-Original-From: sobereva <sobjubao*_*yahoo.com.cn>
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Date: Thu, 15 Jul 2010 19:04:08 +0800 (CST)
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Sent to CCL by: sobereva [sobjubao|yahoo.com.cn]
Hello

If you are using windows platform, I suggest you use Multiwfn program instead of cubegen, Multiwfn is free of charge, can be downloaded at http://multiwfn.codeplex.com

There is a examples file within Multiwfn package, a triplet water calculated at UB3LYP/6-31G*, assuming you want to generate the 2th beta orbital. Boot up multiwfn and input commands as follows, the text after "//" is comment:
examples\h2o-m3ub3lyp.fch    //Input file name. Program prompts there are 10 occupied MOs, the first six orbitals is alpha spin, the last four is beta spin.
-1   //Select a MO
8   //The 8th MO equals the 2th beta MO
5   //Generate cube file
4   //Select wavefunction value as property
80,80,80  //Number of grid in each direction
n  //Use default origin and spacing setting. Now multiwfn start to generate cube file
n  //Don't preview isosurface

As you can see, the cube file "MOvalue.cub" has been saved to current folder.

Tian Lu


--- On Thu, 7/15/10, Will James McDonald mcdonald*_*chemistry.ucsc.edu <owner-chemistry###ccl.net> wrote:

> From: Will James McDonald mcdonald*_*chemistry.ucsc.edu <owner-chemistry###ccl.net>
> Subject: CCL: G03: How to generate a beta spin-orbital cube file using cubegen?
> To: "Lu, Tian " <sobjubao###yahoo.com.cn>
> Date: Thursday, July 15, 2010, 8:28 AM
> 
> Sent to CCL by: "Will James McDonald"
> [mcdonald.:.chemistry.ucsc.edu]
> Dear all,
> 
> I have a spin-unrestricted PBE0 density and I would like to
> visualize a few of the beta spin-orbitals. However, if I use
> the cubegen utility and the MO=n keyword, only the n-th
> alpha spin-orbital is generated. Am I missing something
> obvious? How can one generate a cube file for a beta spin
> orbital without generating files for all beta spin-orbitals
> using the OccB keyword (there are 100 occupied beta
> orbitals)?
> Your help is greatly appreciated.
> 
> Will McDonald
> mcdonald::chemistry.ucsc.edu
> Dept. Chem. and Biochem.
> University of CA, Santa Cruz
> 
> 
> 
> -= This is automatically added to each message by the
> mailing script =-
> To recover the email address of the author of the message,
> please change
> the strange characters on the top line to the ### sign. You
> can also> 
> E-mail to subscribers: CHEMISTRY###ccl.net
> or use:
>      > 
> E-mail to administrators: CHEMISTRY-REQUEST###ccl.net
> or use
>      >      >      > 
> 
>


From owner-chemistry@ccl.net Thu Jul 15 13:24:00 2010
From: "Faranak Teimoory teimoory _ ualberta.ca" <owner-chemistry . server.ccl.net>
To: CCL
Subject: CCL:G: Question in Gar2ped
Message-Id: <-42283-100715122434-17907-VBVu2qo9k81j5OWJ+jl0vw . server.ccl.net>
X-Original-From: "Faranak Teimoory" <teimoory*_*ualberta.ca>
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Sent to CCL by: "Faranak Teimoory" [teimoory#ualberta.ca]
Hello,

I have a question in using Gar2ped after frequency optimization by
Gaussian. Could anybody help me regarding that? I miss one coordinate
when I define my molecule for it. It is a bi-cyclic molecule.I don't  
know if it is possible to use Gar2ped for getting internal coordinates  
of a bi-cyclic molecule.
Thanks in advance,


Faranak Teimoory
Department of Chemistry
University of Alberta


From owner-chemistry@ccl.net Thu Jul 15 13:59:00 2010
From: "RITESH RUHELA riteshruhela*|*gmail.com" <owner-chemistry*server.ccl.net>
To: CCL
Subject: CCL:G: Use of memory in Gaussian G09 A.01
Message-Id: <-42284-100715123042-28829-hYPIuKdwJ1hjp0dMZQfPuA*server.ccl.net>
X-Original-From: "RITESH  RUHELA" <riteshruhela!^!gmail.com>
Date: Thu, 15 Jul 2010 12:30:41 -0400


Sent to CCL by: "RITESH  RUHELA" [riteshruhela_._gmail.com]
Dear Sirs,

During submission of input files to Gaussian setup I have allocated the memory  %Mem=3GB (4 GB RAM installed on computer) but that is not used and only 98MB to 100MB is used which may be the default amount of memory to be used.
Please suggest solution
My input file is like this
#!/bin/csh
g09 <<END >Butanol.log
%Chk=Butanol
%nproc=2
%mem=3GB
# opt freq b3lyp/6-31g geom=connectivity maxdisk=50GB

Butanol

0 2
 C
 C                  1              B1
 H                  2              B2    1              A1
 H                  1              B3    2              A2    3              D1
 H                  1              B4    2              A3    3              D2
 H                  1              B5    2              A4    3              D3
 C                  2              B6    1              A5    5              D4
 C                  2              B7    1              A6    7              D5
 H                  7              B8    2              A7    1              D6
 H                  7              B9    2              A8    1              D7
 H                  7             B10    2              A9    1              D8
 H                  8             B11    2             A10    1              D9
 H                  8             B12    2             A11    1             D10
 H                  8             B13    2             A12    1             D11
 O                  2             B14    1             A13    8             D12
 H                 15             B15    2             A14    1             D13

   B1             1.51406800
   B2             1.07000000
   B3             1.11644874
   B4             1.11644381
   B5             1.11664517
   B6             1.51402453
   B7             1.51404109
   B8             1.11645622
   B9             1.11666091
   B10            1.11645245
   B11            1.11667599
   B12            1.11644791
   B13            1.11645747
   B14            1.43000000
   B15            0.96000000
   A1           108.30952950
   A2           110.36644929
   A3           110.36741915
   A4           110.54594623
   A5           110.61815801
   A6           110.60280120
   A7           110.37143826
   A8           110.54211016
   A9           110.37419373
   A10          110.54205025
   A11          110.36772166
   A12          110.36672078
   A13           71.68271412
   A14          109.50000006
   D1           -60.04506197
   D2            60.01052251
   D3           179.98317110
   D4           -58.54739125
   D5          -122.89278591
   D6           178.57049716
   D7           -61.45604764
   D8            58.51719315
   D9            61.42348809
   D10         -178.59986516
   D11          -58.54459103
   D12           61.46250331
   D13           60.01634167

 1 2 1.0 4 1.0 5 1.0 6 1.0
 2 7 1.0 8 1.0 3 1.0 15 1.0
 3
 4
 5
 6
 7 9 1.0 10 1.0 11 1.0
 8 12 1.0 13 1.0 14 1.0
 9
 10
 11
 12
 13
 14
 15 16 1.0
 16

 
END
echo "Job done. "

also how i can permanently allocate 2-3GB memory 
i have tried the command %Mem=3GB like this

itesh()linux-fhmj:~> csh
gr=/home/ritesh: Command not found.
if: Expression Syntax.
/home/ritesh> cd gussion
ritesh/gussion> cd g09
gussion/g09> %Mem=3GB
%Mem=3GB: No such job.
gussion/g09>

please suggest the solution for this also

thankyou with regards


From owner-chemistry@ccl.net Thu Jul 15 15:37:00 2010
From: "Serdar Bado?lu sbadoglu(_)gazi.edu.tr" <owner-chemistry{}server.ccl.net>
To: CCL
Subject: CCL:G: Use of memory in Gaussian G09 A.01
Message-Id: <-42285-100715153523-31459-MEAxJg+sxvq2MVgktdvekA{}server.ccl.net>
X-Original-From: "Serdar Bado?lu" <sbadoglu!A!gazi.edu.tr>
Content-Type: text/plain; charset="iso-8859-9" 
Date: Thu, 15 Jul 2010 19:35:14 -0000


Sent to CCL by: "Serdar Bado?lu" [sbadoglu[]gazi.edu.tr]
Dear Ritesh,

I'm using Gaussian 03 not 09, but I suppose settings are the same. Now if
I'm not wrong, %mem stands for the memory per core. Because %nproc=2 in
your case, Gaussian looks for 2 x 3 GB = 6 GB of memory, but your total
physical memory is 4 GB. So, that's why it used only 98-100 MB (default
memory setting is 6 MW which is roughly equal to 96 MB). Try %mem=1500MB,
this should work. With %nproc=2, this means that Gaussian will use 3GB of
memory. Also, try not to spend all of the memory for Gaussian, keep some
for the operating system and other stuff.

Regards


-- 
Serdar BADOGLU
Gazi University
Department of Physics


From owner-chemistry@ccl.net Thu Jul 15 16:12:00 2010
From: "Jamin Krinsky jamink%a%berkeley.edu" <owner-chemistry_+_server.ccl.net>
To: CCL
Subject: CCL:G: Use of memory in Gaussian G09 A.01
Message-Id: <-42286-100715152410-29106-6FSp5qT5fshJ0OD9khptIQ_+_server.ccl.net>
X-Original-From: Jamin Krinsky <jamink|,|berkeley.edu>
Content-Type: multipart/alternative; boundary=000e0cd29e10515fc5048b720b76
Date: Thu, 15 Jul 2010 12:23:59 -0700
MIME-Version: 1.0


Sent to CCL by: Jamin Krinsky [jamink]![berkeley.edu]
--000e0cd29e10515fc5048b720b76
Content-Type: text/plain; charset=ISO-8859-1

Dear Ritesh,

It looks like you are doing things correctly (you might need to specify
nprocshared instead of nproc). Your example is a small molecule so it's
probable that your calculation only needs 100MB of memory. You should try
running a frequency calculation on something with 100 atoms or so and see
how much memory it's using then. If you do that and still only see 100MB
being used then there is probably a problem with your system's memory
allocation, not a problem with how you're setting up your Gaussian jobs. FYI
according to the manual G09's default memory usage is 256MB. Finally, I'd
recommend making a Default.Route file as per the instructions in the
"Efficient use of Gaussian" section, putting in values for mem and maxdisk.

Regards,
Jamin


On Thu, Jul 15, 2010 at 9:30 AM, RITESH RUHELA riteshruhela*|*gmail.com <
owner-chemistry:-:ccl.net> wrote:

>
> Sent to CCL by: "RITESH  RUHELA" [riteshruhela_._gmail.com]
> Dear Sirs,
>
> During submission of input files to Gaussian setup I have allocated the
> memory  %Mem=3GB (4 GB RAM installed on computer) but that is not used and
> only 98MB to 100MB is used which may be the default amount of memory to be
> used.
> Please suggest solution
> My input file is like this
> #!/bin/csh
> g09 <<END >Butanol.log
> %Chk=Butanol
> %nproc=2
> %mem=3GB
> # opt freq b3lyp/6-31g geom=connectivity maxdisk=50GB
>
> Butanol
>
> 0 2
>  C
>  C                  1              B1
>  H                  2              B2    1              A1
>  H                  1              B3    2              A2    3
>  D1
>  H                  1              B4    2              A3    3
>  D2
>  H                  1              B5    2              A4    3
>  D3
>  C                  2              B6    1              A5    5
>  D4
>  C                  2              B7    1              A6    7
>  D5
>  H                  7              B8    2              A7    1
>  D6
>  H                  7              B9    2              A8    1
>  D7
>  H                  7             B10    2              A9    1
>  D8
>  H                  8             B11    2             A10    1
>  D9
>  H                  8             B12    2             A11    1
> D10
>  H                  8             B13    2             A12    1
> D11
>  O                  2             B14    1             A13    8
> D12
>  H                 15             B15    2             A14    1
> D13
>
>   B1             1.51406800
>   B2             1.07000000
>   B3             1.11644874
>   B4             1.11644381
>   B5             1.11664517
>   B6             1.51402453
>   B7             1.51404109
>   B8             1.11645622
>   B9             1.11666091
>   B10            1.11645245
>   B11            1.11667599
>   B12            1.11644791
>   B13            1.11645747
>   B14            1.43000000
>   B15            0.96000000
>   A1           108.30952950
>   A2           110.36644929
>   A3           110.36741915
>   A4           110.54594623
>   A5           110.61815801
>   A6           110.60280120
>   A7           110.37143826
>   A8           110.54211016
>   A9           110.37419373
>   A10          110.54205025
>   A11          110.36772166
>   A12          110.36672078
>   A13           71.68271412
>   A14          109.50000006
>   D1           -60.04506197
>   D2            60.01052251
>   D3           179.98317110
>   D4           -58.54739125
>   D5          -122.89278591
>   D6           178.57049716
>   D7           -61.45604764
>   D8            58.51719315
>   D9            61.42348809
>   D10         -178.59986516
>   D11          -58.54459103
>   D12           61.46250331
>   D13           60.01634167
>
>  1 2 1.0 4 1.0 5 1.0 6 1.0
>  2 7 1.0 8 1.0 3 1.0 15 1.0
>  3
>  4
>  5
>  6
>  7 9 1.0 10 1.0 11 1.0
>  8 12 1.0 13 1.0 14 1.0
>  9
>  10
>  11
>  12
>  13
>  14
>  15 16 1.0
>  16
>
>
> END
> echo "Job done. "
>
> also how i can permanently allocate 2-3GB memory
> i have tried the command %Mem=3GB like this
>
> itesh++linux-fhmj:~> csh
> gr=/home/ritesh: Command not found.
> if: Expression Syntax.
> /home/ritesh> cd gussion
> ritesh/gussion> cd g09
> gussion/g09> %Mem=3GB
> %Mem=3GB: No such job.
> gussion/g09>
>
> please suggest the solution for this also
>
> thankyou with regards>
>
>


-- 
Jamin L Krinsky, Ph.D.
Molecular Graphics and Computation Facility
175 Tan Hall, University of California, Berkeley, CA 94720
jamink:-:berkeley.edu, 510-643-0616
http://glab.cchem.berkeley.edu

--000e0cd29e10515fc5048b720b76
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Dear Ritesh,<br><br>It looks like you are doing things correctly (you might=
 need to specify nprocshared instead of nproc). Your example is a small mol=
ecule so it&#39;s probable that your calculation only needs 100MB of memory=
. You should try running a frequency calculation on something with 100 atom=
s or so and see how much memory it&#39;s using then. If you do that and sti=
ll only see 100MB being used then there is probably a problem with your sys=
tem&#39;s memory allocation, not a problem with how you&#39;re setting up y=
our Gaussian jobs. FYI according to the manual G09&#39;s default memory usa=
ge is 256MB. Finally, I&#39;d recommend making a Default.Route file as per =
the instructions in the &quot;Efficient use of Gaussian&quot; section, putt=
ing in values for mem and maxdisk.<br>
<br>Regards,<br>Jamin<br><br><br><div class=3D"gmail_quote">On Thu, Jul 15,=
 2010 at 9:30 AM, RITESH RUHELA riteshruhela*|*<a href=3D"http://gmail.com"=
>gmail.com</a> <span dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry:-:ccl.=
net">owner-chemistry:-:ccl.net</a>&gt;</span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin: 0pt 0pt 0pt 0.8ex; borde=
r-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><br>
Sent to CCL by: &quot;RITESH =A0RUHELA&quot; [riteshruhela_._<a href=3D"htt=
p://gmail.com" target=3D"_blank">gmail.com</a>]<br>
Dear Sirs,<br>
<br>
During submission of input files to Gaussian setup I have allocated the mem=
ory =A0%Mem=3D3GB (4 GB RAM installed on computer) but that is not used and=
 only 98MB to 100MB is used which may be the default amount of memory to be=
 used.<br>

Please suggest solution<br>
My input file is like this<br>
#!/bin/csh<br>
g09 &lt;&lt;END &gt;Butanol.log<br>
%Chk=3DButanol<br>
%nproc=3D2<br>
%mem=3D3GB<br>
# opt freq b3lyp/6-31g geom=3Dconnectivity maxdisk=3D50GB<br>
<br>
Butanol<br>
<br>
0 2<br>
=A0C<br>
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0B1<br>
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0B2 =A0=
 =A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0A1<br>
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0B3 =A0=
 =A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0A2 =A0 =A03 =A0 =A0 =A0 =A0 =A0 =A0 =A0D1<=
br>
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0B4 =A0=
 =A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0A3 =A0 =A03 =A0 =A0 =A0 =A0 =A0 =A0 =A0D2<=
br>
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0B5 =A0=
 =A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0A4 =A0 =A03 =A0 =A0 =A0 =A0 =A0 =A0 =A0D3<=
br>
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0B6 =A0=
 =A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0A5 =A0 =A05 =A0 =A0 =A0 =A0 =A0 =A0 =A0D4<=
br>
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0B7 =A0=
 =A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0A6 =A0 =A07 =A0 =A0 =A0 =A0 =A0 =A0 =A0D5<=
br>
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A07 =A0 =A0 =A0 =A0 =A0 =A0 =A0B8 =A0=
 =A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0A7 =A0 =A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0D6<=
br>
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A07 =A0 =A0 =A0 =A0 =A0 =A0 =A0B9 =A0=
 =A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0A8 =A0 =A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0D7<=
br>
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A07 =A0 =A0 =A0 =A0 =A0 =A0 B10 =A0 =
=A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0A9 =A0 =A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0D8<b=
r>
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A08 =A0 =A0 =A0 =A0 =A0 =A0 B11 =A0 =
=A02 =A0 =A0 =A0 =A0 =A0 =A0 A10 =A0 =A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0D9<br>
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A08 =A0 =A0 =A0 =A0 =A0 =A0 B12 =A0 =
=A02 =A0 =A0 =A0 =A0 =A0 =A0 A11 =A0 =A01 =A0 =A0 =A0 =A0 =A0 =A0 D10<br>
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A08 =A0 =A0 =A0 =A0 =A0 =A0 B13 =A0 =
=A02 =A0 =A0 =A0 =A0 =A0 =A0 A12 =A0 =A01 =A0 =A0 =A0 =A0 =A0 =A0 D11<br>
=A0O =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A02 =A0 =A0 =A0 =A0 =A0 =A0 B14 =A0 =
=A01 =A0 =A0 =A0 =A0 =A0 =A0 A13 =A0 =A08 =A0 =A0 =A0 =A0 =A0 =A0 D12<br>
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 15 =A0 =A0 =A0 =A0 =A0 =A0 B15 =A0 =A0=
2 =A0 =A0 =A0 =A0 =A0 =A0 A14 =A0 =A01 =A0 =A0 =A0 =A0 =A0 =A0 D13<br>
<br>
 =A0 B1 =A0 =A0 =A0 =A0 =A0 =A0 1.51406800<br>
 =A0 B2 =A0 =A0 =A0 =A0 =A0 =A0 1.07000000<br>
 =A0 B3 =A0 =A0 =A0 =A0 =A0 =A0 1.11644874<br>
 =A0 B4 =A0 =A0 =A0 =A0 =A0 =A0 1.11644381<br>
 =A0 B5 =A0 =A0 =A0 =A0 =A0 =A0 1.11664517<br>
 =A0 B6 =A0 =A0 =A0 =A0 =A0 =A0 1.51402453<br>
 =A0 B7 =A0 =A0 =A0 =A0 =A0 =A0 1.51404109<br>
 =A0 B8 =A0 =A0 =A0 =A0 =A0 =A0 1.11645622<br>
 =A0 B9 =A0 =A0 =A0 =A0 =A0 =A0 1.11666091<br>
 =A0 B10 =A0 =A0 =A0 =A0 =A0 =A01.11645245<br>
 =A0 B11 =A0 =A0 =A0 =A0 =A0 =A01.11667599<br>
 =A0 B12 =A0 =A0 =A0 =A0 =A0 =A01.11644791<br>
 =A0 B13 =A0 =A0 =A0 =A0 =A0 =A01.11645747<br>
 =A0 B14 =A0 =A0 =A0 =A0 =A0 =A01.43000000<br>
 =A0 B15 =A0 =A0 =A0 =A0 =A0 =A00.96000000<br>
 =A0 A1 =A0 =A0 =A0 =A0 =A0 108.30952950<br>
 =A0 A2 =A0 =A0 =A0 =A0 =A0 110.36644929<br>
 =A0 A3 =A0 =A0 =A0 =A0 =A0 110.36741915<br>
 =A0 A4 =A0 =A0 =A0 =A0 =A0 110.54594623<br>
 =A0 A5 =A0 =A0 =A0 =A0 =A0 110.61815801<br>
 =A0 A6 =A0 =A0 =A0 =A0 =A0 110.60280120<br>
 =A0 A7 =A0 =A0 =A0 =A0 =A0 110.37143826<br>
 =A0 A8 =A0 =A0 =A0 =A0 =A0 110.54211016<br>
 =A0 A9 =A0 =A0 =A0 =A0 =A0 110.37419373<br>
 =A0 A10 =A0 =A0 =A0 =A0 =A0110.54205025<br>
 =A0 A11 =A0 =A0 =A0 =A0 =A0110.36772166<br>
 =A0 A12 =A0 =A0 =A0 =A0 =A0110.36672078<br>
 =A0 A13 =A0 =A0 =A0 =A0 =A0 71.68271412<br>
 =A0 A14 =A0 =A0 =A0 =A0 =A0109.50000006<br>
 =A0 D1 =A0 =A0 =A0 =A0 =A0 -60.04506197<br>
 =A0 D2 =A0 =A0 =A0 =A0 =A0 =A060.01052251<br>
 =A0 D3 =A0 =A0 =A0 =A0 =A0 179.98317110<br>
 =A0 D4 =A0 =A0 =A0 =A0 =A0 -58.54739125<br>
 =A0 D5 =A0 =A0 =A0 =A0 =A0-122.89278591<br>
 =A0 D6 =A0 =A0 =A0 =A0 =A0 178.57049716<br>
 =A0 D7 =A0 =A0 =A0 =A0 =A0 -61.45604764<br>
 =A0 D8 =A0 =A0 =A0 =A0 =A0 =A058.51719315<br>
 =A0 D9 =A0 =A0 =A0 =A0 =A0 =A061.42348809<br>
 =A0 D10 =A0 =A0 =A0 =A0 -178.59986516<br>
 =A0 D11 =A0 =A0 =A0 =A0 =A0-58.54459103<br>
 =A0 D12 =A0 =A0 =A0 =A0 =A0 61.46250331<br>
 =A0 D13 =A0 =A0 =A0 =A0 =A0 60.01634167<br>
<br>
=A01 2 1.0 4 1.0 5 1.0 6 1.0<br>
=A02 7 1.0 8 1.0 3 1.0 15 1.0<br>
=A03<br>
=A04<br>
=A05<br>
=A06<br>
=A07 9 1.0 10 1.0 11 1.0<br>
=A08 12 1.0 13 1.0 14 1.0<br>
=A09<br>
=A010<br>
=A011<br>
=A012<br>
=A013<br>
=A014<br>
=A015 16 1.0<br>
=A016<br>
<br>
<br>
END<br>
echo &quot;Job done. &quot;<br>
<br>
also how i can permanently allocate 2-3GB memory<br>
i have tried the command %Mem=3D3GB like this<br>
<br>
itesh++linux-fhmj:~&gt; csh<br>
gr=3D/home/ritesh: Command not found.<br>
if: Expression Syntax.<br>
/home/ritesh&gt; cd gussion<br>
ritesh/gussion&gt; cd g09<br>
gussion/g09&gt; %Mem=3D3GB<br>
%Mem=3D3GB: No such job.<br>
gussion/g09&gt;<br>
<br>
please suggest the solution for this also<br>
<br>
thankyou with regards<br>
<br>
<br>
<br>
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<br>
<br>
</blockquote></div><br><br clear=3D"all"><br>-- <br>Jamin L Krinsky, Ph.D.<=
br>Molecular Graphics and Computation Facility<br>175 Tan Hall, University =
of California, Berkeley, CA 94720<br><a href=3D"mailto:jamink:-:berkeley.edu"=
>jamink:-:berkeley.edu</a>, 510-643-0616<br>
<a href=3D"http://glab.cchem.berkeley.edu">http://glab.cchem.berkeley.edu</=
a><br><br>

--000e0cd29e10515fc5048b720b76--


From owner-chemistry@ccl.net Thu Jul 15 16:47:00 2010
From: "Jamin Krinsky jamink]|[berkeley.edu" <owner-chemistry- -server.ccl.net>
To: CCL
Subject: CCL:G: Use of memory in Gaussian G09 A.01
Message-Id: <-42287-100715163611-24596-oZxhrTzQV+8BE9HOYcjBnw- -server.ccl.net>
X-Original-From: Jamin Krinsky <jamink.- -.berkeley.edu>
Content-Type: multipart/alternative; boundary=000e0cd304eafa8140048b730c99
Date: Thu, 15 Jul 2010 13:36:01 -0700
MIME-Version: 1.0


Sent to CCL by: Jamin Krinsky [jamink]-[berkeley.edu]
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In Gaussian the mem keyword specifies the total for the job, NOT per cpu (if
running network parallel with LINDA than it is the memory for each node).
Also, if you specify more memory than exists and the job asks for the
specified amount of memory the job will die, it won't revert to the default.
Jamin


2010/7/15 Serdar Bado?lu sbadoglu(_)gazi.edu.tr <owner-chemistry[a]ccl.net>

>
> Sent to CCL by: "Serdar Bado?lu" [sbadoglu[]gazi.edu.tr]
> Dear Ritesh,
>
> I'm using Gaussian 03 not 09, but I suppose settings are the same. Now if
> I'm not wrong, %mem stands for the memory per core. Because %nproc=2 in
> your case, Gaussian looks for 2 x 3 GB = 6 GB of memory, but your total
> physical memory is 4 GB. So, that's why it used only 98-100 MB (default
> memory setting is 6 MW which is roughly equal to 96 MB). Try %mem=1500MB,
> this should work. With %nproc=2, this means that Gaussian will use 3GB of
> memory. Also, try not to spend all of the memory for Gaussian, keep some
> for the operating system and other stuff.
>
> Regards
>
>
> --
> Serdar BADOGLU
> Gazi University
> Department of Physics>
>
>


-- 
Jamin L Krinsky, Ph.D.
Molecular Graphics and Computation Facility
175 Tan Hall, University of California, Berkeley, CA 94720
jamink[a]berkeley.edu, 510-643-0616
http://glab.cchem.berkeley.edu

--000e0cd304eafa8140048b730c99
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

In Gaussian the mem keyword specifies the total for the job, NOT per cpu (i=
f running network parallel with LINDA than it is the memory for each node).=
 Also, if you specify more memory than exists and the job asks for the spec=
ified amount of memory the job will die, it won&#39;t revert to the default=
.<br>
Jamin<br><br><br><div class=3D"gmail_quote">2010/7/15 Serdar Bado?lu sbadog=
lu(_)<a href=3D"http://gazi.edu.tr">gazi.edu.tr</a> <span dir=3D"ltr">&lt;<=
a href=3D"mailto:owner-chemistry[a]ccl.net">owner-chemistry[a]ccl.net</a>&gt;</=
span><br>
<blockquote class=3D"gmail_quote" style=3D"margin: 0pt 0pt 0pt 0.8ex; borde=
r-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><br>
Sent to CCL by: &quot;Serdar Bado?lu&quot; [sbadoglu[]<a href=3D"http://gaz=
i.edu.tr" target=3D"_blank">gazi.edu.tr</a>]<br>
Dear Ritesh,<br>
<br>
I&#39;m using Gaussian 03 not 09, but I suppose settings are the same. Now =
if<br>
I&#39;m not wrong, %mem stands for the memory per core. Because %nproc=3D2 =
in<br>
your case, Gaussian looks for 2 x 3 GB =3D 6 GB of memory, but your total<b=
r>
physical memory is 4 GB. So, that&#39;s why it used only 98-100 MB (default=
<br>
memory setting is 6 MW which is roughly equal to 96 MB). Try %mem=3D1500MB,=
<br>
this should work. With %nproc=3D2, this means that Gaussian will use 3GB of=
<br>
memory. Also, try not to spend all of the memory for Gaussian, keep some<br=
>
for the operating system and other stuff.<br>
<br>
Regards<br>
<br>
<br>
--<br>
Serdar BADOGLU<br>
Gazi University<br>
Department of Physics<br>
<br>
<br>
<br>
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<br>
</blockquote></div><br><br clear=3D"all"><br>-- <br>Jamin L Krinsky, Ph.D.<=
br>Molecular Graphics and Computation Facility<br>175 Tan Hall, University =
of California, Berkeley, CA 94720<br><a href=3D"mailto:jamink[a]berkeley.edu"=
>jamink[a]berkeley.edu</a>, 510-643-0616<br>
<a href=3D"http://glab.cchem.berkeley.edu">http://glab.cchem.berkeley.edu</=
a><br><br>

--000e0cd304eafa8140048b730c99--


From owner-chemistry@ccl.net Thu Jul 15 17:22:00 2010
From: "zborowsk^^chemia.uj.edu.pl" <owner-chemistry..server.ccl.net>
To: CCL
Subject: CCL:G: Question in Gar2ped
Message-Id: <-42288-100715171648-22000-A8EkbBD9/gMINN3xCPEd1g..server.ccl.net>
X-Original-From: zborowsk*|*chemia.uj.edu.pl
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;charset=iso-8859-2
Date: Thu, 15 Jul 2010 23:16:37 +0200 (CEST)
MIME-Version: 1.0


Sent to CCL by: zborowsk[]chemia.uj.edu.pl
Hi

I have not used gar2ped for a bicyclic molecule so far. But, if you do not
have very old version of gar2ped, you should have the butterfly coordinate
that can help you.

>
> Sent to CCL by: "Faranak Teimoory" [teimoory#ualberta.ca]
> Hello,
>
> I have a question in using Gar2ped after frequency optimization by
> Gaussian. Could anybody help me regarding that? I miss one coordinate
> when I define my molecule for it. It is a bi-cyclic molecule.I don't
> know if it is possible to use Gar2ped for getting internal coordinates
> of a bi-cyclic molecule.
> Thanks in advance,
>
>
> Faranak Teimoory
> Department of Chemistry
> University of Alberta>
>
>


-- 
http://www.youtube.com/watch?v=EXh0PT2lovk&feature=channel




Krzysztof K. Zborowski
Faculty of Chemistry
Jagiellonian University
3 Ingardena Street
30-060 Krakow
Poland
phone: +48(12)632-4888 ext. 2064 or 2067
fax:  +48(12)634-05-15
email: zborowsk++chemia.uj.edu.pl
gg 3817259
skype kzys70
www.chemia.uj.edu.pl/~zborowsk


From owner-chemistry@ccl.net Thu Jul 15 17:57:00 2010
From: "Alex Allardyce aa() chemaxon.hu" <owner-chemistry::server.ccl.net>
To: CCL
Subject: CCL: Program announcement and call for participants: ChemAxon's US UGM: September 14-15, Boston, MA
Message-Id: <-42289-100715142456-15696-0NrimKqTNnRhLZi9CperXA::server.ccl.net>
X-Original-From: Alex Allardyce <aa(!)chemaxon.hu>
Content-Type: multipart/alternative;
 boundary="------------070009090606000204060102"
Date: Thu, 15 Jul 2010 20:24:45 +0200
MIME-Version: 1.0


Sent to CCL by: Alex Allardyce [aa,+,chemaxon.hu]
This is a multi-part message in MIME format.
--------------070009090606000204060102
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Content-Transfer-Encoding: 7bit

  Please excuse cross postings.

The program is now available for ChemAxon's 2010 US User Group Meeting 
which will be held on Tuesday and Wednesday September 14-15 at the Omni 
Parker House, Downtown Boston. The meeting will preceded by a end user & 
developer training day on September 13th and followed by a Markush Forum 
on the morning of September 16th.

Program: http://www.chemaxon.com/events/2010-us-ugm/#program

The meeting will feature presentations from ChemAxon users, introduce a 
focus session on* SharePoint*, lightning presentations/exhibition from 
ChemAxon Partners and the latest updates on product developments.

Preceding the meeting will be a dual track developer and end user 
Training Day on May 18th. To see the topics and schedule visit:

    * Developer Training Day:
      http://www.chemaxon.com/events/2010-us-ugm/#training--developer
    * End user: Application Focus Training Day:
      http://www.chemaxon.com/events/2010-us-ugm/#training--application-focus

Following the UGM we have the first meeting of the *Markush Forum*, an 
open morning for interested organizations (users and content developers) 
to participate in the further development of ChemAxon's tools for 
Markush structure enumeration and search. More information here: 
http://www.chemaxon.com/events/2010-us-ugm/#markush-forum

To find out more about the meeting , register or submit a poster 
abstract (open until September 6th) and view the program, please visit: 
http://www.chemaxon.com/events/2010-eugm/. To review the archives of 
previous meetings, including original presentations (slides and video) 
and meeting reports from Yvonne Martin and Wendy Warr visit: 
http://www.chemaxon.com/library/ugm-presentations/. Yvonne Martin's 
meeting report from San Diego 2009 is here 
https://www.chemaxon.com/library/ugm-presentations/2009-us/#2

We hope you can join us for a very interesting event.

BR
Alex

Selected user presentations:

    * Evaluation of pKa Estimation Methods on 211 Druglike Compounds.  
      Joann Prescott Roy, AstraZeneca
    * A Robotic Chemistry System for the Discovery of Cancer-Specific
      Targeting Ligands. John Frangioni, Harvard Medical School
    * Migrating Chemical Toolkits. Dan Durkin, Broad Institute
    * 2004-2010 - 6 years of using ChemAxon tools at Evotec. Ian Berry,
      Evotec (UK) Ltd
    * Chemical-text hybrid search engines. Yingyao Zhou, GNF
    * Implementation of ChemAxon in a SOA environment, Brett Hiemenz,
      GlaxoSmithKline
    * Helium: An EXCEL based User Tool for SAR analysis. Charles
      Wilkins, GlaxoSmithKline
    * Using J Chem Base - in a  Db 2  environment & no chemical
      cartridge. Stephen Boyer, IBM Research
    * logD comparison with in-house data. Yvonne Martin, Martin Associates
    * Structure-based approaches to the indexing and retrieval of patent
      chemistry. Don Walter, Thomson Reuters
    * Fast flexible search in ZINC. John Irwin, University of California
      San Francisco

ChemAxon Partners participants (tbc) - see partner listing here: 
http://www.chemaxon.com/partners/integrators.html
-- 
*Alex Allardyce*
Marketing Dir.
*ChemAxon* *Ltd*.
Maramaros koz 3/A, Budapest, 1037, Hungary
Tel: +361 453 0435
skype: alex_allardyce

--------------070009090606000204060102
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
  <head>
    <meta http-equiv="content-type" content="text/html;
      charset=ISO-8859-1">
  </head>
  <body bgcolor="#ffffff" text="#000000">
    Please excuse cross postings.<br>
    <br>
    The program is now available for ChemAxon's 2010 US User Group
    Meeting which will be held on Tuesday and Wednesday September 14-15
    at the Omni Parker House, Downtown Boston. The meeting will preceded
    by a end user &amp; developer training day on September 13th and
    followed by a Markush Forum on the morning of September 16th. <br>
    <br>
    Program: <a class="moz-txt-link-freetext"
      href="http://www.chemaxon.com/events/2010-eugm/#1">http://www.chemaxon.com/events/2010-us-ugm/#program</a><br>
    <br>
    The meeting will feature presentations from ChemAxon users,
    introduce a focus session on<b> SharePoint</b>, lightning
    presentations/exhibition from ChemAxon Partners and the latest
    updates on product developments. <br>
    <br>
    Preceding the meeting will be a dual track developer and end user
    Training Day on May 18th. To see the topics and schedule visit: <br>
    <ul>
      <li> Developer Training Day: <a class="moz-txt-link-freetext"
          href="http://www.chemaxon.com/events/2010-us-ugm/#training--developer">http://www.chemaxon.com/events/2010-us-ugm/#training--developer</a></li>
      <li> End user: Application Focus Training Day: <a
          class="moz-txt-link-freetext"
          href="http://www.chemaxon.com/events/2010-eugm/#2">http://www.chemaxon.com/events/2010-us-ugm/#training--application-focus</a></li>
    </ul>
    Following the UGM we have the first meeting of the <b>Markush Forum</b>,
    an open morning for interested organizations (users and content
    developers) to participate in the further development of ChemAxon&#8217;s
    tools for Markush structure enumeration and search. More information
    here: <a class="moz-txt-link-freetext"
      href="http://www.chemaxon.com/events/2010-eugm/#4">http://www.chemaxon.com/events/2010-us-ugm/#markush-forum</a><br>
    <br>
    To find out more about the meeting , register or submit a poster
    abstract (open until September 6th) and view the program, please
    visit: <a class="moz-txt-link-freetext"
      href="http://www.chemaxon.com/events/2010-eugm/">http://www.chemaxon.com/events/2010-eugm/</a>.
    To review the archives of previous meetings, including original
    presentations (slides and video) and meeting reports from Yvonne
    Martin and Wendy Warr visit: <a class="moz-txt-link-freetext"
      href="http://www.chemaxon.com/library/ugm-presentations/">http://www.chemaxon.com/library/ugm-presentations/</a>.
    Yvonne Martin's meeting report from San Diego 2009 is here <a
      class="moz-txt-link-freetext"
      href="https://www.chemaxon.com/library/ugm-presentations/2009-us/#2">https://www.chemaxon.com/library/ugm-presentations/2009-us/#2</a><br>
    <br>
    We hope you can join us for a very interesting event.<br>
    <br>
    BR<br>
    Alex<br>
    <br>
    Selected user presentations:<br>
    <ul>
      <li> Evaluation of pKa Estimation Methods on 211 Druglike
        Compounds. &nbsp; Joann Prescott Roy, AstraZeneca </li>
      <li>A Robotic Chemistry System for the Discovery of
        Cancer-Specific Targeting Ligands. John Frangioni, Harvard
        Medical School </li>
      <li>Migrating Chemical Toolkits. Dan Durkin, Broad Institute </li>
      <li>2004-2010 - 6 years of using ChemAxon tools at Evotec. Ian
        Berry, Evotec (UK) Ltd </li>
      <li>Chemical-text hybrid search engines. Yingyao Zhou, GNF</li>
      <li>Implementation of ChemAxon in a SOA environment, Brett
        Hiemenz, GlaxoSmithKline </li>
      <li>Helium: An EXCEL based User Tool for SAR analysis. Charles
        Wilkins, GlaxoSmithKline </li>
      <li>Using J Chem Base - in a&nbsp; Db 2&nbsp; environment &amp; no chemical
        cartridge. Stephen Boyer, IBM Research </li>
      <li>logD comparison with in-house data. Yvonne Martin, Martin
        Associates</li>
      <li>Structure-based approaches to the indexing and retrieval of
        patent chemistry. Don Walter, Thomson Reuters </li>
      <li>Fast flexible search in ZINC. John Irwin, University of
        California San Francisco </li>
    </ul>
    ChemAxon Partners participants (tbc) - see partner listing here: <a
      class="moz-txt-link-freetext"
      href="http://www.chemaxon.com/partners/integrators.html">http://www.chemaxon.com/partners/integrators.html</a><br>
    <div class="moz-signature">-- <br>
      <div class="moz-signature">
        <div class="moz-signature">
          <title></title>
          <small><font color="#077179" face="Verdana"><small><b>Alex
                  Allardyce</b></small></font></small><br>
          <div class="moz-signature"><small><font face="Verdana"><font
                  color="#666666"><small>Marketing Dir.</small></font><br>
              </font><font color="#fca311"><small><small><font
                      face="Verdana"><b><big>ChemAxon</big></b></font></small></small></font><font
                face="Verdana"><font color="#fca311"><small> <b>Ltd</b>.</small></font><br>
                <small><font color="#666666">Maramaros koz 3/A,
                    Budapest, 1037, Hungary</font><br>
                  <font color="#666666">Tel: +361 453 0435<br>
                    skype: alex_allardyce<br>
                  </font></small></font></small></div>
          <small><font face="Verdana"><font color="#666666"> </font></font></small></div>
        <small><font face="Verdana"><font color="#666666"> </font></font></small></div>
    </div>
  </body>
</html>

--------------070009090606000204060102--


From owner-chemistry@ccl.net Thu Jul 15 18:32:01 2010
From: "Eric Scerri scerri|,|chem.ucla.edu" <owner-chemistry ~~ server.ccl.net>
To: CCL
Subject: CCL: program for - Oxford conference on Philosophy of Chemistry
Message-Id: <-42290-100715145608-15382-p6139HDVlE6ofJwEiacyrg ~~ server.ccl.net>
X-Original-From: Eric Scerri <scerri^_^chem.ucla.edu>
Content-Type: multipart/alternative; boundary=Apple-Mail-81-264589651
Date: Thu, 15 Jul 2010 11:45:00 -0700
Mime-Version: 1.0 (Apple Message framework v753.1)


Sent to CCL by: Eric Scerri [scerri/a\chem.ucla.edu]

--Apple-Mail-81-264589651
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain;
	charset=WINDOWS-1252;
	delsp=yes;
	format=flowed

ISPC 2010 Oxford

http://ispc.sas.upenn.edu/

Program

Monday 9 August

2 pm Registration/Check in
4.45 Welcome

5.30 =96 6.30 `How Oxygen is Detected: A Chemist at Work=92
Christopher  Schofield (Oxford)

Dinner
Tuesday 10 August

9 =96 9.40 `Prigogine and the many voices of nature=92
Olimpia Lombardi (Buenos Aires)



9.40 =96 10.20 `Chemistry and Martin Buber=92s philosophy of dialogue=92

                   Ewa Zielonaska-Lis (Adam Mickiewicz University, =20
Poznan)


10.20 =96 11.00 `Should history and philosophy of chemistry be left to =20=

professional historians and philosophers?'

                   Eric Scerri (University of California, Los Angeles)
Coffee Break

11.15 =96 11.55 `The ontological function of first-order and second-=20
order corupouscles in the chemical philosophy of Robert Boyle: The =20
reintegration of potassium nitrate=92

                   Madrina Banchetti-Robino (Florida Atlantic =20
University)

11.55 =96 12.35 `Bohr=92s atom amd the schism at the heart of chemistry=92=


                   Mark Leach (Salford University)
Lunch

2.  =96 2.40 `The prospects for fusion emergence in chemistry=92
Alexander Manifu (University of Western Ontario)



2.40 =96 3.30 `Quantum chemistry and emergence=92

                   Jean-Pierre Llored (Centre de Recherche en =20
=C9pist=E9mologie Appliqu=E9e, Paris)

Tea Break

4.00  =96 4.40 `The chemical experiment=92

			     Jos=E9 Chamizo (UNA Mexico)

4.40 - 5.20 xxx
Banquet

Wednesday  11 August

9 =96 9.40 `The Contributions of Jaap van Brackel=92
         K. Von Reuthenberg (Technical University of Coburg) & Rom =20
Harr=E9 (Oxford)



9.40 =96 10.20 `How properties hang together in chemical entities=92

                   Joseph Earley (Georgetown University)


10.20 =96 11.00 `Logical foundations of the chemical sciences in =20
relation to the perplex number system=92
                   Jerry L. R. Chandler (George Mason University)

Coffee Break

11.15 =96 11. 55
11.55 =96 12.35
Lunch
2.00 ISPC Business Meeting
3.00 Visit to Museum of the History of Science.


------------------------------------------------------------------------=20=

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

The Periodic Table: Its Story and Its Significance, by Eric Scerri, =20
Oxford University Press, 2007.
	=09
http://www.amazon.com/Periodic-Table-Its-Story-Significance/dp/=20
0195305736/ref=3Dsr_1_1?ie=3DUTF8&s=3Dbooks&qid=3D1246750502&sr=3D1-1





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Content-Transfer-Encoding: quoted-printable
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	charset=WINDOWS-1252

<html><body style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; =
-webkit-line-break: after-white-space; ">
<!--StartFragment--><p class=3D"MsoNormal" =
style=3D"mso-outline-level:1"><span lang=3D"EN-GB" =
style=3D"font-size:20.0pt;mso-ansi-language:EN-GB"><b>ISPC 2010 =
Oxford<span class=3D"Apple-style-span" style=3D"font-size: 21px; =
">&nbsp;&nbsp; &nbsp;</span></b></span></p><p class=3D"MsoNormal" =
style=3D"mso-outline-level:1"><font class=3D"Apple-style-span" =
size=3D"6"><span class=3D"Apple-style-span" style=3D"font-size: =
21px;"><b><a =
href=3D"http://ispc.sas.upenn.edu">http://ispc.sas.upenn.edu</a>/</b></spa=
n></font></p><p class=3D"MsoNormal" style=3D"mso-outline-level:1"><span =
class=3D"Apple-style-span" style=3D"font-size: 21px; font-weight: bold; =
">Program</span></p><p class=3D"MsoNormal" =
style=3D"mso-outline-level:1"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB"><u>Monday 9 =
August<o:p></o:p></u></span></p> <div class=3D"MsoNormal"><span =
lang=3D"EN-GB" style=3D"mso-ansi-language:EN-GB">2 pm Registration/Check =
in<o:p></o:p></span></div> <div class=3D"MsoNormal"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB">4.45 =
Welcome<o:p></o:p></span></div><div class=3D"MsoNormal"><br></div> <div =
class=3D"MsoNormal"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB">5.30 =96 6.30 `How Oxygen is Detected: =
A Chemist at Work=92 <o:p></o:p></span></div><p class=3D"MsoNormal" =
style=3D"text-indent:.5in"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language: EN-GB">Christopher<span style=3D"mso-spacerun:=
 yes">&nbsp; </span>Schofield (Oxford)<o:p></o:p></span></p> <div =
class=3D"MsoNormal"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB"><i>Dinner<o:p></o:p></i></span></div><p =
class=3D"MsoNormal" style=3D"mso-outline-level:1"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB"><u>Tuesday 10 =
August<o:p></o:p></u></span></p> <div class=3D"MsoNormal"><span =
lang=3D"EN-GB" style=3D"mso-ansi-language:EN-GB">9 =96 9.40 `Prigogine =
and the many voices of nature=92 <o:p></o:p></span></div><p =
class=3D"MsoNormal" style=3D"text-indent:.5in"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language: EN-GB">Olimpia Lombardi (Buenos =
Aires)<o:p></o:p></span></p><p class=3D"MsoNormal" =
style=3D"text-indent:.5in"><br></p><p class=3D"MsoNormal" =
style=3D"mso-outline-level:1"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB">9.40 =96 10.20 `Chemistry and Martin =
Buber=92s philosophy of dialogue=92<o:p></o:p></span></p> <div =
class=3D"MsoNormal"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB"><span =
style=3D"mso-tab-count:1">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Ewa =
Zielonaska-Lis (Adam Mickiewicz University, =
Poznan)<o:p></o:p></span></div><div class=3D"MsoNormal"><br></div><div =
class=3D"MsoNormal"><br></div> <div class=3D"MsoNormal"><span =
lang=3D"EN-GB" style=3D"mso-ansi-language:EN-GB">10.20 =96 11.00 `Should =
history and philosophy of chemistry be left to professional historians =
and philosophers?'<o:p></o:p></span></div><div =
class=3D"MsoNormal"><br></div> <div class=3D"MsoNormal"><span =
lang=3D"EN-GB" style=3D"mso-ansi-language:EN-GB"><span =
style=3D"mso-tab-count:1">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Eric =
Scerri (University of California, Los Angeles)<o:p></o:p></span></div><p =
class=3D"MsoNormal" style=3D"mso-outline-level:1"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB"><i>Coffee =
Break<o:p></o:p></i></span></p> <div class=3D"MsoNormal"><span =
lang=3D"EN-GB" style=3D"mso-ansi-language:EN-GB">11.15 =96 11.55 `The =
ontological function of first-order and second-order corupouscles in the =
chemical philosophy of Robert Boyle: The reintegration of potassium =
nitrate=92 <o:p></o:p></span></div><div class=3D"MsoNormal"><br></div> =
<div class=3D"MsoNormal"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB"><span =
style=3D"mso-tab-count:1">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Madrina =
Banchetti-Robino (Florida Atlantic =
University)<o:p></o:p></span></div><div class=3D"MsoNormal"><br></div><p =
class=3D"MsoNormal" style=3D"mso-outline-level:1"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB">11.55 =96 12.35 `Bohr=92s atom amd the =
schism at the heart of chemistry=92<o:p></o:p></span></p> <div =
class=3D"MsoNormal"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB"><span =
style=3D"mso-tab-count:1">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Mark Leach =
(Salford University)<o:p></o:p></span></div><p class=3D"MsoNormal" =
style=3D"mso-outline-level:1"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB"><i>Lunch<o:p></o:p></i></span></p> =
<div class=3D"MsoNormal"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB">2.<span style=3D"mso-spacerun: =
yes">&nbsp; </span>=96 2.40 `The prospects for fusion emergence in =
chemistry=92<o:p></o:p></span></div><p class=3D"MsoNormal" =
style=3D"text-indent:.5in"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language: EN-GB">Alexander Manifu (University of =
Western Ontario)<o:p></o:p></span></p><p class=3D"MsoNormal" =
style=3D"text-indent:.5in"><br></p><p class=3D"MsoNormal" =
style=3D"mso-outline-level:1"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB">2.40 =96 3.30 `Quantum chemistry and =
emergence=92<o:p></o:p></span></p> <div class=3D"MsoNormal"><span =
lang=3D"EN-GB" style=3D"mso-ansi-language:EN-GB"><span =
style=3D"mso-tab-count:1">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
</span>Jean-Pierre Llored (Centre de Recherche en =C9pist=E9mologie =
Appliqu=E9e, Paris)<o:p></o:p></span></div><div =
class=3D"MsoNormal"><br></div> <div class=3D"MsoNormal"><span =
lang=3D"EN-GB" style=3D"mso-ansi-language:EN-GB"><i>Tea Break =
<o:p></o:p></i></span></div><div class=3D"MsoNormal"><i><br></i></div> =
<div class=3D"MsoNormal"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB">4.00<span style=3D"mso-spacerun: =
yes">&nbsp; </span>=96 4.40 `The chemical =
experiment=92<o:p></o:p></span></div> <div class=3D"MsoNormal"><span =
lang=3D"EN-GB" style=3D"mso-ansi-language:EN-GB"><span =
style=3D"mso-tab-count:1">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span></span>=
</div><div class=3D"MsoNormal"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB"><span =
style=3D"mso-tab-count:1"></span><span class=3D"Apple-tab-span" =
style=3D"white-space:pre">			</span>&nbsp;&nbsp; =
&nbsp;&nbsp;Jos=E9 Chamizo (UNA Mexico)<o:p></o:p></span></div><div =
class=3D"MsoNormal"><br></div> <div class=3D"MsoNormal"><span =
lang=3D"EN-GB" style=3D"mso-ansi-language:EN-GB">4.40 - 5.20 =
xxx<o:p></o:p></span></div> <div class=3D"MsoNormal"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB"><i>Banquet<o:p></o:p></i></span></div> =
<div class=3D"MsoNormal"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB"><i>&nbsp;<o:p></o:p></i></span></div><p =
class=3D"MsoNormal" style=3D"mso-outline-level:1"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB"><u>Wednesday<span style=3D"mso-spacerun:=
 yes">&nbsp; </span>11 August<o:p></o:p></u></span></p> <div =
class=3D"MsoNormal"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB">9 =96 9.40 `The Contributions of Jaap =
van Brackel=92 <o:p></o:p></span></div><p class=3D"MsoNormal" =
style=3D"text-indent:.5in"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language: EN-GB"><span =
style=3D"mso-tab-count:1">&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;</span>K. Von =
Reuthenberg (Technical University of Coburg) &amp; Rom Harr=E9 =
(Oxford)<o:p></o:p></span></p><p class=3D"MsoNormal" =
style=3D"text-indent:.5in"><br></p><p class=3D"MsoNormal" =
style=3D"mso-outline-level:1"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB">9.40 =96 10.20 `How properties hang =
together in chemical entities=92<o:p></o:p></span></p> <div =
class=3D"MsoNormal"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB"><span =
style=3D"mso-tab-count:1">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Joseph =
Earley (Georgetown University)<o:p></o:p></span></div><div =
class=3D"MsoNormal"><br></div><div class=3D"MsoNormal"><br></div> <div =
class=3D"MsoNormal"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB">10.20 =96 11.00 `Logical foundations =
of the chemical sciences in relation to the perplex number =
system=92<o:p></o:p></span></div> <div class=3D"MsoNormal"><span =
lang=3D"EN-GB" style=3D"mso-ansi-language:EN-GB"><span =
style=3D"mso-tab-count:1">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Jerry L. =
R. Chandler (George Mason University)<o:p></o:p></span></div> <div =
class=3D"MsoNormal"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB">&nbsp;<o:p></o:p></span></div><p =
class=3D"MsoNormal" style=3D"mso-outline-level:1"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB"><i>Coffee =
Break<o:p></o:p></i></span></p> <div class=3D"MsoNormal"><span =
lang=3D"EN-GB" style=3D"mso-ansi-language:EN-GB">11.15 =96 11. =
55<o:p></o:p></span></div> <div class=3D"MsoNormal"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB">11.55 =96 =
12.35<o:p></o:p></span></div> <div class=3D"MsoNormal"><span =
lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB"><i>Lunch<o:p></o:p></i></span></div> =
<div class=3D"MsoNormal"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB">2.00 ISPC Business =
Meeting<o:p></o:p></span></div> <div class=3D"MsoNormal"><span =
lang=3D"EN-GB" style=3D"mso-ansi-language:EN-GB">3.00 Visit to Museum of =
the History of Science.<o:p></o:p></span></div> <div =
class=3D"MsoNormal"><span lang=3D"EN-GB" =
style=3D"mso-ansi-language:EN-GB"><u>&nbsp;<o:p></o:p></u></span></div> =
<!--EndFragment--> <br><div> <span class=3D"Apple-style-span" =
style=3D"border-collapse: separate; color: rgb(0, 0, 0); font-family: =
Helvetica; font-size: medium; font-style: normal; font-variant: normal; =
font-weight: normal; letter-spacing: normal; line-height: normal; =
orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; =
widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; =
-webkit-border-vertical-spacing: 0px; =
-webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: =
auto; -webkit-text-stroke-width: 0px; "><span class=3D"Apple-style-span" =
style=3D"border-collapse: separate; color: rgb(0, 0, 0); font-family: =
Helvetica; font-size: medium; font-style: normal; font-variant: normal; =
font-weight: normal; letter-spacing: normal; line-height: normal; =
orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; =
widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; =
-webkit-border-vertical-spacing: 0px; =
-webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: =
auto; -webkit-text-stroke-width: 0px; "><span class=3D"Apple-style-span" =
style=3D"border-collapse: separate; color: rgb(0, 0, 0); font-family: =
Helvetica; font-size: 16px; font-style: normal; font-variant: normal; =
font-weight: normal; letter-spacing: normal; line-height: normal; =
orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; =
widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; =
-webkit-border-vertical-spacing: 0px; =
-webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: =
auto; -webkit-text-stroke-width: 0px; "><span class=3D"Apple-style-span" =
style=3D"border-collapse: separate; color: rgb(0, 0, 0); font-family: =
Helvetica; font-size: 16px; font-style: normal; font-variant: normal; =
font-weight: normal; letter-spacing: normal; line-height: normal; =
orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; =
widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; =
-webkit-border-vertical-spacing: 0px; =
-webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: =
auto; -webkit-text-stroke-width: 0px; "><span class=3D"Apple-style-span" =
style=3D"border-collapse: separate; color: rgb(0, 0, 0); font-family: =
Helvetica; font-size: 16px; font-style: normal; font-variant: normal; =
font-weight: normal; letter-spacing: normal; line-height: normal; =
orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; =
widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; =
-webkit-border-vertical-spacing: 0px; =
-webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: =
auto; -webkit-text-stroke-width: 0px; "><span class=3D"Apple-style-span" =
style=3D"border-collapse: separate; color: rgb(0, 0, 0); font-family: =
Helvetica; font-size: 16px; font-style: normal; font-variant: normal; =
font-weight: normal; letter-spacing: normal; line-height: normal; =
orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; =
widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; =
-webkit-border-vertical-spacing: 0px; =
-webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: =
auto; -webkit-text-stroke-width: 0px; "><span class=3D"Apple-style-span" =
style=3D"border-collapse: separate; color: rgb(0, 0, 0); font-family: =
Helvetica; font-size: 16px; font-style: normal; font-variant: normal; =
font-weight: normal; letter-spacing: normal; line-height: normal; =
orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; =
widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; =
-webkit-border-vertical-spacing: 0px; =
-webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: =
auto; -webkit-text-stroke-width: 0px; "><span class=3D"Apple-style-span" =
style=3D"border-collapse: separate; color: rgb(0, 0, 0); font-family: =
Helvetica; font-size: 16px; font-style: normal; font-variant: normal; =
font-weight: normal; letter-spacing: normal; line-height: normal; =
orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; =
widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; =
-webkit-border-vertical-spacing: 0px; =
-webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: =
auto; -webkit-text-stroke-width: 0px; "><span class=3D"Apple-style-span" =
style=3D"border-collapse: separate; color: rgb(0, 0, 0); font-family: =
Helvetica; font-size: 16px; font-style: normal; font-variant: normal; =
font-weight: normal; letter-spacing: normal; line-height: normal; =
orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; =
widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; =
-webkit-border-vertical-spacing: 0px; =
-webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: =
auto; -webkit-text-stroke-width: 0px; "><span class=3D"Apple-style-span" =
style=3D"border-collapse: separate; color: rgb(0, 0, 0); font-family: =
Helvetica; font-size: 16px; font-style: normal; font-variant: normal; =
font-weight: normal; letter-spacing: normal; line-height: normal; =
orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; =
widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; =
-webkit-border-vertical-spacing: 0px; =
-webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: =
auto; -webkit-text-stroke-width: 0px; "><div><div><font =
class=3D"Apple-style-span" color=3D"#C80B56" size=3D"5"><span =
class=3D"Apple-style-span" style=3D"font-size: 18px; =
"><i>---------------------------------------------------------------------=
--------------------------------------------------------------------------=
</i></span></font></div><div><font class=3D"Apple-style-span" =
color=3D"#C80B56" size=3D"5"><span class=3D"Apple-style-span" =
style=3D"font-size: 18px; "><i><br></i></span></font></div><div><font =
class=3D"Apple-style-span" color=3D"#C80B56" size=3D"5"><span =
class=3D"Apple-style-span" style=3D"font-size: 18px; "><i style=3D"color: =
rgb(200, 11, 86); font-size: 18px; font-style: italic; ">The Periodic =
Table: Its Story and Its Significance, by Eric Scerri, Oxford University =
Press, 2007.</i></span></font></div><div><span class=3D"Apple-tab-span" =
style=3D"white-space: pre; color: rgb(27, 17, 255); font-size: 18px; =
font-style: italic; ">		</span></div><div><span =
class=3D"Apple-tab-span" style=3D"white-space: pre; color: rgb(27, 17, =
255); font-size: 18px; font-style: italic; "></span><a =
href=3D"http://www.amazon.com/Periodic-Table-Its-Story-Significance/dp/019=
5305736/ref=3Dsr_1_1?ie=3DUTF8&amp;s=3Dbooks&amp;qid=3D1246750502&amp;sr=3D=
1-1">http://www.amazon.com/Periodic-Table-Its-Story-Significance/dp/019530=
5736/ref=3Dsr_1_1?ie=3DUTF8&amp;s=3Dbooks&amp;qid=3D1246750502&amp;sr=3D1-=
1</a></div><div><br></div></div></span></span></span></span></span></span>=
</span></span><br class=3D"Apple-interchange-newline"></span><br =
class=3D"Apple-interchange-newline"></span> </div><br></body></html>=

--Apple-Mail-81-264589651--


From owner-chemistry@ccl.net Thu Jul 15 19:07:01 2010
From: "Govender, Penny pennyg(!)uj.ac.za" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL: Announcement: Chemistry Conference
Message-Id: <-42291-100715135530-9111-+pisV4fndezOlX5MJbayfg+*+server.ccl.net>
X-Original-From: "Govender, Penny" <pennyg-.-uj.ac.za>
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Date: Thu, 15 Jul 2010 19:55:01 +0200
MIME-Version: 1.0


Sent to CCL by: "Govender, Penny" [pennyg::uj.ac.za]
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Dear Colleagues
Please take note of the following upcomming convention.
SACI 2011
40th South African Chemical Institute
(SACI) Convention incorporating the 15th
Inorganic Conference (INORG2011) and
the 3rd Federation of African Societies of
Chemistry (FASC) Congress
16 - 21 January 2011
Please visit www.saci2011.org.za<http://www.saci2011.org.za> for more detai=
ls.

Currently, we are still open to have keynote speakers where the convention =
is willing to waiver the registration fees of the successful candidate but =
due to financial constraints the cost of air travel and accommodation will =
be the candidates responsibility.  Any interested parties can submit their =
abstracts to me, pennyg(a)uj.ac.za<mailto:pennyg(a)uj.ac.za> as soon as possibl=
e.
Thank you.
Ms Penny Govender (AMRSC)
Lecturer: Organic Chemistry

University of Johannesburg
Department of Chemical Technology
Doornfontein Campus
(w) 011-5596555
(fax) 011-5596425
(c) 0845002689
pennyg(a)uj.ac.za

[cid:image002.gif(a)01CB2455.37260610]
Louis Pasteur "There are no such things as applied sciences, only applicati=
ons of science"

Please don't print this e-mail unless you really have to. Think Green.


________________________________
This email and all contents are subject to the following disclaimer:

http://disclaimer.uj.ac.za

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<div class=3D"WordSection1">
<p class=3D"MsoNormal"><span style=3D"font-family:&quot;Arial&quot;,&quot;s=
ans-serif&quot;;color:#666600">Dear Colleagues<o:p></o:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-family:&quot;Arial&quot;,&quot;s=
ans-serif&quot;;color:#666600">Please take note of the following upcomming =
convention.&nbsp;
<o:p></o:p></span></p>
<p class=3D"MsoNormal" style=3D"margin:0cm;margin-bottom:.0001pt;text-autos=
pace:none">
<b><span style=3D"font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;co=
lor:black">SACI 2011<o:p></o:p></span></b></p>
<p class=3D"MsoNormal" style=3D"margin:0cm;margin-bottom:.0001pt;text-autos=
pace:none">
<b><span style=3D"font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;co=
lor:black">40th South African Chemical Institute<o:p></o:p></span></b></p>
<p class=3D"MsoNormal" style=3D"margin:0cm;margin-bottom:.0001pt;text-autos=
pace:none">
<b><span style=3D"font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;co=
lor:black">(SACI) Convention incorporating the 15th<o:p></o:p></span></b></=
p>
<p class=3D"MsoNormal" style=3D"margin:0cm;margin-bottom:.0001pt;text-autos=
pace:none">
<b><span style=3D"font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;co=
lor:black">Inorganic Conference (INORG2011) and<o:p></o:p></span></b></p>
<p class=3D"MsoNormal" style=3D"margin:0cm;margin-bottom:.0001pt;text-autos=
pace:none">
<b><span style=3D"font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;co=
lor:black">the 3rd Federation of African Societies of<o:p></o:p></span></b>=
</p>
<p class=3D"MsoNormal" style=3D"margin:0cm;margin-bottom:.0001pt;text-autos=
pace:none">
<b><span style=3D"font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;co=
lor:black">Chemistry (FASC) Congress<o:p></o:p></span></b></p>
<p class=3D"MsoNormal"><b><span style=3D"font-family:&quot;Calibri&quot;,&q=
uot;sans-serif&quot;;
color:black">16 - 21 January 2011</span></b><span style=3D"font-family:&quo=
t;Calibri&quot;,&quot;sans-serif&quot;;
color:black"><o:p></o:p></span></p>
<p class=3D"MsoNormal" style=3D"margin:0cm;margin-bottom:.0001pt;text-autos=
pace:none">
<b><span style=3D"font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;co=
lor:black">Please visit <a href=3D"http://www.saci2011.org.za">
www.saci2011.org.za</a> for more details.<o:p></o:p></span></b></p>
<p class=3D"MsoNormal" style=3D"margin:0cm;margin-bottom:.0001pt;text-autos=
pace:none">
<b><span style=3D"font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;co=
lor:black"><o:p>&nbsp;</o:p></span></b></p>
<p class=3D"MsoNormal" style=3D"margin:0cm;margin-bottom:.0001pt;text-autos=
pace:none">
<b><span style=3D"font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;co=
lor:black">Currently, we are still open to have keynote speakers where the =
convention is willing to waiver the registration fees of the successful can=
didate but due to financial constraints the cost of air
 travel and accommodation will be the candidates responsibility.&nbsp; Any =
interested parties can submit their abstracts to me,
<a href=3D"mailto:pennyg(a)uj.ac.za">pennyg(a)uj.ac.za</a> as soon as possible.=
<o:p></o:p></span></b></p>
<p class=3D"MsoNormal"><span style=3D"color:black">Thank you.<o:p></o:p></s=
pan></p>
<div>
<p class=3D"MsoNormal"><span lang=3D"EN-ZA" style=3D"font-size:11.0pt;font-=
family:&quot;Calibri&quot;,&quot;sans-serif&quot;;
color:black">Ms Penny Govender (AMRSC)<o:p></o:p></span></p>
<p class=3D"MsoNormal" style=3D"margin:0cm;margin-bottom:.0001pt"><span lan=
g=3D"EN-ZA" style=3D"font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot=
;sans-serif&quot;;color:black">Lecturer: Organic Chemistry<o:p></o:p></span=
></p>
<p class=3D"MsoNormal" style=3D"margin:0cm;margin-bottom:.0001pt"><span lan=
g=3D"EN-ZA" style=3D"font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot=
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--_005_FF60AD4A80240949BC2B59CE743B217D66E168C87DAPKEXCMS01adu_--


From owner-chemistry@ccl.net Thu Jul 15 19:42:00 2010
From: "Joy Ku joyku+/-stanford.edu" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL: OpenMM 2.0 Supports Accelerated Molecular Dynamics on NVIDIA & ATI GPU
Message-Id: <-42292-100715192849-2885-0+JoP4+mMH46tBI8hzVvvw-#-server.ccl.net>
X-Original-From: "Joy  Ku" <joyku[A]stanford.edu>
Date: Thu, 15 Jul 2010 19:28:46 -0400


Sent to CCL by: "Joy  Ku" [joyku{:}stanford.edu]
Simbios is excited to announce the release of OpenMM 2.0.  OpenMM is an extensible library designed to enhance the performance of almost any molecular dynamics simulation package  (MD package) by allowing the code to be executed on high performance computer architectures, in particular Graphics Processor Units (GPUs).  It also provides custom forces for the rapid development of novel methods.

Major features for this release include:

1)  Support for NVIDIA GPU cards (using either CUDA or OpenCL) and ATI GPU cards (using OpenCL)
2)  New custom force types, such as a custom H-bond force and extension of the custom GB force to support implicit membrane models
3)  Pressure coupling with long range dispersion correction
4)  A number of performance enhancements, especially for PME
 
Download the latest version  from http://simtk.org/home/openmm.  OpenMM 2.0 is available to GROMACS users (via OpenMM-Accelerated GROMACS) and to AMBER users (via an AMBER/Sander-compatible interface to OpenMM, available at http://simtk.org/home/sander_openmm).

OpenMM was developed by Simbios, the NIH National Center for Physics-Based Simulation of Biological Structures at Stanford University, funded under grant U54 GM072970.  Learn more about Simbios at http://simbios.stanford.edu.


From owner-chemistry@ccl.net Thu Jul 15 21:41:00 2010
From: "Cheri A McFerrin cmcfer1[*]lsu.edu" <owner-chemistry||server.ccl.net>
To: CCL
Subject: CCL: calculation of bader electron density distribution w/ GAMESS .dat file
Message-Id: <-42293-100715170655-9002-995VNH2IwKtpkFCtZ9G9Zw||server.ccl.net>
X-Original-From: "Cheri A McFerrin" <cmcfer1]*[lsu.edu>
Date: Thu, 15 Jul 2010 17:06:52 -0400


Sent to CCL by: "Cheri A McFerrin" [cmcfer1 : lsu.edu]
hi all:

i have run a GAMESS job after having included aimpac=.true. in the $CONTRL section of my input.  this 
aimpac keyword generates a section in the output (.dat file) that contains the information needed for 
calculating bader electron density (per nucleus in a cluster).

i have copied the bader portion of this .dat file to a .wfn (wavefunction) file.

could anyone please help me w understanding which code (in the series of aimpac codes) is useful for 
calculating bader electron densities?   in other words, has anyone out there calculated bader electron 
densities (per nucleus) using a .dat file generated by GAMESS?  sos.

thank you!!

cheri mcferrin. lsu dept of chemistry


From owner-chemistry@ccl.net Thu Jul 15 23:16:00 2010
From: "Jason Stephen D Acchioli jdacchio#uwsp.edu" <owner-chemistry=server.ccl.net>
To: CCL
Subject: CCL:G: Potential energy surface scans
Message-Id: <-42294-100715231441-5141-cvaocfg4VKboJcBhkRAXNA=server.ccl.net>
X-Original-From: "Jason  Stephen D Acchioli" <jdacchio__uwsp.edu>
Date: Thu, 15 Jul 2010 23:14:40 -0400


Sent to CCL by: "Jason  Stephen D Acchioli" [jdacchio-$-uwsp.edu]
Hi all, 

I've got a question that's been bugging me for quite some time. I'm attempting to calculate the 
potential energy surface for the barrier of rotation in a piano-stool complex, but I'm having 
extreme difficulty assigning the correct dihedral angle to use. I'm attaching the input file of the 
optimization I've performed on the structure. I've tried using dummy atoms (I'm assuming this is 
OK; it took some playing around for me to figure out "Dummy" is a dummy atom in Orca!), but I still 
can't get the structure to rotate. I've tried doing this in other packages, but I'm having the same 
problem. I'd prefer to use Orca at the moment! 

In the attached file, you'll see an acyclic pentadienyl ring, and a Fe(CO)2(PPH3), which I'm trying to 
rotate. The coordinates in the file are already optimized at the listed level of theory; my problem is 
trying to get the scan set up. Any suggestions or help would be greatly appreciated. 

On a different note, does anyone know why I can't use dummy atoms in G03 to specify the dihedral 
of a coordinate I'd like to scan? This would apply to the coordinates I have below as well.

Be well, 

Jason 

#Geom. of normal bonding with ; 
%pal nprocs=2 end 
!RKS B3LYP/G TightSCF Opt 
%basis basis SV 
newgto Fe "TZVP" end 
end 
%rel method ZORA #or IORA 
modelpot 1,1,1,1 
modeldens rhoZORA 
velit 137.0359895 #speed of light used 
end 
* xyz 1 1 
Fe -3.171920 -0.438610 0.886377 
P -0.920800 -0.772046 0.330849 
C -3.861155 -0.368678 -1.211233 
H -4.829928 0.128955 -1.186782 
H -3.196067 0.011011 -1.997061 
C -3.891820 -3.785487 0.648549 
H -3.854867 -4.010793 1.728276 
H -2.939655 -4.102886 0.188413 
H -4.689663 -4.416399 0.209112 
C -3.101755 1.337692 0.793522 
C -4.195061 -2.327944 0.383182 
C -5.325899 -0.223406 1.266415 
H -5.657148 0.262898 2.191902 
H -5.750647 0.216249 0.364273 
C -3.662636 -1.703478 -0.794882 
H -2.899947 -2.294928 -1.319655 
O -3.092286 2.500144 0.725650 
O -2.415530 -0.726138 3.733160 
C -2.707886 -0.621877 2.611221 
C -4.934940 -1.577632 1.362738 
H -5.043675 -2.073258 2.336377 
H 0.048970 -0.039281 1.071523 
H -0.551586 -0.436492 -1.002157 
H -0.390399 -2.090412 0.434113 
Dummy -4.396 -1.240 0.201 
Dummy -2.243 -0.019 1.245 
* 



******************************************* 
Jason D'Acchioli 
Assistant Professor of Chemistry 
University of Wisconsin-Stevens Point 
2001 Fourth Avenue 
Stevens Point, WI 54481 
http://chemdac.uwsp.edu