From owner-chemistry@ccl.net Fri Mar 10 09:43:01 2006
From: "Marius Retegan marius.retegan]*[yahoo.com" <owner-chemistry[]server.ccl.net>
To: CCL
Subject: CCL: charge decomposion analysis for W(CO)6
Message-Id: <-31169-060310094043-13566-++6jXE/YOA/nYVClny3sqA[]server.ccl.net>
X-Original-From: Marius Retegan <marius.retegan%a%yahoo.com>
Content-Transfer-Encoding: 8bit
Content-Type: multipart/alternative; boundary="0-1656675843-1142001594=:18477"
Date: Fri, 10 Mar 2006 06:39:54 -0800 (PST)
MIME-Version: 1.0


Sent to CCL by: Marius Retegan [marius.retegan ~~ yahoo.com]
--0-1656675843-1142001594=:18477
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 8bit

Hello,
I have some problems with performing the charge decomposition analysis with CDA 2.1, which I hope it's still free. I've performed the analysis on W(CO)6, but I get the following error:

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
      CHARGE DECOMPOSITION ANALYSIS   <cda>

             S. Dapprich and G. Frenking
         Philipps-Universitaet Marburg, 1995
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

/Execution started at Fri Mar 10 15:18:41 2006

--- Chemical system information ---

 Complex  C:  C6O6W
 Fragment A:  CO
 Fragment B:  C5O5W

/Reading basis set information...OK.

--- Basis set information ---

 alpha electrons  C: 49  A:  7  B: 42
 beta  electrons  C: 49  A:  7  B: 42
 basis functions  C:130  A: 18  B:112

/Testing integrity of files...OK.
Segmentation fault

I think it's something related to the way I've specified the geometries in the input files, but they were done according to the manual.
For W(CO)6:
#p nosym pop=no iop(3/33=1) iop(3/36=-1) density mp2/lanl2dz

no title

0 1
6        0.000000000      0.000000000      2.053337000
8        0.000000000      3.203337000      0.000000000
74       0.000000000      0.000000000      0.000000000
6        0.000000000      2.053337000      0.000000000
8        0.000000000      0.000000000      3.203337000
8        3.203337000      0.000000000      0.000000000
8        0.000000000     -3.203337000      0.000000000
6        0.000000000      0.000000000     -2.053337000
6        0.000000000     -2.053337000      0.000000000
6        2.053337000      0.000000000      0.000000000
8        0.000000000      0.000000000     -3.203337000
6       -2.053337000      0.000000000      0.000000000
8       -3.203337000      0.000000000      0.000000000 
where the first 2 row from the cartesian coordinates represent the donor fragment, and the rest the acceptor.
If someone has some experience with CDA, please give me some suggestions.
Thank you
Marius RETEGAN

--0-1656675843-1142001594=:18477
Content-Type: text/html; charset=iso-8859-1
Content-Transfer-Encoding: 8bit

Hello,<br>I have some problems with performing the charge decomposition analysis with CDA 2.1, which I hope it's still free. I've performed the analysis on W(CO)6, but I get the following error:<br><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; CHARGE DECOMPOSITION ANALYSIS&nbsp;&nbsp; &lt;cda&gt;<br><br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; S. Dapprich and G. Frenking<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Philipps-Universitaet Marburg, 1995<br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br><br>/Execution started at Fri Mar 10 15:18:41 2006<br><br>--- Chemical system information ---<br><br>&nbsp;Complex&nbsp; C:&nbsp; C6O6W<br>&nbsp;Fragment A:&nbsp; CO<br>&nbsp;Fragment B:&nbsp; C5O5W<br><br>/Reading basis set information...OK.<br><br>--- Basis set information ---<br><br>&nbsp;alpha electrons&nbsp; C: 49&nbsp; A:&nbsp; 7&nbsp; B: 42<br>&nbsp;beta&nbsp; electrons&nbsp; C:
 49&nbsp; A:&nbsp; 7&nbsp; B: 42<br>&nbsp;basis functions&nbsp; C:130&nbsp; A: 18&nbsp; B:112<br><br>/Testing integrity of files...OK.<br>Segmentation fault<br><br>I think it's something related to the way I've specified the geometries in the input files, but they were done according to the manual.<br>For W(CO)6:<br>#p nosym pop=no iop(3/33=1) iop(3/36=-1) density mp2/lanl2dz<br><br>no title<br><br>0 1<br>6&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2.053337000<br>8&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3.203337000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000000000<br>74&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000000000<br>6&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2.053337000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 0.000000000<br>8&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3.203337000<br>8&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3.203337000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000000000<br>8&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000000000&nbsp;&nbsp;&nbsp;&nbsp; -3.203337000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000000000<br>6&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000000000&nbsp;&nbsp;&nbsp;&nbsp; -2.053337000<br>6&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000000000&nbsp;&nbsp;&nbsp;&nbsp; -2.053337000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000000000<br>6&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2.053337000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000000000<br>8&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000000000&nbsp;&nbsp;&nbsp;&nbsp;
 -3.203337000<br>6&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -2.053337000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000000000<br>8&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -3.203337000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000000000 <br>where the first 2 row from the cartesian coordinates represent the donor fragment, and the rest the acceptor.<br>If someone has some experience with CDA, please give me some suggestions.<br>Thank you<br>Marius RETEGAN<br>
--0-1656675843-1142001594=:18477--


From owner-chemistry@ccl.net Fri Mar 10 16:22:00 2006
From: "Sengen Sun sengensun : yahoo.com" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL: A breakthrough in mechanism of concerted cycloadditions?
Message-Id: <-31170-060310161844-9212-rcRRmzEPqNgFcY5EVzbQ2Q:server.ccl.net>
X-Original-From: Sengen Sun <sengensun*yahoo.com>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=iso-8859-1
Date: Fri, 10 Mar 2006 13:18:38 -0800 (PST)
MIME-Version: 1.0


Sent to CCL by: Sengen Sun [sengensun__yahoo.com]
---------
I forward the following message I posted in ORGLIST.
---------- 
----------
Thanks to Drs. Darren Rhodes and Yuehui Zhou for
suggestions.

It took me 20+ years before I figured out how
electrons move in concerted cycloadditions. It was
my solid computational data that led me to propose a
new and general electronic mechanism. I have been
struggling for about 7 years to get this thing
published. 

I am not trying to attack any referees or editors
> from a few journals. But they did use fierce languages
to reject my papers. The 70-years old puzzles already
had caused a strongly divided scientific community.
And
the conceptual confusion derived from the orbital
control theories flooded in the chemical literature
for nearly a half of century. And the referees had a
very limited time to evaluate my manuscript. It is
understandable to me that no one in the community can
immediately accept my new thinking. If I were one of
the referees, it is highly likely that I would reject
this kind of papers too!

Therefore, as a scientist responsible for science, I
had to stand up and took the challenge to spread the
new knowledge from my computational studies. I am
really grateful to the modern human civilization of
the Internet communications. Initially I set up my
own web site - Coulombiclab.com and my home office -
the Coulombic Lab of Computational Chemistry. But
later, I realized I could afford all the costs
including computational softwares and hardwares as we
have three kids to feed. I started to seek alternative
websites.....

I have no interest to attack any people. But science
has to be made correct unconditionally no matter
where and no matter who you are. Science will move
forward and no body can stop it.

I welcome any comments to my papers. I am ready to
explain my theory anywhere and anytime as allowed by
by my busy life. I have the confidence that I can
convince the public of my explanations of concerted
cycloadditions if I am given a chance.

Thanks to every one for attention.

Sengen
 
> --- Yuehui Zhou <yuehuizhou_._hotmail.com> wrote:

> ---------------------------------
> 
> Why not send to peer reviewed journals first? That's
> the usual way to get acknowledged.
>  
> >
> >On 2/21/06, Sengen Sun <sengensun_._yahoo.com> wrote:
> > >
> > > Recently, I claimed that I have made a
> breakthrough in
> > > the fundamental understanding of concerted
> > > cycloadditions.
> > >
> > > Now I have uploaded to the CCL site one of my
> papers
> > > and a ppt presentation I used twice in 2005 for
> two
> > > international symposiums. The paper was the
> first
> > > paper I posted in the Chemistry Preprint Server
> 5
> > > years ago. Some people already have it.
> > >
> > >
>
http://server.ccl.net/cca/documents/ConcertedCycloadditons/
> > >
> > >
>
http://server.ccl.net/cca/documents/ConcertedCycloadditons_2/
> > >
> > > My findings on the theoretical knowledge of
> concerted
> > > cycloadditions are based on such a
> "ridiculously"
> > > simple method that it may be simply ridiculous
> to
> some
> > > people. I evaluated some arbitrary colliding
> complexes
> > > and learned some new and very important
> knowledge
> that
> > > is valid in understanding the concerted pathway.
> I
> > > formulated some new and interesting concepts
> such
> as
> > > conjugation hindrances and easiness of
> electronic
> > > migration that decide organic chemical
> reactivity.
> > >
> > > I invite every one to criticize my theory on a
> > > scientific basis. I invite you to defeat my
> > > sensational claims I made in the Conclusions of
> my
> ppt
> > > presentation. If I am convinced anything I made
> wrong,
> > > I will correct or withdraw it.
> > >
> > > Thanks to every one.
> > >
> > > Sengen
> > >
> > > _______________________________________________
> > > ORGLIST - Organic Chemistry Mailing List
> > > Website / Archive / FAQ: http://www.orglist.net
> > > To post a message (TO EVERYBODY) send to
> everybody_._orglist.net
> > > To unsubscribe, send to
> everybody-request_._orglist.net the message:
> unsubscribe
> your_orglist_password your_address
> > >
> >
> >
> >--
> >http://pgpkeys.mit.edu:11371/
> >Key ID:- 0xB76FE0B9
> >_______________________________________________
> >ORGLIST - Organic Chemistry Mailing List
> >Website / Archive / FAQ: http://www.orglist.net
> >To post a message (TO EVERYBODY) send to
> everybody_._orglist.net
> >To unsubscribe, send to
> everybody-request_._orglist.net
> the message: unsubscribe your_orglist_password
> your_address
> 
> 
--- Darren Rhodes <darren.rhodes_._gmail.com> wrote:

> Date: Fri, 10 Mar 2006 15:59:06 +0000
> From: "Darren Rhodes" <darren.rhodes_._gmail.com>
> To: "everybody_._orglist.net" <everybody_._orglist.net>
> Subject: Re: ORGLIST: A breakthrough in mechanism of
> concerted cycloadditions?
> 
> Why not post it on wikipedia?
> 
> On 2/21/06, Sengen Sun <sengensun_._yahoo.com> wrote:
> >
> > Recently, I claimed that I have made a
> breakthrough in
> > the fundamental understanding of concerted
> > cycloadditions.
> >


__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com


From owner-chemistry@ccl.net Fri Mar 10 18:17:00 2006
From: "Osman Guner oguner|a|turquoisecons.com" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL: Call for Papers - ACS Fall : San Francisco
Message-Id: <-31171-060310120227-27366-ZY/7HEncFmbVLSTqt46L5Q:server.ccl.net>
X-Original-From: "Osman Guner" <oguner^^turquoisecons.com>
Content-Type: multipart/alternative;
	boundary="----=_NextPart_000_0024_01C64421.57488DA0"
Date: Fri, 10 Mar 2006 09:02:19 -0800
MIME-Version: 1.0


Sent to CCL by: "Osman Guner" [oguner{=}turquoisecons.com]
This is a multi-part message in MIME format.

------=_NextPart_000_0024_01C64421.57488DA0
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

While we are still gearing up for the Spring ACS meeting at Atlanta that =
is
about to start in two weeks, I would like to get a head start for the =
San
Francisco meeting for those people who like planning in advance.  This =
is
one of the symposia that I recycle every two years in order to review =
and
evaluate most recent developments in the field.

=20

ADVANCES IN VIRTUAL HIGH-THROUGHPUT SCREENING

=20

at 232nd ACS National Meeting, San Francisco, CA (September 10-14, 2006)

=20

Organized by Chemical Information Division (CINF)

Co-sponsored by the Division of Medicinal Chemistry (MEDI)

Co-sponsored by the Computers in Chemistry Division (COMP)

=20

We invite you to present your recent work in the area of virtual
high-throughput screening.  We will likely have at least two =
subsections:
1- new methods and approaches, and 2- recent applications.  Depending on =
the
level of participation, we may open additional subsections.

=20

Topics of interest may include:

*         2D structure- or similarity-based database searching=20

*         Pharmacophore perception techniques and pharmacophore-based
screening

*         High-throughput docking and scoring

*         ADME/Tox based screening.

=20

Please submit your abstracts through the OASYS
(http://oasys.acs.org/acs/232nm/cinf/papers/index.cgi ).  The deadline =
for
submitting the abstract is sometime in late April (I will post the =
actual
deadline date once it is fixed).  Feel free to contact me for any =
questions
or suggestions.

=20

Osman F, G=FCner, PhD

Principal, Turquoise Consulting

oguner.:.turquoisecons.com

http://www.turquoisecons.com

=20


------=_NextPart_000_0024_01C64421.57488DA0
Content-Type: text/html;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<html xmlns:o=3D"urn:schemas-microsoft-com:office:office" =
xmlns:w=3D"urn:schemas-microsoft-com:office:word" =
xmlns:st1=3D"urn:schemas-microsoft-com:office:smarttags" =
xmlns=3D"http://www.w3.org/TR/REC-html40">

<head>
<meta http-equiv=3DContent-Type content=3D"text/html; =
charset=3Diso-8859-1">
<meta name=3DGenerator content=3D"Microsoft Word 11 (filtered medium)">
<o:SmartTagType =
namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags"
 name=3D"State"/>
<o:SmartTagType =
namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags"
 name=3D"City"/>
<o:SmartTagType =
namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags"
 name=3D"place"/>
<!--[if !mso]>
<style>
st1\:*{behavior:url(#default#ieooui) }
</style>
<![endif]-->
<style>
<!--
 /* Font Definitions */
 .:.font-face
	{font-family:Wingdings;
	panose-1:5 0 0 0 0 0 0 0 0 0;}
 /* Style Definitions */
 p.MsoNormal, li.MsoNormal, div.MsoNormal
	{margin:0in;
	margin-bottom:.0001pt;
	font-size:12.0pt;
	font-family:"Times New Roman";}
a:link, span.MsoHyperlink
	{color:blue;
	text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
	{color:purple;
	text-decoration:underline;}
span.EmailStyle17
	{mso-style-type:personal-compose;
	font-family:Arial;
	color:windowtext;}
.:.page Section1
	{size:8.5in 11.0in;
	margin:1.0in 1.25in 1.0in 1.25in;}
div.Section1
	{page:Section1;}
 /* List Definitions */
 .:.list l0
	{mso-list-id:1528832198;
	mso-list-type:hybrid;
	mso-list-template-ids:392479120 67698689 67698691 67698693 67698689 =
67698691 67698693 67698689 67698691 67698693;}
.:.list l0:level1
	{mso-level-number-format:bullet;
	mso-level-text:\F0B7;
	mso-level-tab-stop:39.0pt;
	mso-level-number-position:left;
	margin-left:39.0pt;
	text-indent:-.25in;
	font-family:Symbol;}
ol
	{margin-bottom:0in;}
ul
	{margin-bottom:0in;}
-->
</style>

</head>

<body lang=3DEN-US link=3Dblue vlink=3Dpurple>

<div class=3DSection1>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>While we are still gearing up for the Spring ACS =
meeting at
Atlanta that is about to start in two weeks, I would like to get a head =
start for
the San Francisco meeting for those people who like planning in =
advance.=A0 This
is one of the symposia that I recycle every two years in order to review =
and evaluate
most recent developments in the field.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>ADVANCES IN VIRTUAL HIGH-THROUGHPUT =
SCREENING<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>at 232nd ACS National Meeting, <st1:place =
w:st=3D"on"><st1:City
 w:st=3D"on">San Francisco</st1:City>, <st1:State =
w:st=3D"on">CA</st1:State></st1:place>
(September 10-14, 2006)<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Organized by Chemical Information Division =
(CINF)<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Co-sponsored by the Division of Medicinal Chemistry =
(MEDI)<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Co-sponsored by the Computers in Chemistry Division =
(COMP)<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>We invite you to present your recent work in the area =
of
virtual high-throughput screening.=A0 We will likely have at least two
subsections:=A0 1- new methods and approaches, and 2- recent =
applications.=A0
Depending on the level of participation, we may open additional =
subsections.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Topics of interest may =
include:<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'margin-left:39.0pt;text-indent:-.25in;mso-list:l0 level1 =
lfo1'><![if !supportLists]><font
size=3D2 face=3DSymbol><span =
style=3D'font-size:10.0pt;font-family:Symbol'><span
style=3D'mso-list:Ignore'>=B7<font size=3D1 face=3D"Times New =
Roman"><span
style=3D'font:7.0pt "Times New =
Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></font></span></span></font><![endif]><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>2D structure- or =
similarity-based database
searching <o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'margin-left:39.0pt;text-indent:-.25in;mso-list:l0 level1 =
lfo1'><![if !supportLists]><font
size=3D2 face=3DSymbol><span =
style=3D'font-size:10.0pt;font-family:Symbol'><span
style=3D'mso-list:Ignore'>=B7<font size=3D1 face=3D"Times New =
Roman"><span
style=3D'font:7.0pt "Times New =
Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></font></span></span></font><![endif]><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>Pharmacophore perception =
techniques and
pharmacophore-based screening<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'margin-left:39.0pt;text-indent:-.25in;mso-list:l0 level1 =
lfo1'><![if !supportLists]><font
size=3D2 face=3DSymbol><span =
style=3D'font-size:10.0pt;font-family:Symbol'><span
style=3D'mso-list:Ignore'>=B7<font size=3D1 face=3D"Times New =
Roman"><span
style=3D'font:7.0pt "Times New =
Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></font></span></span></font><![endif]><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>High-throughput docking and =
scoring<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'margin-left:39.0pt;text-indent:-.25in;mso-list:l0 level1 =
lfo1'><![if !supportLists]><font
size=3D2 face=3DSymbol><span =
style=3D'font-size:10.0pt;font-family:Symbol'><span
style=3D'mso-list:Ignore'>=B7<font size=3D1 face=3D"Times New =
Roman"><span
style=3D'font:7.0pt "Times New =
Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></font></span></span></font><![endif]><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>ADME/Tox based =
screening.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Please submit your abstracts through the OASYS (<a
href=3D"http://oasys.acs.org/acs/232nm/cinf/papers/index.cgi">http://oasy=
s.acs.org/acs/232nm/cinf/papers/index.cgi</a>
).=A0 The deadline for submitting the abstract is sometime in late April =
(I will
post the actual deadline date once it is fixed).=A0 Feel free to contact =
me for
any questions or suggestions.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Osman F, G=FCner, PhD</span></font><o:p></o:p></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Principal, Turquoise =
Consulting</span></font><o:p></o:p></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><a =
href=3D"mailto:oguner.:.turquoisecons.com">oguner.:.turquoisecons.com</a></sp=
an></font><o:p></o:p></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><a =
href=3D"http://www.turquoisecons.com">http://www.turquoisecons.com</a></s=
pan></font><o:p></o:p></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><o:p>&nbsp;</o:p></span></font></p>

</div>

</body>

</html>

------=_NextPart_000_0024_01C64421.57488DA0--


From owner-chemistry@ccl.net Fri Mar 10 22:08:00 2006
From: "Renata Kwiecien renee:p.lodz.pl" <owner-chemistry]^[server.ccl.net>
To: CCL
Subject: CCL: CHARMM - adding hydrogens
Message-Id: <-31172-060310181407-16653-dXpaISzTfOpwYaM12spFcg]^[server.ccl.net>
X-Original-From: "Renata  Kwiecien" <renee-$-p.lodz.pl>
Date: Fri, 10 Mar 2006 18:14:06 -0500


Sent to CCL by: "Renata  Kwiecien" [renee.^-^.p.lodz.pl]
Dear Subscribers,

I have basic problem with correct adding hydrogen atoms to Leu and Pro when using hbuilt module. Model consists of four parts:
Chain A,
Chain B,
Chain P,
INH covalently bounded to the His B 73 and Ser P 230.
Inhibitor is a protein-derived chain: Phe-Pro-Arg, has its own unique atom names. I assigned unique atom names to His and Ser and named them Hsi and Sre, respectively, but it did not help.
Covalent bond was made by patching His B 73 and Ser P 230. I also patched four Cys-Cys bridges. Parameters for covalently bounded INH are based on CHARMM22 All-Hydrogen Parameter File for Proteins. 
Part of my input file:

! read in coordinates of subunit B 
open read form unit 13 name "bppa12.pdb"
read sequ pdb unit 13
generate B setup first NTER last CTER
rewind unit 13
read coord pdb unit 13
hbuild
ic para
ic build
close unit 13

! His 73
patch PHS INH 1 B 73 
auto angl dihe
! Cys5--Cys149
patch DISU A 5 B 149
auto angl dihe
! Cys58--Cys74
patch DISU B 58 B 74
auto angl dihe

CHARMM generates patched active site correctly, but has problems with all Leu B and Leu P and with Pro B 78, Pro B 79, Pro P 196 and Pro P 217. In chain A all hydrogen atoms are placed correctly. 
What is the source of the problem and how to correct it?
Renata Kwiecien