From owner-chemistry@ccl.net Fri Nov 12 00:12:00 2010
From: "baljinder baljinder7- -gmail.com" <owner-chemistry-x-server.ccl.net>
To: CCL
Subject: CCL:G: HOMA analysis
Message-Id: <-43149-101111221009-29427-U3MnvKgIE5kfDo/sgxV0zQ-x-server.ccl.net>
X-Original-From: baljinder <baljinder7{:}gmail.com>
Content-Type: multipart/alternative; boundary=000e0ce048e029715f0494d26dcc
Date: Fri, 12 Nov 2010 08:40:02 +0530
MIME-Version: 1.0


Sent to CCL by: baljinder [baljinder7|gmail.com]
--000e0ce048e029715f0494d26dcc
Content-Type: text/plain; charset=ISO-8859-1

Thank You Eduard for suggestion and informative link

On Thu, Nov 11, 2010 at 8:35 PM, Eduard Matito ematito!=!gmail.com <
owner-chemistry**ccl.net> wrote:

>
> Sent to CCL by: Eduard Matito [ematito%a%gmail.com]
> I'm afraid HOMA it's not implemented in Gaussian, but its calculation can
> be done
> on the back of an envelope, you only need distances and few constants.
> This topic was already discussed in CCL. See e.g.:
>
> http://www.ccl.net/cgi-bin/ccl/message-new?2009+05+11+010
>
> Eduard
>
>
> On Nov 11, 2010, at 5:15 AM, baljinder grewal baljinder7]^[gmail.comwrote:
>
>
>> Sent to CCL by: "baljinder  grewal" [baljinder7%a%gmail.com]
>> Dear all,
>> I need to quantify the extent of -electron delocalization of series of
>> compound.In  literature it is reported to be done by HOMA (harmonic
>> oscillator measure of aromaticity) analysis using gaussian software , but
>> method to do same is not reported .Kindly suggest any keyword or specific
>> tutorial i have to refer .
>>
>> Thanks in advance>
>>
>>
> --
> Eduard Matito
> Postdoctoral researcher
> Institute of Physics
> University of Szczecin
> Wielkopolska 15
> 70451 Szczecin (Poland)
> Phone: +48914441436
> http://ematito.webs.comhttp://www.ccl.net/chemistry/sub_unsub.shtml>
> Job: http://www.ccl.net/jobsConferences:
> http://server.ccl.net/chemistry/announcements/conferences/>
>
>

--000e0ce048e029715f0494d26dcc
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

<div dir=3D"ltr">Thank You Eduard for suggestion and informative link<br><b=
r><div class=3D"gmail_quote">On Thu, Nov 11, 2010 at 8:35 PM, Eduard Matito=
 ematito!=3D!<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>&g=
t;</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: Eduard Matito [ematito%a%<a href=3D"http://gmail.com" targe=
t=3D"_blank">gmail.com</a>]<br>
I&#39;m afraid HOMA it&#39;s not implemented in Gaussian, but its calculati=
on can be done<br>
on the back of an envelope, you only need distances and few constants.<br>
This topic was already discussed in CCL. See e.g.:<br>
<br>
<a href=3D"http://www.ccl.net/cgi-bin/ccl/message-new?2009+05+11+010" targe=
t=3D"_blank">http://www.ccl.net/cgi-bin/ccl/message-new?2009+05+11+010</a><=
br>
<br>
Eduard<div class=3D"im"><br>
<br>
On Nov 11, 2010, at 5:15 AM, baljinder grewal baljinder7]^[<a href=3D"http:=
//gmail.com" target=3D"_blank">gmail.com</a> wrote:<br>
<br>
</div><blockquote class=3D"gmail_quote" style=3D"margin: 0pt 0pt 0pt 0.8ex;=
 border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class=
=3D"im">
<br>
Sent to CCL by: &quot;baljinder =A0grewal&quot; [baljinder7%a%<a href=3D"ht=
tp://gmail.com" target=3D"_blank">gmail.com</a>]<br>
Dear all,<br>
I need to quantify the extent of -electron delocalization of series of comp=
ound.In =A0literature it is reported to be done by HOMA (harmonic oscillato=
r measure of aromaticity) analysis using gaussian software , but method to =
do same is not reported .Kindly suggest any keyword or specific tutorial i =
have to refer .<br>

<br>
Thanks in advance<br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
<br></div&gt=
; Conferences: <a href=3D"http://server.ccl.net/chemistry/announcements/con=
ferences/" target=3D"_blank">http://server.ccl.net/chemistry/announcements/=
conferences/</a>&gt;<br>

<br>
</blockquote>
<br>
--<br>
Eduard Matito<br>
Postdoctoral researcher<br>
Institute of Physics<br>
University of Szczecin<br>
Wielkopolska 15<br>
70451 Szczecin (Poland)<br>
Phone: +48914441436<br>
<a href=3D"http://ematito.webs.com" target=3D"_blank">http://ematito.webs.c=
om</a><div class=3D"im"><br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
<br<br=<br<br>
<br>
E-mail to subscribers: <a href=3D"mailto:CHEMISTRY**ccl.net" target=3D"_blan=
k">CHEMISTRY**ccl.net</a> or use:<br>
 =A0 =A0 <a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message" target=
=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br>
<br>
E-mail to administrators: <a href=3D"mailto:CHEMISTRY-REQUEST**ccl.net" targ=
et=3D"_blank">CHEMISTRY-REQUEST**ccl.net</a> or use<br>
 =A0 =A0 <a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message" target=
=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br>
<br=A0 =A0 <a href=3D"http://www.ccl.net/chemistry/sub_=
unsub.shtml" target=3D"_blank">http://www.ccl.net/chemistry/sub_unsub.shtml=
</a><br>
<br>
Before posting, check wait time at: <a href=3D"http://www.ccl.net" target=
=3D"_blank">http://www.ccl.net</a><br>
<br></div>
Job: <a href=3D"http://www.ccl.net/jobsConferences" target=3D"_blank">http:=
//www.ccl.net/jobsConferences</a>: <a href=3D"http://server.ccl.net/chemist=
ry/announcements/conferences/" target=3D"_blank">http://server.ccl.net/chem=
istry/announcements/conferences/</a><div>
<div></div><div class=3D"h5"><br>
<br>
Search Messages: <a href=3D"http://www.ccl.net/chemistry/searchccl/index.sh=
tml" target=3D"_blank">http://www.ccl.net/chemistry/searchccl/index.shtml</=
a><br>
<br<br>
 =A0 =A0 <a href=3D"http://www.ccl.net/spammers.txt" target=3D"_blank">http=
://www.ccl.net/spammers.txt</a><br>
<br>
RTFI: <a href=3D"http://www.ccl.net/chemistry/aboutccl/instructions/" targe=
t=3D"_blank">http://www.ccl.net/chemistry/aboutccl/instructions/</a><br>
<br>
<br>
</div></div></blockquote></div><br><div style=3D"visibility: hidden; displa=
y: inline;" id=3D"avg_ls_inline_popup"></div><style type=3D"text/css">#avg_=
ls_inline_popup {  position:absolute;  z-index:9999;  padding: 0px 0px;  ma=
rgin-left: 0px;  margin-top: 0px;  width: 240px;  overflow: hidden;  word-w=
rap: break-word;  color: black;  font-size: 10px;  text-align: left;  line-=
height: 13px;}</style></div>

--000e0ce048e029715f0494d26dcc--


From owner-chemistry@ccl.net Fri Nov 12 00:47:00 2010
From: "Joaquin Barroso Flores joaco_barroso!A!yahoo.com" <owner-chemistry|a|server.ccl.net>
To: CCL
Subject: CCL: Structure and property
Message-Id: <-43150-101111180049-19603-qcQqvXOXLkucMGqhMnWLkw|a|server.ccl.net>
X-Original-From: Joaquin Barroso Flores <joaco_barroso[a]yahoo.com>
Content-Type: multipart/alternative; boundary="0-995048478-1289516442=:94486"
Date: Thu, 11 Nov 2010 15:00:42 -0800 (PST)
MIME-Version: 1.0


Sent to CCL by: Joaquin Barroso Flores [joaco_barroso=-=yahoo.com]
--0-995048478-1289516442=:94486
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: quoted-printable

Deer Neeraj=0A=0AAntonio is right, you have to dive deep into QSAR and ther=
e is plenty of info in =0Athe CCL archives. BUT when Antonio says:=0A"... c=
alculate any property  you can think of [...] and checking wether there =0A=
are any  correlation..."=0Ayou have to beware that a correlation does not n=
ecessarily establish a causality =0A(wearing a particular color wont increa=
se risk of heart failure in humans =0Aalthough you can certainly inquire wh=
at is the color most often worn by people =0Awith heart attacks)=0A=0ABest =
wishes=0A=0A=0A=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=0ADr. Joaquin Barroso-Flores, Ph. D.=0A-> http:=
//joaquinbarroso.wordpress.com=0A=0ACentro Conjunto de Investigacion en Qui=
mica Sustentable=0AInstituto de Quimica=0AUNAM=0Ajbarroso"a"unam.mx=0Ajoaqu=
in.barroso''a''gmail.com =0A=0A=0A"Blogastronom=EDa": http://joaquinbarroso=
.blogspot.com =0A=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=0A=0A=0A=0A=0A___________________________=
_____=0ADe: Antonio Chana achana _ iqfr.csic.es <owner-chemistry_._ccl.net>=
=0APara: "Flores, Joaquin Barroso " <joaco_barroso_._yahoo.com>=0AEnv=
iado: jueves, 11 de noviembre, 2010 10:05:53=0AAsunto: CCL: Structure and p=
roperty=0A=0A=0ASent to CCL by: Antonio Chana [achana ~ iqfr.csic.es]=0ADea=
r Neeraj,=0A=0Athat's actually the underlying idea of any SAR or -getting q=
uantitative- QSAR =0Astudy. Basically you must calculate any property  you =
can think of (in your case =0AusingDFT, although why being so close minded?=
), and checking wether there are =0Aany correlation between the  properties=
 you obtained and the bioactivity.=0A=0ASo the answer is yes, you can do it=
. Inet is plenty of information about such =0Aapproaches.=0A=0ARegards,=0A=
=0AAntonio=0A=0A=0A=0AEl 11/11/2010 16:18, neeraj misra neerajmisra^hotmail=
.com escribi=F3:=0A> Sent to CCL by: "neeraj  misra" [neerajmisra]=3D[hotma=
il.com]=0A> DEAR CCLER'S=0A>               I AM WORKING ON TWO ANALOGUES OF=
 A BIOMOLECULE, AND I WONDER HOW =0A>TO RELATE/CALCULATE THE STRUCTURAL PRO=
PERTIES(USING DFT) WITH ITS =0A>BIOACTIVITY.CAN THE BIOACTIVITY BE RELATED/=
INTERPRETED IN TERMS OF RESULTS =0A>OBTAINED BY QUANTUM CHEMICAL CALCULATIO=
NS(DFT).ANY SUGGESTION IN THIS REGARD =0A>WOULD BE GREATLY APPRECIATED.=0A>=
 =0A> REGARDS=0A> NEERAJ>=0A> =0A> =0A=0A=0A=0A-=3D This is automatically a=
dded to each message by the mailing script =3D-=0ATo recover the email addr=
ess of the author of the message, please change=0Athe strange characters on=
 the top line to the _._ sign. You can also=0Alook up the X-Original-From: li=
ne in the mail header.=0A=0AE-mail to subscribers: CHEMISTRY_._ccl.net or use=
:=0A=0A=0AE-mail to admi=
nistrators: CHEMISTRY-REQUEST_._ccl.net or use=0A    http://www.ccl.net/cgi-b=
in/ccl/send_ccl_message=0A=0Ahttp://www.ccl.net=
/chemistry/sub_unsub.shtml=0A=0ABefore posting, check wait time at: http://=
www.ccl.net=0A=0AConferences: =0Ahttp://server=
.ccl.net/chemistry/announcements/conferences/=0A=0ASearch Messages: http://=
www.ccl.net/chemistry/searchccl/index.shtml=0A=0AIf your mail bounces from =
CCL with 5.7.1 error, check:=0A=0A=0ARTF=
I: http://www.ccl.net/chemistry/aboutccl/instructions/=0A=0A=0A      
--0-995048478-1289516442=:94486
Content-Type: text/html; charset=iso-8859-1
Content-Transfer-Encoding: quoted-printable

<html><head><style type=3D"text/css"><!-- DIV {margin:0px;} --></style></he=
ad><body><div style=3D"font-family:times new roman,new york,times,serif;fon=
t-size:12pt">Deer Neeraj<br><br>Antonio is right, you have to dive deep int=
o QSAR and there is plenty of info in the CCL archives. BUT when Antonio sa=
ys:<br>"... calculate any property&nbsp; you can think of [...] and checkin=
g wether there are any =0Acorrelation..."<br>you have to beware that a corr=
elation does not necessarily establish a causality (wearing a particular co=
lor wont increase risk of heart failure in humans although you can certainl=
y inquire what is the color most often worn by people with heart attacks)<b=
r><br>Best wishes<br><div><br>=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<br></div>Dr. Joaquin Barroso-Flo=
res, Ph. D.<br><span>-&gt; <a target=3D"_blank" href=3D"http://joaquinbarro=
so.wordpress.com">http://joaquinbarroso.wordpress.com</a></span><br><br>Cen=
tro Conjunto de Investigacion en Quimica Sustentable<br>Instituto de Quimic=
a<br>UNAM<br>jbarroso"a"unam.mx<br>joaquin.barroso''a''gmail.com <br><br><d=
iv><span>"Blogastronom=EDa": <a target=3D"_blank" href=3D"http://joaquinbar=
roso.blogspot.com">http://joaquinbarroso.blogspot.com</a> </span><br>=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<div><br></div><div style=3D"font-family: times new roman,new york=
,times,serif;
 font-size: 12pt;"><br><div style=3D"font-family: arial,helvetica,sans-seri=
f; font-size: 10pt;"><font face=3D"Tahoma" size=3D"2"><hr size=3D"1"><b><sp=
an style=3D"font-weight: bold;">De:</span></b> Antonio Chana achana _ iqfr.=
csic.es &lt;owner-chemistry_._ccl.net&gt;<br><b><span style=3D"font-weight: b=
old;">Para:</span></b> "Flores, Joaquin Barroso " &lt;joaco_barroso=
_._yahoo.com&gt;<br><b><span style=3D"font-weight: bold;">Enviado:</span></b>=
 jueves, 11 de noviembre, 2010 10:05:53<br><b><span style=3D"font-weight: b=
old;">Asunto:</span></b> CCL: Structure and property<br></font><br><br>Sent=
 to CCL by: Antonio Chana [achana ~ iqfr.csic.es]<br>Dear Neeraj,<br><br>th=
at's actually the underlying idea of any SAR or -getting quantitative- QSAR=
 study. Basically you must calculate any property&nbsp; you can think of (i=
n your case usingDFT, although why being so close minded?), and checking we=
ther there are any correlation between the&nbsp; properties you obtained an=
d the
 bioactivity.<br><br>So the answer is yes, you can do it. Inet is plenty of=
 information about such approaches.<br><br>Regards,<br><br>Antonio<br><br><=
br><br>El 11/11/2010 16:18, neeraj misra neerajmisra^hotmail.com escribi=F3=
:<br>&gt; Sent to CCL by: "neeraj&nbsp; misra" [neerajmisra]=3D[hotmail.com=
]<br>&gt; DEAR CCLER'S<br>&gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nb=
sp;  I AM WORKING ON TWO ANALOGUES OF A BIOMOLECULE, AND I WONDER HOW TO RE=
LATE/CALCULATE THE STRUCTURAL PROPERTIES(USING DFT) WITH ITS BIOACTIVITY.CA=
N THE BIOACTIVITY BE RELATED/INTERPRETED IN TERMS OF RESULTS OBTAINED BY QU=
ANTUM CHEMICAL CALCULATIONS(DFT).ANY SUGGESTION IN THIS REGARD WOULD BE GRE=
ATLY APPRECIATED.<br>&gt; <br>&gt; REGARDS<br>&gt; NEERAJ&gt;<br>&gt; <br>&=
gt; <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 the m=
essage, please change<br<br>look up the X-Original-From: line in the mail header=
.<br><br>E-mail to subscribers: <a ymailto=3D"mailto:CHEMISTRY_._ccl.net" hre=
f=3D"mailto:CHEMISTRY_._ccl.net">CHEMISTRY_._ccl.net</a> or use:<br>&nbsp; &nbs=
p;  <a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message" target=3D"_=
blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br><br>E-mail to=
 administrators: <a ymailto=3D"mailto:CHEMISTRY-REQUEST_._ccl.net" href=3D"ma=
ilto:CHEMISTRY-REQUEST_._ccl.net">CHEMISTRY-REQUEST_._ccl.net</a> or use<br>&nb=
sp; &nbsp;  <a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message" tar=
get=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br><br>S=
ubscribe/Unsubscribe:&nbsp; &nbsp; &nbsp; <a href=3D"http://www.ccl.net/che=
mistry/sub_unsub.shtml" target=3D"_blank">http://www.ccl.net/chemistry/sub_=
unsub.shtml</a><br><br>Before posting, check wait time at: <a href=3D"http:=
//www.ccl.net" target=3D"_blank">http://www.ccl.net</a><br><br>Job: <a
 href=3D"http://www.ccl.net/jobs" target=3D"_blank">http://www.ccl.net/jobs=
</a> Conferences: <a href=3D"http://server.ccl.net/chemistry/announcements/=
conferences/" target=3D"_blank">http://server.ccl.net/chemistry/announcemen=
ts/conferences/</a><br><br>Search Messages: <a href=3D"http://www.ccl.net/c=
hemistry/searchccl/index.shtml" target=3D"_blank">http://www.ccl.net/chemis=
try/searchccl/index.shtml</a><br><br>If your mail bounces from CCL with 5.7=
.1 error, check:<br>&nbsp; &nbsp;  <a href=3D"http://www.ccl.net/spammers.t=
xt" target=3D"_blank">http://www.ccl.net/spammers.txt</a><br><br>RTFI: <a h=
ref=3D"http://www.ccl.net/chemistry/aboutccl/instructions/" target=3D"_blan=
k">http://www.ccl.net/chemistry/aboutccl/instructions/</a><br><br><br></div=
></div></div>=0A</div><br>=0A=0A=0A=0A      &nbsp;</body></html>
--0-995048478-1289516442=:94486--


From owner-chemistry@ccl.net Fri Nov 12 01:21:00 2010
From: "Simon Halstead joyjoyhappyjoy**yahoo.co.uk" <owner-chemistry=-=server.ccl.net>
To: CCL
Subject: CCL: Hardware suggestions for CPMD calculations
Message-Id: <-43151-101112001257-14354-2wsPTNjnNjOuiRYHUeIXmg=-=server.ccl.net>
X-Original-From: Simon Halstead <joyjoyhappyjoy(0)yahoo.co.uk>
Content-Type: text/plain; charset=us-ascii
Date: Fri, 12 Nov 2010 05:12:51 +0000 (GMT)
MIME-Version: 1.0


Sent to CCL by: Simon Halstead [joyjoyhappyjoy!A!yahoo.co.uk]
Dear CCLers,
 
I am starting a new research project which will require CPMD calculations. 
However, my current cluster is not especially powerful and I feel it will not be 
up to the task. So, I am looking to buy and build a new machine. I have very 
little experience with running CPMD, so I am not sure about what kind of 
hardware requirements it has. 

 
I am planning to run CPMD calculations with something on the order of 200 to 400 
relatively light atoms, primarily C, H and O. I do not need to run large 
quantities of simulations, and would be perfectly happy with only being able to 
run one simulation at a time as long as it is within a reasonable time scale. 
With this in mind, does anybody have any suggestions about what hardware I 
should be looking to use, especially which CPU? Also, would should be my primary 
concern with the cluster? I am currently assuming that the most important thing 
will be large quantities of RAM for each CPU...
 
Any help or advice is appreciated.
 
Regards,
 
Simon Halstead


From owner-chemistry@ccl.net Fri Nov 12 10:20:00 2010
From: "Gopakumar G scschem=gmail.com" <owner-chemistry a server.ccl.net>
To: CCL
Subject: CCL: IRC with Turbomole
Message-Id: <-43152-101112101853-3819-7es7j06aK/6xlSNqrj/dug a server.ccl.net>
X-Original-From: "Gopakumar  G" <scschem=-=gmail.com>
Date: Fri, 12 Nov 2010 10:18:51 -0500


Sent to CCL by: "Gopakumar  G" [scschem!A!gmail.com]
Hi,

  I was just wondering whether it is possible to do an IRC calculation
with Turbomole. Is it available in the latest version? Or the developers
are planning to make that available for the future release.

Thanks in advance for the reply.

Sincerely

-Gopakumar


From owner-chemistry@ccl.net Fri Nov 12 13:14:00 2010
From: "Andreas Bender, PhD Andreas.Bender++cantab.net" <owner-chemistry::server.ccl.net>
To: CCL
Subject: CCL: "Visions of a Semantic Molecular Future" - Symposium for Peter Murray-Rust, Cambridge/UK, 17 Jan 2011
Message-Id: <-43153-101112115432-1758-1oayn+DcuXTPNn4vRaCnRg::server.ccl.net>
X-Original-From: "Andreas Bender, PhD" <Andreas.Bender:_:cantab.net>
Content-Type: text/plain; charset=ISO-8859-1
Date: Fri, 12 Nov 2010 16:54:20 +0000
MIME-Version: 1.0


Sent to CCL by: "Andreas Bender, PhD" [Andreas.Bender:_:cantab.net]
Dear CCL'lers,

In order to celebrate the life and scientific contributions of
Professor Peter Murray-Rust in both industry and academia the Unilever
Centre for Molecular Sciences in Cambridge/UK would like to cordially
invite you to the following event:

"Visions of a Semantic Molecular Future" - A Symposium to celebrate
the Career of Professor Peter Murray-Rust
(for a full programme please see
http://www.cheminformatics.org/PMR_Symposium_20110117.pdf)

The symposium will take place on 17 January 2011 in the Unilever
Centre, part of the Department of Chemistry of the University of
Cambridge.

Professor Murray-Rust's career spans academic positions in Stirling,
Nottingham and Cambridge and the establishment of one of the earliest
Molecular Graphics laboratories with Glaxo in the early 80's. More
recently, he has become well known for his contributions to the Open
Data movement and various Open Source developments, such as within the
Blue Obelisk framework.

In order to acknowledge Professor Murray-Rust's contributions to
science we are now organizing this symposium. Everyone is welcome to
attend, in particular of course the large number of people he has been
involved with on a scientific, as well as a personal basis.
Participation at the symposium is free, please just register your
interest via e-mail with Susan Begg (smb28^-^cam.ac.uk) until the end of
November.

Best wishes and we are looking forward to welcoming you to Cambridge soon,

Cheers,
Andreas

--
Andreas Bender, PhD
Lecturer for Molecular Informatics
Unilever Centre, Cambridge University
http://www-ucc.ch.cam.ac.uk
Personal: http://www.andreasbender.de


From owner-chemistry@ccl.net Fri Nov 12 13:48:00 2010
From: "Bjoern Baumeier baumeier- -mpip-mainz.mpg.de" <owner-chemistry%a%server.ccl.net>
To: CCL
Subject: CCL:G: XC potential matrix elements output
Message-Id: <-43154-101112133631-20349-tvgWYgaXviiiv2ZuBR7q7g%a%server.ccl.net>
X-Original-From: "Bjoern  Baumeier" <baumeier(_)mpip-mainz.mpg.de>
Date: Fri, 12 Nov 2010 13:36:29 -0500


Sent to CCL by: "Bjoern  Baumeier" [baumeier|a|mpip-mainz.mpg.de]
Hi people,

does anyone of you know whether it is possible to output the matrix elements of the XC potential 
either in Gaussian or in Turbomole?

Thanks, 
Bjoern


From owner-chemistry@ccl.net Fri Nov 12 14:25:00 2010
From: "Jamin Krinsky jamink-$-berkeley.edu" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL:G: Reading fchk files in gv 3.0
Message-Id: <-43155-101112142149-20266-z5416we8AKZrGd2PVZhJXA++server.ccl.net>
X-Original-From: Jamin Krinsky <jamink{:}berkeley.edu>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=ISO-8859-1
Date: Fri, 12 Nov 2010 11:21:38 -0800
MIME-Version: 1.0


Sent to CCL by: Jamin Krinsky [jamink#%#berkeley.edu]
David is correct, in general you need to run formchk on the system
that created the .chk file. If that system has G03 and G09, be sure
you are using the formchk utility for G09 by specifying the full path
to the executable, for example "/software/gaussian/g09/formchk
yourfilename" if the G09 installation were located in
/software/gaussian. You can then read the .fchk file directly into
GaussView on your Ubuntu machine, but keep in mind that certain output
generated by G09 will not be compatible with GaussView3.

Regards,
Jamin

On Thu, Nov 11, 2010 at 5:37 PM, Close, David M. CLOSED a
mail.etsu.edu <owner-chemistry#ccl.net> wrote:
>
> Sent to CCL by: "Close, David M." [CLOSED]=[mail.etsu.edu]
> Jacqueline:
>  This topic was discussed on the CCL just 1-2 months ago.  I seem to recall that there were several solutions offered.  One solution was to generate the .fchk file in the actual calculation by adding the keyword formcheck on the command line.  Also someone mentioned that G03 may not be able to convert a check file generated by G09.  So you could do a quick check at try to generate the 'fchk file on the remote computer, and then see if you can read it locally.
>  Regards, Dave Close.
>
> -----Original Message-----
>> From: owner-chemistry+closed==etsu.edu\a/ccl.net [mailto:owner-chemistry+closed==etsu.edu\a/ccl.net] On Behalf Of jacqueline cawthray jcawth01:+:gmail.com
> Sent: Thursday, November 11, 2010 8:08 PM
> To: Close, David M.
> Subject: CCL:G: Reading fchk files in gv 3.0
>
>
> Sent to CCL by: "jacqueline  cawthray" [jcawth01##gmail.com]
> Hi
>
> I have g09 optimization jobs run on a remote computer and want to view the results (particularly surfaces) using Gaussview 3.0 on Ubuntu on a local computer. I have tried reading the file.chk directly but get the error "can't find the formchk utility". It is there but I'm not sure how to go about this.
>
> I have also tried converting the file.chk to file.fchk using either g09 or g03. Using g03 generates an error writing the fchk file and using g09, gview won't open it.
>
> Thanks for your time.
>
> Regards
>
> JChttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt>
>
>


From owner-chemistry@ccl.net Fri Nov 12 21:13:00 2010
From: "Wojciech Kolodziejczyk dziecial()icnanotox.org" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL:G: Reading fchk files in gv 3.0
Message-Id: <-43156-101112165012-26387-tg5YG542XPFpq0EYTT4AdQ**server.ccl.net>
X-Original-From: Wojciech Kolodziejczyk <dziecial__icnanotox.org>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=ISO-8859-1
Date: Fri, 12 Nov 2010 22:50:01 +0100
MIME-Version: 1.0


Sent to CCL by: Wojciech Kolodziejczyk [dziecial\a/icnanotox.org]
Hi
Jamin. You are not right. I made G09 fchk files and run them in
GaussViev3. I have never had problems with reading that. G09 fchk
files made with formchk works with gaussView with no problem.I use GV3
for Windows.

2010/11/12 Jamin Krinsky jamink-$-berkeley.edu <owner-chemistry(0)ccl.net>:
>
> Sent to CCL by: Jamin Krinsky [jamink#%#berkeley.edu]
> David is correct, in general you need to run formchk on the system
> that created the .chk file. If that system has G03 and G09, be sure
> you are using the formchk utility for G09 by specifying the full path
> to the executable, for example "/software/gaussian/g09/formchk
> yourfilename" if the G09 installation were located in
> /software/gaussian. You can then read the .fchk file directly into
> GaussView on your Ubuntu machine, but keep in mind that certain output
> generated by G09 will not be compatible with GaussView3.
>
> Regards,
> Jamin
>
> On Thu, Nov 11, 2010 at 5:37 PM, Close, David M. CLOSED a
> mail.etsu.edu <owner-chemistry/a\ccl.net> wrote:
>>
>> Sent to CCL by: "Close, David M." [CLOSED]=[mail.etsu.edu]
>> Jacqueline:
>>  This topic was discussed on the CCL just 1-2 months ago.  I seem to recall that there were several solutions offered.  One solution was to generate the .fchk file in the actual calculation by adding the keyword formcheck on the command line.  Also someone mentioned that G03 may not be able to convert a check file generated by G09.  So you could do a quick check at try to generate the 'fchk file on the remote computer, and then see if you can read it locally.
>>  Regards, Dave Close.
>>
>> -----Original Message-----
>>> From: owner-chemistry+closed==etsu.edu\a/ccl.net [mailto:owner-chemistry+closed==etsu.edu\a/ccl.net] On Behalf Of jacqueline cawthray jcawth01:+:gmail.com
>> Sent: Thursday, November 11, 2010 8:08 PM
>> To: Close, David M.
>> Subject: CCL:G: Reading fchk files in gv 3.0
>>
>>
>> Sent to CCL by: "jacqueline  cawthray" [jcawth01##gmail.com]
>> Hi
>>
>> I have g09 optimization jobs run on a remote computer and want to view the results (particularly surfaces) using Gaussview 3.0 on Ubuntu on a local computer. I have tried reading the file.chk directly but get the error "can't find the formchk utility". It is there but I'm not sure how to go about this.
>>
>> I have also tried converting the file.chk to file.fchk using either g09 or g03. Using g03 generates an error writing the fchk file and using g09, gview won't open it.
>>
>> Thanks for your time.
>>
>> Regards
>>
>> JChttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt>
>
>