From owner-chemistry@ccl.net Mon Oct  6 17:46:00 2008
From: "javier MAURICIO vallejos javier33###vtr.net" <owner-chemistry||server.ccl.net>
To: CCL
Subject: CCL:G: NBODEL OPTIMITATION
Message-Id: <-37846-081006115741-26790-3dj57W49Xcm0YkNL5nxHag||server.ccl.net>
X-Original-From: "javier MAURICIO vallejos" <javier33(0)vtr.net>
Date: Mon, 6 Oct 2008 11:57:37 -0400


Sent to CCL by: "javier MAURICIO vallejos" [javier33(a)vtr.net]
Dear All,

With Gaussian03, I tried to do reoptimize the geometry after deleting some
orbitals. I test the example given by NBO5 Tutorials. But the program gives
error messages as follows,
************************************************
 ** ERROR IN INITNF. NUMBER OF VARIABLES (  0) **
 **   INCORRECT (SHOULD BE BETWEEN 1 AND 50)   **
 ************************************************

 Error termination via Lnk1e in /opt/g03/revD01//g03/l114.exe at Mon 06/10
19:0


*
The input is:

* %Mem=1000MB
 #N HF/6-31G*  NOSYMM POP=NBODel OPT

 CHF::CHF (cis)

   0  1
  C
  C   1   1.34
  F   1   1.33   2  120.0
  F   2   1.33   1  120.0  3    0.0
  H   1   1.08   2  120.0  3  180.0
  H   2   1.08   1  120.0  4  180.0

 $NBO file=dfe_c $END
 $DEL
 delete 2 orbitals
   63 64
 $END


From owner-chemistry@ccl.net Mon Oct  6 18:20:00 2008
From: "Iain Wallace iain.m.wallace/./gmail.com" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL: Purchasing compounds
Message-Id: <-37847-081006174559-23115-YEkwq8kAyWsiojjstlR87A(0)server.ccl.net>
X-Original-From: "Iain Wallace" <iain.m.wallace*|*gmail.com>
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Date: Mon, 6 Oct 2008 17:45:48 -0400
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Sent to CCL by: "Iain Wallace" [iain.m.wallace*o*gmail.com]
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Hi,

A question slightly out of left field, but I was wondering if anybody knew a
source of purchasing compounds that have either failed in Phase I,II or III
or that have been withdrawn.
Drugbank has a list of compounds that are withdrawn but it would be cool to
know if there was a database that contained the information of compounds
that failed Phase I-III

Thanks

Iain

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<div dir="ltr">Hi,<br><br>A question slightly out of left field, but I was wondering if anybody knew a source of purchasing compounds that have either failed in Phase I,II or III or that have been withdrawn.<br>Drugbank has a list of compounds that are withdrawn but it would be cool to know if there was a database that contained the information of compounds that failed Phase I-III<br>
<br>Thanks<br><br>Iain <br></div>

------=_Part_47043_28561441.1223329548238--


From owner-chemistry@ccl.net Mon Oct  6 19:38:01 2008
From: "Jorge Rodriguez jorberr/./ciq.uchile.cl" <owner-chemistry- -server.ccl.net>
To: CCL
Subject: CCL: Problem with Autodock 4 _ Halogen Bound
Message-Id: <-37848-081006193624-2463-gynGQ2pnIlbCNIfo+Slqlw- -server.ccl.net>
X-Original-From: "Jorge  Rodriguez" <jorberr-x-ciq.uchile.cl>
Date: Mon, 6 Oct 2008 19:36:20 -0400


Sent to CCL by: "Jorge  Rodriguez" [jorberr%x%ciq.uchile.cl]
Hi, I have a system that present carbon-halogen bond in the active site. So, in the autodock 4 program I can`t use this system becouse autodock don't consider the carbon-halogen bond in its description (the halogen bond was not defined). If someone can help me. Because I don't knwon, how I can define an carbon-halogen bond in the AD4_parameters.dat?

I will greatly appreciate it if someone helps me

Jorge R


From owner-chemistry@ccl.net Mon Oct  6 21:40:00 2008
From: "Jeff Woodford jwoodfor]|[eou.edu" <owner-chemistry!^!server.ccl.net>
To: CCL
Subject: CCL:G: NBODEL OPTIMITATION
Message-Id: <-37849-081006213806-10397-Mq1Mdq8sq5MgWcUTJHqT/A!^!server.ccl.net>
X-Original-From: "Jeff Woodford" <jwoodfor~~eou.edu>
Content-Transfer-Encoding: 7bit
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	charset="US-ASCII"
Date: Mon, 6 Oct 2008 20:37:46 -0500
MIME-Version: 1.0


Sent to CCL by: "Jeff Woodford" [jwoodfor###eou.edu]
Hi Javier,
I also came across the same error.  If you put variables into your Z-matrix
and then define the variables below, then it should work.  As far as I know
this isn't documented.

-Jeff

Jeffrey N. Woodford
Associate Professor of Chemistry
Eastern Oregon University
Tel: 541-962-3321
Fax: 541-962-3873

-----Original Message-----
> From: owner-chemistry^ccl.net [mailto:owner-chemistry^ccl.net] 
Sent: Monday, October 06, 2008 10:58 AM
To: Woodford, Jeffrey N 
Subject: CCL:G: NBODEL OPTIMITATION


Sent to CCL by: "javier MAURICIO vallejos" [javier33(a)vtr.net]
Dear All,

With Gaussian03, I tried to do reoptimize the geometry after deleting some
orbitals. I test the example given by NBO5 Tutorials. But the program gives
error messages as follows,
************************************************
 ** ERROR IN INITNF. NUMBER OF VARIABLES (  0) **
 **   INCORRECT (SHOULD BE BETWEEN 1 AND 50)   **
 ************************************************

 Error termination via Lnk1e in /opt/g03/revD01//g03/l114.exe at Mon 06/10
19:0


*
The input is:

* %Mem=1000MB
 #N HF/6-31G*  NOSYMM POP=NBODel OPT

 CHF::CHF (cis)

   0  1
  C
  C   1   1.34
  F   1   1.33   2  120.0
  F   2   1.33   1  120.0  3    0.0
  H   1   1.08   2  120.0  3  180.0
  H   2   1.08   1  120.0  4  180.0

 $NBO file=dfe_c $END
 $DEL
 delete 2 orbitals
   63 64
 $ENDhttp://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 Mon Oct  6 22:14:00 2008
From: "Vincent Xianlong Wang xloongw(~)yahoo.com" <owner-chemistry*|*server.ccl.net>
To: CCL
Subject: CCL: Purchasing compounds
Message-Id: <-37850-081006215441-18630-OBtMms360IT1noGRDqvxNw*|*server.ccl.net>
X-Original-From: Vincent Xianlong Wang <xloongw . yahoo.com>
Content-Type: multipart/alternative; boundary="0-1767891538-1223340864=:3656"
Date: Mon, 6 Oct 2008 17:54:24 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: Vincent Xianlong Wang [xloongw(0)yahoo.com]
--0-1767891538-1223340864=:3656
Content-Type: text/plain; charset=us-ascii

Hi Iain,

ZINC (http://zinc.docking.org/) has collected vendor information under the "Subsets' menu.  You may check if the failed compounds of your inerest are included there.  

Best regards,
Vincent





----- Original Message ----
> From: Iain Wallace iain.m.wallace/./gmail.com <owner-chemistry+/-ccl.net>
To: "Wang, Xianlong " <xloongw+/-yahoo.com>
Sent: Tuesday, October 7, 2008 5:45:48 AM
Subject: CCL: Purchasing compounds


Hi,

A question slightly out of left field, but I was wondering if anybody knew a source of purchasing compounds that have either failed in Phase I,II or III or that have been withdrawn.
Drugbank has a list of compounds that are withdrawn but it would be cool to know if there was a database that contained the information of compounds that failed Phase I-III

Thanks

Iain 



      
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Content-Type: text/html; charset=us-ascii

<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><div>Hi Iain,<br><br>ZINC (http://zinc.docking.org/) has collected vendor information under the "Subsets' menu.&nbsp; You may check if the failed compounds of your inerest are included there.&nbsp; <br><br>Best regards,<br>Vincent<br><br><br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">----- Original Message ----<br>From: Iain Wallace iain.m.wallace/./gmail.com &lt;owner-chemistry+/-ccl.net&gt;<br>To: "Wang, Xianlong " &lt;xloongw+/-yahoo.com&gt;<br>Sent: Tuesday, October 7, 2008 5:45:48 AM<br>Subject: CCL: Purchasing compounds<br><br>
<div dir="ltr">Hi,<br><br>A question slightly out of left field, but I was wondering if anybody knew a source of purchasing compounds that have either failed in Phase I,II or III or that have been withdrawn.<br>Drugbank has a list of compounds that are withdrawn but it would be cool to know if there was a database that contained the information of compounds that failed Phase I-III<br>
<br>Thanks<br><br>Iain <br></div>
</div></div></div><br>



      </body></html>
--0-1767891538-1223340864=:3656--


From owner-chemistry@ccl.net Mon Oct  6 23:22:00 2008
From: "Leo yao nuo.yao%x%yahoo.com.cn" <owner-chemistry~!~server.ccl.net>
To: CCL
Subject: CCL:G: How to keep Initial guess orbital symmetries in opt calculation?
Message-Id: <-37851-081006220333-23081-1bWQpb8zKvQ2ihZTvsy3JQ~!~server.ccl.net>
X-Original-From: "Leo  yao" <nuo.yao],[yahoo.com.cn>
Date: Mon, 6 Oct 2008 22:03:29 -0400


Sent to CCL by: "Leo  yao" [nuo.yao===yahoo.com.cn]
attached is my input file, and the initial guess orbital symmetries gived by G03.
Input file:
%chk=scs3
#p B3LYP/6-311+G** opt=(maxcyc=100) scf=(maxcyc=2000,tight,qc,symm)
   guess=(only,alter)
    
scs3

1,3
Sc
S,1,r
 
r= 2.3452 

19,21

19,21

the initial guess orbital symmetries gived by G03.
Harris En= -1158.72654891472    
 Pairs of Alpha orbitals switched:
   19  21
 Pairs of Beta  orbitals switched:
   19  21
 Initial guess orbital symmetries:
 Alpha Orbitals:
       Occupied  (SG) (SG) (SG) (SG) (PI) (PI) (SG) (SG) (PI) (PI)
                 (SG) (SG) (PI) (PI) (SG) (SG) (PI) (PI) (DLTA)
       Virtual   (DLTA) (SG) (PI) (PI) (SG) (PI) (PI) (SG) (SG)
                 (PI) (PI) (SG) (SG) (DLTA) (DLTA) (PI) (PI) (SG)
                 (SG) (PI) (PI) (SG) (SG) (PI) (PI) (PI) (PI) (SG)
                 (DLTA) (DLTA) (DLTA) (DLTA) (SG) (PI) (PI) (SG)
                 (PI) (PI) (SG) (SG) (PI) (PI) (DLTA) (DLTA) (PHI)
                 (PHI) (PI) (PI) (SG) (SG) (DLTA) (DLTA) (PI) (PI)
                 (SG) (PI) (PI) (SG) (SG) (SG) (PI) (PI) (SG) (PI)
                 (PI) (SG) (SG) (SG) (SG)
 Beta  Orbitals:
       Occupied  (SG) (SG) (SG) (SG) (PI) (PI) (SG) (SG) (PI) (PI)
                 (SG) (SG) (PI) (PI) (SG) (SG) (PI)
       Virtual   (PI) (DLTA) (DLTA) (SG) (PI) (PI) (SG) (PI) (PI)
                 (SG) (SG) (PI) (PI) (SG) (SG) (DLTA) (DLTA) (PI)
                 (PI) (SG) (SG) (PI) (PI) (SG) (SG) (PI) (PI) (PI)
                 (PI) (SG) (DLTA) (DLTA) (DLTA) (DLTA) (SG) (PI)
                 (PI) (SG) (PI) (PI) (SG) (SG) (PI) (PI) (DLTA)
                 (DLTA) (PHI) (PHI) (PI) (PI) (SG) (SG) (DLTA)
                 (DLTA) (PI) (PI) (SG) (PI) (PI) (SG) (SG) (SG)
                 (PI) (PI) (SG) (PI) (PI) (SG) (SG) (SG) (SG)


> "leo yao nuo.yao(!)yahoo.com.cn"  wrote:
> 
> Sent to CCL by: "leo  yao" [nuo.yao+/-yahoo.com.cn]
> 
> Dear all,
>    
>   I meet a problem in Gaussian calc.
>   The problem is How to keep Initial guess orbital symmetries?
>   I have used the key:scf=symm, but the orbital symmetries were atered.
> 
> my work resulted show:
> 
>             Population analysis using the SCF density.
> 
>  **********************************************************************
> 
>  Orbital symmetries:
>  Alpha Orbitals:
>        Occupied  (SG) (SG) (SG) (SG) (PI) (PI) (SG) (PI) (SG) (PI)
>                  (SG) (PI) (SG) (PI) (SG) (?A) (SG) (?A) (?B)
>        Virtual   (?B) (?A) (?A) (?B) (?B) (PI) (PI) (SG) (SG) (?B)
>                  (PI) (PI) (?B) (?B) (PI) (PI) (?B) (?B) (SG) (PI)
>                  (PI) (SG) (PI) (SG) (PI) (?A) (?A) (?C) (?C) (?C)
>                  (?C) (?C) (?C) (?A) (?C) (?A) (?D) (?D) (SG) (?D)
>                  (?D) (DLTA) (?D) (?D) (DLTA) (SG) (SG) (?D) (?D)
>                  (SG) (DLTA) (DLTA) (PI) (PI) (SG) (PI) (PI) (SG)
>                  (SG) (SG) (PI) (PI) (SG) (PI) (PI) (SG) (SG) (SG)
>                  (SG) 
> 
> Have more suggestion?
> 
>


From owner-chemistry@ccl.net Mon Oct  6 23:56:00 2008
From: "Sengen Sun sengensun*o*yahoo.com" <owner-chemistry^_^server.ccl.net>
To: CCL
Subject: CCL: Thomas Kuhn Paradigm Shift Award
Message-Id: <-37852-081006232733-11927-8JEhQrscR1FaR/YPzFvZDQ^_^server.ccl.net>
X-Original-From: Sengen Sun <sengensun-*-yahoo.com>
Content-Type: text/plain; charset=us-ascii
Date: Mon, 6 Oct 2008 20:27:20 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: Sengen Sun [sengensun(~)yahoo.com]
I am still concerned with the AWARD that may cause philosophical 
confusion in this human society.

According to Kuhn, a truly theoretical paradigm shift is often 
a long-term struggle, induces confrontation, and eventually 
changes our very fundamental view how human understands the nature.

I'd like to give an example what a Kuhn paradigm shift is really 
about to me. During my graduate study for my PhD degree at 
McMaster University from 1989-1994, I found that Professor 
Richard Bader had been struggling for many years for his 
revolutionary philosophy about the role of electron density 
in atoms and molecules. I did not work directly with Bader 
but was a close spectator. Nowadays, Bader's theory is quite 
popular. But I don't think the resistance is over until his 
work is awarded what it really deserves.

This case of Kuhn's paradigm shift leads me to think that 
even in our highly civilized society today, it is very 
difficult to adjust our minds to accept a fundamental revolution 
of scientific theory. At least, there are two reasons for this 
difficulty. One is our limited ability to judge no matter what 
kind of experts we are; The other is the political correctness as
 recognized by Kuhn. As soon as human is not free from these two 
factors, awarding Kuhn paradigm shift is likely just a joke.

Also imagine we are in an era when Kuhn paradigm shift happens 
every year! And recognized every year! After 50 years, we will 
have a big list. Is that really what Kuhn meant about theoretical 
paradigm shift?

The awarded works under this AWARD in the past are excellent works, 
but no more than some technical changes, improvements or modifications in 
a field. They do change things in a particular field, even very
 significantly. To me, it is exaggerated and philosophically 
misleading to use the words "Kuhn paradigm shift". They should 
be awarded in many other ways.

How could you tell the difference between normal scientific progress and truly a revolution?
  
Thanks for attention and welcome any comments.

Sengen

>
>
>
>
> From: "carlos simmerling" <carlos.simmerling ~ gmail.com> 
Subject: CCL: Thomas Kuhn Paradigm Shift Award symposium at Spring ACS meeting 
Date: Wed, 1 Oct 2008 15:44:40 -0400 

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

Sent to CCL by: "carlos  simmerling" [carlos.simmerling:-:gmail.com]
Please forward this announcement of an award symposium to be held in the COMP
division at the Spring ACS national meeting in Salt lake City.
The Thomas Kuhn Paradigm Shift Award is given each year to the talk that most
captures the spirit of Kuhn's writings, exemplified in his landmark book,
"The Structure of Scientific Revolutions". The symposium at each
Spring ACS is open to all and attempts to attract those whose work has the
potential to change the way we think about an aspect of science. Kuhn's words
for this, a "Paradigm Shift", have been much over used and as such can
be an intimidating standard to approach, but the intent is for talks that
represent a fresh way of looking at an aspect of our field. As an example, the
2006 winner, Christopher Bayly of Merck-Frosst, proposed that focused screening
was a more efficient path to drug discovery than high throughput screening and
in 2008 Derek Debe of Abbott Laboratories presented the case for knowing
confidence intervals in molecular modeling. Talks are usually within the
computational sphere. They are judged on novelty, potential impact and quality
of presentation by a panel of independent scientists with extensive
computational experience. It is hoped the Award, which carries a stipend of  one
thousand dollars, can provide a platform to researchers extending a mirror to
our field and questioning the scientific status quo.
Abstracts can be submitted on the OASYS web site (oasys.acs.org) and four will
be selected for 40 minute presentations to take place during a half-day
symposium at the national meeting.  Abstracts not selected for the symposium
competition can be moved into consideration for the general symposia (which are
always well attended!) if desired.
More information on awards offered by the ACS COMP division can be found on the
web site at http://www.acscomp.org/Awards/index.html