From chemistry-request@ccl.net Tue Jun 14 22:53:36 2005
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Date: Tue, 14 Jun 2005 22:53:34 -0400
From: Gustavo Seabra <gustavo.seabra ^^^ gmail.com>
Reply-To: 
To: chemistry ^^^ ccl.net
Subject: Re: CCL:W:isotope calculations
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On 6/14/05, kono, , lemke <klemke04 ^^^ yahoo.com> wrote:
>=20
> i am running cbs-4 calculations on small deuterated organics and
> can not get gaussian to rerun for heavier isotopes. does gaussian
> require a blank line at the input end? any suggestion
> as how to edit the input below would be appreciated. thanks
> kono


Yes. I've had calculations crashing for missing the blank line=20
in the end. HTH.


--=20
---------------------------------------------------------------------------=
------------------
Gustavo Seabra Postdoctoral Associate
Quantum Theory Project University of Florida
Registered Linux user number 381680
Say NO! to software patents: http://www.nosoftwarepatents.com
---------------------------------------------------------------------------=
------------------
If at first you don't succeed...
...skydiving is not for you.

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On 6/14/05, <b class=3D"gmail_sendername">kono, , lemke</b> &lt;<a href=3D"=
mailto:klemke04 ^^^ yahoo.com">klemke04 ^^^ yahoo.com</a>&gt; wrote:<div><span clas=
s=3D"gmail_quote"></span><blockquote class=3D"gmail_quote" style=3D"border-=
left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left=
: 1ex;">
i am running cbs-4 calculations on small deuterated organics and<br>can not=
 get gaussian to rerun for heavier isotopes. does gaussian<br>require a bla=
nk line at the input end? any suggestion<br>as how to edit the input below =
would be appreciated. thanks
<br>kono</blockquote><div><br>
Yes. I've had calculations crashing for missing the blank line <br>
in the end. HTH.<br>
</div><br></div><br>-- <br>------------------------------------------------=
---------------------------------------------<br>Gustavo
Seabra&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pos=
tdoctoral
Associate<br>Quantum Theory
Project&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&n=
bsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp=
;&nbsp;&nbsp;&nbsp;&nbsp;
University of Florida<br>Registered Linux user number 381680<br>Say NO! to =
software patents: <a href=3D"http://www.nosoftwarepatents.com">http://www.n=
osoftwarepatents.com</a><br>-----------------------------------------------=
----------------------------------------------
<br>If at first you don't succeed...<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp=
;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&n=
bsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;...sk=
ydiving
is not for you.

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From chemistry-request@ccl.net Tue Jun 14 21:51:29 2005
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From: renyanliang <yanliangren_2002 ^^^ yahoo.com.cn>
Subject: How to print overlap matrix in gaussian 03
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Dear All:
    Now, I want to check the overlap integral matrix
(S) in the output file of the gaussian 03 program, who
can give me some advice to make gaussian 03 print this
matrix. or which program can print it.  
   Best Wish!
   


		
___________________________________________________________
QE;"Cb7QGSJOd#-VP9zWnG?Cb7Q7@6>74@,;x3,4sSJOd
http://cn.mail.yahoo.com/?id=77072


From chemistry-request@ccl.net Wed Jun 15 02:15:53 2005
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To: chemistry ^^^ ccl.net
Subject: Re: CCL:QSAR Software
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An interesting question! I can't wait to see the answers. But, in the 
meantime, I have a question:

Apparently, you are a "consultant" because you provide expert advice to 
your client. But since you are asking us for expert advice, does this 
make us into "consultants" if we provide expert advice to you? And, 
maybe more to the point, will we get paid by you for our answers?

-Alan

Lisa M. Balbes, Ph.D. wrote:

> Good Afternoon!
>
> I am evaluating QSAR packages for a client, and am looking for 
> opinions on what's currently available.
>
> I am especially interested in what features people love, hate, can't 
> live without, wish they had, and so on. I would be most appreciative 
> of opinions members of this list would care to share, and of course 
> you will remain anonymous. (Hard data comparisons are also welcome!)
>
> You may respond to me directly, and I will summarize to the list if 
> there is enough interest.
>
> Looking forward to hearing > from you!
>
> Lisa
>
> PS  I tried posting this query on the QSAR society list,  
> qsar_society ^^^ accelrys.com, but did not get anything back.  Does anyone 
> know if that list is active?
>
>-- 
>  
>
> -------------------------------------------------------------------------------------------------------------------------------
> Lisa M. Balbes, Ph.D.    lisa ^^^ balbes.com         http://www.balbes.com/
> Balbes Consultants                Scientific Documentation Specialist 
> since 1992 
>                
> American Chemical Society - St Louis Section Treasurer, COMP division 
> WebMaven
> ACS/Dept of Career Services Presenter and Career Consultant
> Chair, Washington University APAP, St Louis South Committee   
> Consultants and Independent Contractors SIG Manager, St Louis Society 
> for Technical Communication
> Technical Coordinator, Cyberworkshop Committee, American Needlepoint Guild
> Advancement Coordinator, Boy Scout Troop 352
>
>-= This is automatically added to each message by the mailing script =-
>To send e-mail to subscribers of CCL put the string CCL: on your Subject: line
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>use the Web based form from CCL Home Page 
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>
>
>  
>

-- 
Alan Shusterman
Chemistry Department
Reed College
Portland, OR 97202-8199
503-517-7699
http://academic.reed.edu/chemistry/alan/
"Yield and overcome; Bend and be straight." Lao Tzu 22


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An interesting question! I can't wait to see the answers. But, in the
meantime, I have a question:<br>
<br>
Apparently, you are a "consultant" because you provide expert advice to
your client. But since you are asking us for expert advice, does this
make us into "consultants" if we provide expert advice to you? And,
maybe more to the point, will we get paid by you for our answers?<br>
<br>
-Alan<br>
<br>
Lisa M. Balbes, Ph.D. wrote:
<blockquote cite="midp06210216bed4fd32a0b5@%5B192.168.1.9%5D"
 type="cite">
  <style type="text/css"><!--
blockquote, dl, ul, ol, li { padding-top: 0 ; padding-bottom: 0 }
 --></style>
  <title>QSAR Software</title>
  <div><font face="Courier New" size="-1">Good Afternoon!</font></div>
  <div><font face="Courier New" size="-1"><br>
  </font></div>
  <div><font face="Courier New" size="-1">I am evaluating QSAR packages
for a client, and am looking for opinions on what's currently
available.</font></div>
  <div><font face="Courier New" size="-1"><br>
  </font></div>
  <div><font face="Courier New" size="-1">I am especially interested in
what features people love, hate, can't live without, wish they had,
and so on. I would be most appreciative of opinions members of this
list would care to share, and of course you will remain anonymous.
(Hard data comparisons are also welcome!)</font></div>
  <div><font face="Courier New" size="-1"><br>
  </font></div>
  <div><font face="Courier New" size="-1">You may respond to me
directly, and I will summarize to the list if there is enough
interest.</font></div>
  <div><font face="Courier New" size="-1"><br>
  </font></div>
  <div><font face="Courier New" size="-1">Looking forward to hearing
&gt; from you!</font></div>
  <div><br>
  </div>
  <div>Lisa</div>
  <div><br>
  </div>
  <div>PS&nbsp; I tried posting this query on the QSAR society list,&nbsp;
<a class="moz-txt-link-abbreviated" href="mailto:qsar_society ^^^ accelrys.com">qsar_society ^^^ accelrys.com</a>, but did not get anything back.&nbsp; Does
anyone know if that list is active?</div>
  <x-sigsep></x-sigsep>
  <pre>-- 
  </pre>
  <div>--------------------------------------------------------------------<span></span>-----------------------------------------------------------<br>
Lisa M. Balbes, Ph.D.<x-tab>&nbsp;&nbsp;&nbsp;
  </x-tab><a class="moz-txt-link-abbreviated" href="mailto:lisa ^^^ balbes.com">lisa ^^^ balbes.com</a><x-tab>
  </x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
  </x-tab><a class="moz-txt-link-freetext" href="http://www.balbes.com/">http://www.balbes.com/</a><br>
Balbes Consultants<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
  </x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
  </x-tab>Scientific Documentation Specialist since 1992<x-tab>&nbsp;
  </x-tab><br>
  <x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
  </x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </x-tab><br>
American Chemical Society - St Louis Section Treasurer, COMP division
WebMaven<br>
ACS/Dept of Career Services Presenter and Career Consultant<br>
Chair, Washington University APAP, St Louis South
Committee<x-tab>&nbsp;&nbsp;&nbsp; </x-tab><br>
Consultants and Independent Contractors SIG Manager, St Louis Society
for Technical Communication<br>
Technical Coordinator, Cyberworkshop Committee, American Needlepoint
Guild<br>
Advancement Coordinator, Boy Scout Troop 352</div>
  <pre>-= This is automatically added to each message by the mailing script =-
To send e-mail to subscribers of CCL put the string CCL: on your Subject: line
and send your message to:  <a class="moz-txt-link-abbreviated" href="mailto:CHEMISTRY ^^^ ccl.net">CHEMISTRY ^^^ ccl.net</a>

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If your is mail bouncing from ccl.net domain due to spam filters, please
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  </pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">-- 
Alan Shusterman
Chemistry Department
Reed College
Portland, OR 97202-8199
503-517-7699
<a class="moz-txt-link-freetext" href="http://academic.reed.edu/chemistry/alan/">http://academic.reed.edu/chemistry/alan/</a>
"Yield and overcome; Bend and be straight." Lao Tzu 22</pre>
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From chemistry-request@ccl.net Wed Jun 15 13:48:19 2005
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In-Reply-To: <42AE6AED.8050002 ^^^ cosmologic.de>
To: chemistry ^^^ ccl.net
Cc: Stephen Warde <swarde ^^^ accelrys.com>
Subject: Re: CCL:Scientific Conference by Accelrys in London, Nov 14-16
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Andreas Klamt wrote on 06/13/2005 10:28:13 PM:

> Dear Dr. Nauss,
> 
> is AccelrysWorld really open to anyone, even to vendors of technology 
> competing (or at least not directly connected) with Accelrys software?

Yes, it is open to all.

Jeff
--
Jeffrey L. Nauss, Ph.D.
Lead Training Scientist
Accelrys
10188 Telesis Court, Suite 100
San Diego, CA 92121-4779

Phone: +1-858-799-5555
Fax: +1-858-799-5100
http://www.accelrys.com/training

*AccelrysWorld 2005, London, Nov 14-16. http://www.accelrysworld.com*



From chemistry-request@ccl.net Wed Jun 15 11:53:52 2005
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From: "car.cardenas" <car.cardenas ## uandresbello.edu>
To: chemistry ## ccl.net
Subject: Re: CCL:How to print overlap matrix in gaussian 03
Date: Wed, 15 Jun 2005 12:47:04 -0200
Message-Id: <20050615143920.M85870 ## uandresbello.edu>
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Hi Dear ...
The overlap matrix in terms of the atomic orbital basis fuctions can be print 
in the output file using the IOP=3/33 (overlay 3 variable 33). De default is 
No Print. The next keyword in the Route secction print the overlap matrix

iop(3/33=4) pop=full

Warning: Do not forget it the pop=full keyword.

The output look as(h20 with the sto-3g basis):
      DENSITY MATRIX.
                           1         2         3         4         5
   1 1   O  1S          2.10786
   2        2S         -0.45534   2.00654
   3        2PX         0.00000   0.00000   2.00000
   4        2PY         0.00000   0.00000   0.00000   0.75066
   5        2PZ        -0.10813   0.60592   0.00000   0.00000   1.17327
   6 2   H  1S         -0.02248  -0.05498   0.00000   0.55045  -0.48420
   7 3   H  1S         -0.02248  -0.05498   0.00000  -0.55045  -0.48420
                           6         7
   6 2   H  1S          0.62617
   7 3   H  1S         -0.18112   0.62617

Best Regards, 

Carlos




Carlos Cardenas
Doctorado en Fmsico Qummica Molecular
Universidad Andris Bello.
Santiago, Chile
Tel (56+2) 6714518

---------- Original Message -----------
From: renyanliang <yanliangren_2002 ## yahoo.com.cn>
To: chemistry ## ccl.net
Sent: Wed, 15 Jun 2005 09:51:21 +0800 (CST)
Subject: CCL:How to print overlap matrix in gaussian 03

> Dear All:
>     Now, I want to check the overlap integral matrix
> (S) in the output file of the gaussian 03 program, who
> can give me some advice to make gaussian 03 print this
> matrix. or which program can print it.  
>    Best Wish!
> 
> 		
> ___________________________________________________________
> QE;"Cb7QGSJOd#-VP9zWnG?Cb7Q7@6>74@,;x3,4sSJOd
> http://cn.mail.yahoo.com/?id=77072
> 
> -= This is automatically added to each message by the mailing script 
> =- To send e-mail to subscribers of CCL put the string CCL: on your 
> Subject: line and send your message to:  CHEMISTRY ## ccl.net
> 
> Send your subscription/unsubscription requests to: CHEMISTRY-
> REQUEST ## ccl.net HOME Page: http://www.ccl.net   | Jobs Page: 
> http://www.ccl.net/jobs
> 
> If your is mail bouncing from ccl.net domain due to spam filters, please
> use the Web based form from CCL Home Page 
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> +-+
------- End of Original Message -------



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Date: Wed, 15 Jun 2005 15:50:07 +0200
From: Uwe Richter <urichter ## jerini.de>
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Subject: CCL: size of ligand binding pocket
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Dear CCLers,

I am looking for software which is able to quantify the
size/depth of ligand binding pockets of proteins?

Thanks in advance,
Uwe



From chemistry-request@ccl.net Wed Jun 15 14:17:52 2005
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Subject: Hard spheres and ewald sum
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Dear Sir/Madam,

I am working on F.10 (Hard sphere) and F.22 (Ewald sum) programs of your
book (Computer simulation of liquids). The program F.10 requires a
configuration file. Where is it? How can I obtain the configuration file
(CNFILE)?
Amir Vahid (amirvahid ## iust.ac.ir)
Thermokinetic Research Laboratory
Chem. Eng. Dept.
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From chemistry-request@ccl.net Wed Jun 15 11:18:46 2005
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Date: Wed, 15 Jun 2005 11:18:41 -0400
From: Gustavo Seabra <gustavo.seabra !! gmail.com>
Reply-To: 
To: chemistry !! ccl.net
Subject: Re: CCL:How to print overlap matrix in gaussian 03
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On 6/14/05, renyanliang <yanliangren_2002 !! yahoo.com.cn> wrote:
>=20
> Dear All:
> Now, I want to check the overlap integral matrix
> (S) in the output file of the gaussian 03 program, who
> can give me some advice to make gaussian 03 print this
> matrix. or which program can print it.
> Best Wish!


Try using IOp(4/34=3D1). But beware: it will print **a lot** of stuff. Try =
it=20
with a single point calculation first.

HTH.


--=20
---------------------------------------------------------------------------=
------------------
Gustavo Seabra Postdoctoral Associate
Quantum Theory Project University of Florida
Registered Linux user number 381680
Say NO! to software patents: http://www.nosoftwarepatents.com
---------------------------------------------------------------------------=
------------------
If at first you don't succeed...
...skydiving is not for you.

------=_Part_3066_15790461.1118848721877
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On 6/14/05, <b class=3D"gmail_sendername">renyanliang</b> &lt;<a href=3D"ma=
ilto:yanliangren_2002 !! yahoo.com.cn">yanliangren_2002 !! yahoo.com.cn</a>&gt; w=
rote:<div><span class=3D"gmail_quote"></span><blockquote class=3D"gmail_quo=
te" style=3D"border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt=
 0.8ex; padding-left: 1ex;">
Dear All:<br>&nbsp;&nbsp;&nbsp;&nbsp;Now, I want to check the overlap integ=
ral matrix<br>(S) in the output file of the gaussian 03 program, who<br>can=
 give me some advice to make gaussian 03 print this<br>matrix. or which pro=
gram can print it.
<br>&nbsp;&nbsp; Best Wish!</blockquote><div><br>
Try using IOp(4/34=3D1). But beware: it will print **a lot** of stuff. Try =
it with a single point calculation first.<br>
<br>
HTH.<br>
&nbsp;<br>
</div><br></div>-- <br>----------------------------------------------------=
-----------------------------------------<br>Gustavo
Seabra&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pos=
tdoctoral
Associate<br>Quantum Theory
Project&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&n=
bsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp=
;&nbsp;&nbsp;&nbsp;&nbsp;
University of Florida<br>Registered Linux user number 381680<br>Say NO! to =
software patents: <a href=3D"http://www.nosoftwarepatents.com">http://www.n=
osoftwarepatents.com</a><br>-----------------------------------------------=
----------------------------------------------
<br>If at first you don't succeed...<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp=
;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&n=
bsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;...sk=
ydiving
is not for you.

------=_Part_3066_15790461.1118848721877--


From chemistry-request@ccl.net Wed Jun 15 08:21:22 2005
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From: =?GB2312?B?Tmljb2xhcyBGZXJyqKY=?= <nicolas.ferre !! up.univ-mrs.fr>
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Subject: Re: CCL:How to print overlap matrix in gaussian 03
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Hi,

Write IOp(3/33=1) in the keywords. You'll get this matrix together with
the kinetic energy, the potential energy and the  core hamiltonian matrices.

renyanliang a (&crit :
> Dear All:
>     Now, I want to check the overlap integral matrix
> (S) in the output file of the gaussian 03 program, who
> can give me some advice to make gaussian 03 print this
> matrix. or which program can print it.  
>    Best Wish!
>    

-- 
 ***********           Dr. Nicolas Ferre'           ***********
 Laboratoire de Chimie Theorique et de Modelisation Moleculaire
 UMR 6517 - CNRS Universites Aix-Marseille             Case 521
 Centre de Saint-Jerome      13397 - Marseille Cedex 20, France
 Tel : (+33)4.91.28.27.33              Fax : (+33)4.91.28.87.58
       http://www.up.univ-mrs.fr/wsrep/ctheo/lctmm.html
***************************************************************


From chemistry-request@ccl.net Wed Jun 15 09:50:11 2005
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Subject: RE: W:isotope calculations
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Your input should be something like this (i.e. what's between the two rows of + signs):
++++++++++++++++++++++++++++++++++++++++++++++++++++++
%chk=formaldehyde
# cbs-4m

formaldehyde

0 1
 c
 o   1 oc2     
 h   1 hc3        2 hco3      
 h   1 hc4        2 hco4         3 dih4   
 
oc2         1.450000
hc3         1.089000
hco3        109.471
hc4         1.089000
hco4        109.471
dih4        120.000

--link1--
%chk=formaldehyde
# cbs-4m=(readfc,readiso) geom=check guess=read

Formaldehyde, deuterated

0 1

298.16 0.0 0.0
12
16
2
2

++++++++++++++++++++++++++++++++++++++++++++++++++++++
--David Shobe, Ph.D., M.L.S.
S|d-Chemie, Inc.
phone (502) 634-7409
fax (502) 634-7724

Don't bother flaming me: I'm behind a firewall.



-----Original Message-----
From: Computational Chemistry List [mailto:chemistry-request !! ccl.net] On Behalf Of kono, , lemke
Sent: Tuesday, June 14, 2005 7:13 PM
To: chemistry !! ccl.net
Subject: CCL:W:isotope calculations

i am running cbs-4 calculations on small deuterated organics and can not get gaussian to rerun for heavier isotopes. does gaussian require a blank line at the input end? any suggestion as how to edit the input below would be appreciated. thanks kono


%chk=formaldehyde
 cbs-4m

formaldehyde

0 1
 c
 o   1 oc2     
 h   1 hc3        2 hco3      
 h   1 hc4        2 hco4         3 dih4   
 
oc2         1.450000
hc3         1.089000
hco3        109.471
hc4         1.089000
hco4        109.471
dih4        120.000

--link1--
%chk=formaldehyde
 cbs-4m

0 1

298.16 0.0 0.0
12
16
2
2



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From chemistry-request@ccl.net Wed Jun 15 06:37:39 2005
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Place IOP(3/33=1) in the route section along with POP=FULL

On Wed, 2005-06-15 at 09:51 +0800, renyanliang wrote:
> Dear All:
>     Now, I want to check the overlap integral matrix
> (S) in the output file of the gaussian 03 program, who
> can give me some advice to make gaussian 03 print this
> matrix. or which program can print it.  
>    Best Wish!
>    
> 
> 
> 		
> ___________________________________________________________
> QE;"Cb7QGSJOd#-VP9zWnG?Cb7Q7@6>74@,;x3,4sSJOd
> http://cn.mail.yahoo.com/?id=77072
> 
> 
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From chemistry-request@ccl.net Wed Jun 15 11:17:54 2005
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Subject: cycloketones
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Dear ccl
I want to compare expremental  of vibrational frequency for the molecules
 cyclopropanone,cyclobutanone,cyclopentanone,.....and cyclooctanone with result of the gaussian .
How I can recognize and assignment frequency?because I do not have expremental data for this compare.
please help me.
thanks


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<DIV>
<DIV>Dear ccl</DIV>
<DIV>I&nbsp;want to compare&nbsp;expremental &nbsp;of vibrational frequency for the molecules</DIV>
<DIV>&nbsp;cyclopropanone,cyclobutanone,cyclopentanone,.....and cyclooctanone with result of the gaussian .</DIV>
<DIV>How I can recognize and assignment frequency?because I do not have expremental data for this compare.</DIV>
<DIV>please help me.</DIV>
<DIV>thanks</DIV></DIV><p>__________________________________________________<br>Do You Yahoo!?<br>Tired of spam?  Yahoo! Mail has the best spam protection around <br>http://mail.yahoo.com 
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From chemistry-request@ccl.net Wed Jun 15 09:36:32 2005
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Dear everyone:
I'm working with the MD simulation of the SO2. Does anyone have the force field parameters for this type molecule?  I'm working in Gromacs so parameters in that form would be particularly useful.

Cheers,

Yong


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Date: Wed, 15 Jun 2005 12:19:27 +0200
From: Pierre Archirel <pierre.archirel _()_ lcp.u-psud.fr>
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Subject: CCL: how to print overlap
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Overlap can be printed but most programs,
provided the right print flag is given:
for Gaussian (98, at least): iop(3/33=1)
for Gamess UK: nprint=3
Best wishes

__________________________________________________________

 Pierre Archirel
 Groupe de Chimie Thiorique
 Laboratoire de Chimie Physique      Tel: 01 69 15 63 86
 Bat 349                             Fax: 01 69 15 61 88
 91405 Orsay Cedex
 France                   pierre.archirel _+_ lcp.u-psud.fr
__________________________________________________________




From chemistry-request@ccl.net Wed Jun 15 07:31:34 2005
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References: <20050615015121.94696.qmail ^^^ web15104.mail.cnb.yahoo.com>
Subject: Re: CCL:How to print overlap matrix in gaussian 03
Date: Wed, 15 Jun 2005 06:30:48 -0500
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Add the following line to your com file:
"%rwf=rwf_file_name.rwf"  (rwf_file_name is any name you want to give to 
this file)
That will force gaussian to save the rwf file

The utility to get the matrix is "rwfdump".  I haven't done this for a while 
but I believe the syntax is:

rwfdump rwf_file_name.rwf yourfile 514r

"yourfile" is the file where the matrix will be stored and 514 is record 
number for the overlap matrix (r is format instruction).  It'll save it as a 
(I believe)lower triangular matrix.  It is formatted in 5 columns so the way 
you read it is, (from left to right and from top to bottom

(1,1) (2,1) (2,2) (3,1) (3,2)
(3,3) (4,1) (4,2) (4,3) (4,4)
...

Check the programmer's reference manual (chapter 3) for the list of other 
matrices you can get from the rwf.

PD
----- Original Message ----- 
From: "renyanliang" <yanliangren_2002 ^^^ yahoo.com.cn>
To: <chemistry ^^^ ccl.net>
Sent: Tuesday, June 14, 2005 8:51 PM
Subject: CCL:How to print overlap matrix in gaussian 03


> Dear All:
>    Now, I want to check the overlap integral matrix
> (S) in the output file of the gaussian 03 program, who
> can give me some advice to make gaussian 03 print this
> matrix. or which program can print it.
>   Best Wish!
>
>
>
>
> ___________________________________________________________
> QE;"Cb7QGSJOd#-VP9zWnG?Cb7Q7@6>74@,;x3,4sSJOd
> http://cn.mail.yahoo.com/?id=77072
>
>
> -= This is automatically added to each message by the mailing script =-
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From chemistry-request@ccl.net Wed Jun 15 08:52:41 2005
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From: Jason Thompson <Thompson.Jason1 %x% mayo.edu>
Subject: Re: CCL:How to print overlap matrix in gaussian 03
Date: Wed, 15 Jun 2005 07:54:38 -0500
To: chemistry %x% ccl.net
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Try:

Iop(3/33=1)

On Jun 14, 2005, at 8:51 PM, renyanliang wrote:

> Dear All:
>     Now, I want to check the overlap integral matrix
> (S) in the output file of the gaussian 03 program, who
> can give me some advice to make gaussian 03 print this
> matrix. or which program can print it.
>    Best Wish!
>
>
>
> 		
> ___________________________________________________________
> QE;"Cb7QGSJOd#-VP9zWnG?Cb7Q7@6>74@,;x3,4sSJOd
> http://cn.mail.yahoo.com/?id=77072
>
>
> -= This is automatically added to each message by the mailing script =-
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> +-+
>
>
>
>
Jason D. Thompson
Molecular Pharmacology and Experimental Therapeutics
Mayo Clinic
Guggenheim 6-93
200 First Street SW
Rochester, MN 55905
(507)-284-1758


From chemistry-request@ccl.net Wed Jun 15 16:02:04 2005
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Date: Wed, 15 Jun 2005 12:20:30 -0700
From: Xavier Deupi <Xavier.Deupi~at~stanford.edu>
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To: chemistry~at~ccl.net
Subject: Re: CCL:size of ligand binding pocket
References: <42B0320F.4090003~at~jerini.de>
In-Reply-To: <42B0320F.4090003~at~jerini.de>
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Hi Uwe,

I've used grasp for that purpose.

Xavi

Uwe Richter wrote:

> Dear CCLers,
>
> I am looking for software which is able to quantify the
> size/depth of ligand binding pockets of proteins?
>
> Thanks in advance,
> Uwe
>
-- 
Xavier Deupi, Ph.D.
Department of Molecular and Cellular Physiology
Beckman Center for Molecular and Genetic Medicine (B161)
279 Campus Drive, Stanford University School of Medicine
Stanford, CA 94305 (USA)

E-mail: Xavier.Deupi~at~stanford.edu
Phone: +1 (650) 725-6497
Fax : +1 (650) 725-8021


From chemistry-request@ccl.net Wed Jun 15 15:29:46 2005
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Date: Wed, 15 Jun 2005 11:32:07 -0700
To: CHEM-EDUCATION$at$JISCMAIL.AC.UK
From: Eric Scerri <scerri$at$chem.ucla.edu>
Subject: link to most viewed articles in Found Chem
Cc: history of chemistry <chem-hist$at$listserv.uni-regensburg.de>,
        ccl <chemistry$at$ccl.net>, PHILCHEM$at$LISTSERV.SC.EDU
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The following link to the most recently viewed and downloaded 
articles from Foundations of Chemistry may be of interest,


http://www.springeronline.com/sgw/cda/frontpage/0,11855,4-40399-70-35545882-detailsPage%253Djournal%257CmostViewedArticles%257CmostViewedArticles,00.html


eric scerri
-- 


Dr. Eric Scerri ,
UCLA,
4077C, Young Hall,
Department of Chemistry & Biochemistry,
607 Charles E. Young Drive East,
Los Angeles,  CA 90095-1569
USA

E-mail :   scerri$at$chem.ucla.edu
tel:  310 206 7443
fax:  310 206 2061
Web Page:    http://www.chem.ucla.edu/dept/Faculty/scerri/index.html

Editor  of  Foundations of Chemistry
http://www.springeronline.com/sgw/cda/frontpage/0,11855,4-0-70-35545882-0,00.html?referer=www.wkap.nl

Also see International Society for the Philosophy of Chemistry
http://ispc.sas.upenn.edu/


From chemistry-request@ccl.net Wed Jun 15 16:05:48 2005
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Date: Wed, 15 Jun 2005 21:14:32 +0200 (MEST)
From: Jana Precechtelova <janap * ncbr.chemi.muni.cz>
To: "CCL.NET" <chemistry * ccl.net>
Subject: CCL: PCM calculation with COSMO
Message-ID: <Pine.NEB.4.62.0506152045580.7054 * ncbr.chemi.muni.cz>
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Dear CClers,
I've done a single-point calculation (in g03) with the PCM-COSMO
model for a molecule solvated by 5 explicit waters.
Moreover, I used partial point charges to model
the solvent (water) within a certain cutoff distance.

The job crashed in the 1st SCF cycle with an error
announcement:

  Cycle   1  Pass 1  IDiag  1:
  FoFCou: FMM=T IPFlag=           0 FMFlag=      100000 FMFlg1=        8193
  NFxFlg=           0 DoJE=T BraDBF=F KetDBF=F FulRan=T.
  Petite list used in FoFCou.
  FMM levels:  10  Number of levels for PrismC:   9
  QIPC2: Lapack GESV/PPSV failed with Info=   107.


Does someone have any idea, what this error message mean
and how I can fix the problem???


Thanks, Jana


=============================================================
         Jana Precechtelova (Ph.D. student)
-------------------------------------------------------------
         Institut fuer Anorganische Chemie
         Bayerische Julius-Maximilians Universitaet Wuerzburg
         Am Hubland, 97074 Wuerzburg, Germany
                    &
         NMR Laboratory
         National Centre for Biomolecular Research (NCBR)
         Faculty of Science, Masaryk University
         Kotlarska 2, 611 37 Brno, Czech Republic
=============================================================
         email: janap * ncbr.chemi.muni.cz
=============================================================



From chemistry-request@ccl.net Wed Jun 15 18:09:38 2005
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Date: Wed, 15 Jun 2005 13:30:19 -0700 (PDT)
From: Andrew Orry <andy %x% molsoft.com>
To: CCL <chemistry %x% ccl.net>
Subject: Re: CCL:size of ligand binding pocket
In-Reply-To: <42B0320F.4090003 %x% jerini.de>
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> I am looking for software which is able to quantify the
> size/depth of ligand binding pockets of proteins?
>
> Thanks in advance,
> Uwe

Dear Uwe

The ICM suite of software has a number of different functions to analyze 
ligand binding pockets. Please see www.molsoft.com or the following 
papers:

An J, Totrov M, Abagyan R. Pocketome via Comprehensive Identification and 
Classification of Ligand Binding Envelopes. Mol Cell Proteomics. 2005 
Jun;4(6):752-761. Epub 2005 Mar 9.

An J, Totrov M, Abagyan R. Comprehensive identification of "druggable"  
protein ligand binding sites. Genome Inform Ser Workshop Genome Inform.
2004;15(2):31-41.

Thanks

Andy

On Wed, 15 Jun 2005, Uwe Richter wrote:

> Dear CCLers,
> 
> I am looking for software which is able to quantify the
> size/depth of ligand binding pockets of proteins?
> 
> Thanks in advance,
> Uwe
> 

From chemistry-request@ccl.net Wed Jun 15 18:18:30 2005
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Subject: RE: cycloketones
Date: Wed, 15 Jun 2005 17:26:51 -0400
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From: "Shobe, David" <dshobe=at=sud-chemieinc.com>
To: <chemistry=at=ccl.net>
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Try this book: Aldrich library of FT-IR spectra. Hopefully in a chem =
library near you.
=20
--David Shobe, Ph.D., M.L.S.=20
S=FCd-Chemie, Inc.=20
phone (502) 634-7409=20
fax (502) 634-7724=20

Don't bother flaming me: I'm behind a firewall.=20


  _____ =20

From: Computational Chemistry List [mailto:chemistry-request=at=ccl.net] On =
Behalf Of talia
Sent: Wednesday, June 15, 2005 10:18 AM
To: CHEMISTRY=at=ccl.net
Subject: CCL:cycloketones


Dear ccl
I want to compare expremental  of vibrational frequency for the =
molecules
 cyclopropanone,cyclobutanone,cyclopentanone,.....and cyclooctanone with =
result of the gaussian .
How I can recognize and assignment frequency?because I do not have =
expremental data for this compare.
please help me.
thanks

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<DIV dir=3Dltr align=3Dleft><FONT face=3DArial color=3D#0000ff =
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class=3D648231221-15062005>Try this book: Aldrich library of FT-IR =
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Hopefully in a chem library near you.</SPAN></FONT></DIV>
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<P><FONT face=3DArial size=3D2>--David Shobe, Ph.D., M.L.S.</FONT> =
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<HR tabIndex=3D-1>
<FONT face=3DTahoma size=3D2><B>From:</B> Computational Chemistry List=20
[mailto:chemistry-request=at=ccl.net] <B>On Behalf Of =
</B>talia<BR><B>Sent:</B>=20
Wednesday, June 15, 2005 10:18 AM<BR><B>To:</B>=20
CHEMISTRY=at=ccl.net<BR><B>Subject:</B> =
CCL:cycloketones<BR></FONT><BR></DIV>
<DIV></DIV>
<DIV>
<DIV>Dear ccl</DIV>
<DIV>I&nbsp;want to compare&nbsp;expremental &nbsp;of vibrational =
frequency for=20
the molecules</DIV>
<DIV>&nbsp;cyclopropanone,cyclobutanone,cyclopentanone,.....and =
cyclooctanone=20
with result of the gaussian .</DIV>
<DIV>How I can recognize and assignment frequency?because I do not have=20
expremental data for this compare.</DIV>
<DIV>please help me.</DIV>
<DIV>thanks</DIV></DIV>
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