From owner-chemistry@ccl.net Thu Mar 23 08:46:00 2006
From: "john furr john.furr . gmail.com" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL: reveal your affiliation
Message-Id: <-31287-060323084426-1657-NYAd8w2awG3ZSdlhihae2g^server.ccl.net>
X-Original-From: "john furr" <john.furr]^[gmail.com>
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Sent to CCL by: "john furr" [john.furr++gmail.com]
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"However, it would make the postings more credible if people who have
yahoo,"

A persons credibility should not be judged by their affiliation.  As soon a=
s
we head down that path then science becomes inherently biased.  Good scienc=
e
(especially computational science) can be done by any person with a desire
to learn and experiment.  You certainly don't need to have a position at on=
e
of the worlds Ivy League Universities to do quality science.  Nor do you
need to be employed in one of the major pharmas.  A person should simply be
judged based on the insights they bring to the discussion.  I do understand
that you weren't implying any of these things with your original request.
However, I feel it could be a very slippery slope to head down.  Also as
noted before many people may not be allowed to post their affiliation.

John
http://www.dynamol.com

On 3/22/06, Andrew D. Fant fant:-:pobox.com <owner-chemistry[A]ccl.net >
wrote:
>
> Sent to CCL by: "Andrew D. Fant" [ fant-x-pobox.com]
> Boyd, D. boyd%chem.iupui.edu wrote:
> > Sent to CCL by: "Boyd, D." [boyd]![chem.iupui.edu]
> > Colleagues,
> > I recommend/request that people who post on CCL include their
> affiliation.
> > I realize that because of spammers people do not want to reveal their
> full particulars.
> > However, it would make the postings more credible if people who have
> yahoo,
> > hotmail, etc. email addresses, include the university or company they
> are
> > associated with.
>
> Many people are employed in situations where they are not allowed to
> speak/post
> in a public setting with reference to their employment status without
> clearing
> it with their public relations or corporate communications
> departments.  This is
> to make management feel secure that nobody is representing themselves in
> any way
> as an official spokesperson for the institution.   I don't think that we
> need
> affiliation information to judge the merits of a posting/email in any
> case.  If
> someone makes a statement that sounds outlandish, the claims should be
> examined
> and validated by the same standards whether it comes from wwcc.cc.wy.us,
> tripos.com, phar.cam.ac.uk, or ru.yahoo.com.  Likewise, I would hope my
> opinions
> here are considered on their merits and my past participation, rather the=
n
>
> whether my circumstances require me to be discreet about my current
> affiliation.
>
> Andy
>
> Andrew Fant    | And when the night is cloudy    | This space to let
> Molecular Geek | There is still a light          |----------------------
> fant+*+pobox.com | That shines on me               | Disclaimer:  I don't
> Boston, MA     | Shine until tomorrow, Let it be | even speak for myself
>
>
>
> -=3D This is automatically added to each message by the mailing script =
=3D->
> Search Messages: http://www.ccl.net/htdig   (login: ccl, Password: search=
)>
>
>
>

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&quot;However, it would make the postings more credible if people who have =
yahoo,&quot;<br>
<br>
A persons credibility should not be judged by their affiliation.&nbsp;
As soon as we head down that path then science becomes inherently
biased.&nbsp; Good science (especially computational science) can be
done by any person with a desire to learn and experiment.&nbsp; You
certainly don't need to have a position at one of the worlds Ivy League
Universities to do quality science.&nbsp; Nor do you need to be
employed in one of the major pharmas.&nbsp; A person should simply be
judged based on the insights they bring to the discussion.&nbsp; I do
understand that you weren't implying any of these things with your
original request.&nbsp; However, I feel it could be a very slippery
slope to head down.&nbsp; Also as noted before many people may not be
allowed to post their affiliation.&nbsp; <br>
<br>
John<br>
<a href=3D"http://www.dynamol.com">http://www.dynamol.com</a><br><br><div><=
span class=3D"gmail_quote">On 3/22/06, <b class=3D"gmail_sendername">Andrew=
 D. Fant fant:-:<a href=3D"http://pobox.com" target=3D"_blank" onclick=3D"r=
eturn top.js.OpenExtLink(window,event,this)">
pobox.com</a></b> &lt;<a href=3D"mailto:owner-chemistry[A]ccl.net" target=3D"=
_blank" onclick=3D"return top.js.OpenExtLink(window,event,this)">owner-chem=
istry[A]ccl.net
</a>&gt; wrote:</span><blockquote class=3D"gmail_quote" style=3D"border-lef=
t: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1=
ex;">Sent to CCL by: &quot;Andrew D. Fant&quot; [<a href=3D"http://fant-x-p=
obox.com" target=3D"_blank" onclick=3D"return top.js.OpenExtLink(window,eve=
nt,this)">

fant-x-pobox.com</a>]<br>Boyd, D. boyd%chem.iupui.edu wrote:<br>&gt; Sent t=
o CCL by: &quot;Boyd, D.&quot; [boyd]![<a href=3D"http://chem.iupui.edu" ta=
rget=3D"_blank" onclick=3D"return top.js.OpenExtLink(window,event,this)">ch=
em.iupui.edu
</a>]<br>&gt; Colleagues,<br>&gt; I recommend/request that people who post =
on CCL include their affiliation.
<br>&gt; I realize that because of spammers people do not want to reveal th=
eir full particulars.<br>&gt; However, it would make the postings more cred=
ible if people who have yahoo,<br>&gt; hotmail, etc. email addresses, inclu=
de the university or company they are
<br>&gt; associated with.<br><br>Many people are employed in situations whe=
re they are not allowed to speak/post<br>in a public setting with reference=
 to their employment status without clearing<br>it with their public relati=
ons or corporate communications departments.&nbsp;&nbsp;This is
<br>to make management feel secure that nobody is representing themselves i=
n any way<br>as an official spokesperson for the institution.&nbsp;&nbsp; I=
 don't think that we need<br>affiliation information to judge the merits of=
 a posting/email in any case.&nbsp;&nbsp;If
<br>someone makes a statement that sounds outlandish, the claims should be =
examined<br>and validated by the same standards whether it comes from <a hr=
ef=3D"http://wwcc.cc.wy.us" target=3D"_blank" onclick=3D"return top.js.Open=
ExtLink(window,event,this)">
wwcc.cc.wy.us</a>,<br><a href=3D"http://tripos.com" target=3D"_blank" oncli=
ck=3D"return top.js.OpenExtLink(window,event,this)">
tripos.com</a>, <a href=3D"http://phar.cam.ac.uk" target=3D"_blank" onclick=
=3D"return top.js.OpenExtLink(window,event,this)">phar.cam.ac.uk</a>, or <a=
 href=3D"http://ru.yahoo.com" target=3D"_blank" onclick=3D"return top.js.Op=
enExtLink(window,event,this)">
ru.yahoo.com</a>.&nbsp;&nbsp;Likewise, I would hope my opinions<br>here are=
 considered on their merits and my past participation, rather then
<br>whether my circumstances require me to be discreet about my current aff=
iliation.<br><br>Andy<br><br>Andrew Fant&nbsp;&nbsp;&nbsp;&nbsp;| And when =
the night is cloudy&nbsp;&nbsp;&nbsp;&nbsp;| This space to let<br>Molecular=
 Geek | There is still a light&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;|----------------------
<br>fant+*+pobox.com
| That shines on
me&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&=
nbsp;&nbsp;
| Disclaimer:&nbsp;&nbsp;I don't<br>Boston, MA&nbsp;&nbsp;&nbsp;&nbsp; | Sh=
ine until tomorrow, Let it be | even speak for myself<br><br><br><br>-=3D T=
his is automatically added to each message by the mailing script =3D-<br>To=
 recover the email address of the author of the message, please change
<br<br>l=
ook up the X-Original-From: line in the mail header.<br><br>E-mail to subsc=
ribers: <a href=3D"mailto:CHEMISTRY[A]ccl.net" target=3D"_blank" onclick=3D"r=
eturn top.js.OpenExtLink(window,event,this)">
CHEMISTRY[A]ccl.net</a> or use:
<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=3D"http://www.ccl.net/cgi-b=
in/ccl/send_ccl_message" target=3D"_blank" onclick=3D"return top.js.OpenExt=
Link(window,event,this)">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a=
><br><br>E-mail to administrators:=20
<a href=3D"mailto:CHEMISTRY-REQUEST[A]ccl.net" target=3D"_blank" onclick=3D"r=
eturn top.js.OpenExtLink(window,event,this)">CHEMISTRY-REQUEST[A]ccl.net
</a> or use<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=3D"http://www.cc=
l.net/cgi-bin/ccl/send_ccl_message" target=3D"_blank" onclick=3D"return top=
.js.OpenExtLink(window,event,this)">http://www.ccl.net/cgi-bin/ccl/send_ccl=
_message</a><br><br<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=3D"http://www.ccl.net/chemi=
stry/sub_unsub.shtml" target=3D"_blank" onclick=3D"return top.js.OpenExtLin=
k(window,event,this)"</a><br><br>Before posting, che=
ck wait time at: <a href=3D"http://www.ccl.net" target=3D"_blank" onclick=
=3D"return top.js.OpenExtLink(window,event,this)">http://www.ccl.net</a><br=
><br>
Job: <a href=3D"http://www.ccl.net/jobs" target=3D"_blank" onclick=3D"retur=
n top.js.OpenExtLink(window,event,this)">http://www.ccl.net/jobs</a><br>
Conferences: <a href=3D"http://server.ccl.net/chemistry/announcements/confe=
rences/" target=3D"_blank" onclick=3D"return top.js.OpenExtLink(window,even=
t,this)">http://server.ccl.net/chemistry/announcements/conferences/</a><br>=
<br>
Search Messages: <a href=3D"http://www.ccl.net/htdig" target=3D"_blank" onc=
lick=3D"return top.js.OpenExtLink(window,event,this)">http://www.ccl.net/ht=
dig
</a>&nbsp;&nbsp;(login: ccl, Password: search)<br><br>If your mail bounces =
> from CCL with 5.7.1 error, check:<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a=
 href=3D"http://www.ccl.net/spammers.txt" target=3D"_blank" onclick=3D"retu=
rn top.js.OpenExtLink(window,event,this)"</a><br><br>RTFI: <a href=3D"http://www.ccl.=
net/chemistry/aboutccl/instructions/" target=3D"_blank" onclick=3D"return t=
op.js.OpenExtLink(window,event,this)">
http://www.ccl.net/chemistry/aboutccl/instructions/</a><br><br>-+-+-+-+-+-+=
-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+<br><br><br><br=
></blockquote></div><br>

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From owner-chemistry@ccl.net Thu Mar 23 09:48:00 2006
From: "Shobe, David dshobe*sud-chemieinc.com" <owner-chemistry,,server.ccl.net>
To: CCL
Subject: CCL: reveal your affiliation
Message-Id: <-31288-060323091522-20122-+Cne4wEJe79VaxAQ51vncA,,server.ccl.net>
X-Original-From: "Shobe, David" <dshobe*sud-chemieinc.com>
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Date: Thu, 23 Mar 2006 15:15:14 +0100
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Sent to CCL by: "Shobe, David" [dshobe:+:sud-chemieinc.com]
Years ago, people used to put a disclaimer in their signature stating that any opinions stated belonged to the individual, and not necessarily to the individual's employer.

I do include the name of my employer in my signature (which my email address identifies anyway), but I hope everyone realizes that I DO NOT speak for Süd-Chemie, Inc. when I post to CCL, CHMINF-L, or any similar discussion list.

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

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



-----Original Message-----
> From: owner-chemistry_-_ccl.net [mailto:owner-chemistry_-_ccl.net] 
Sent: Wednesday, March 22, 2006 5:54 PM
To: Shobe, David
Subject: CCL: reveal your affiliation

Sent to CCL by: "Andrew D. Fant" [fant-x-pobox.com] Boyd, D. boyd%chem.iupui.edu wrote:
> Sent to CCL by: "Boyd, D." [boyd]![chem.iupui.edu] Colleagues, I 
> recommend/request that people who post on CCL include their affiliation.
> I realize that because of spammers people do not want to reveal their full particulars.
> However, it would make the postings more credible if people who have 
> yahoo, hotmail, etc. email addresses, include the university or 
> company they are associated with.

Many people are employed in situations where they are not allowed to speak/post in a public setting with reference to their employment status without clearing it with their public relations or corporate communications departments.  This is to make management feel secure that nobody is representing themselves in any way
as an official spokesperson for the institution.   I don't think that we need
affiliation information to judge the merits of a posting/email in any case.  If someone makes a statement that sounds outlandish, the claims should be examined and validated by the same standards whether it comes from wwcc.cc.wy.us, tripos.com, phar.cam.ac.uk, or ru.yahoo.com.  Likewise, I would hope my opinions here are considered on their merits and my past participation, rather then whether my circumstances require me to be discreet about my current affiliation.

Andy

Andrew Fant    | And when the night is cloudy    | This space to let
Molecular Geek | There is still a light          |----------------------
fant+*+pobox.com | That shines on me               | Disclaimer:  I don't
Boston, MA     | Shine until tomorrow, Let it be | even speak for myselfhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. 
Thank you.


From owner-chemistry@ccl.net Thu Mar 23 10:22:00 2006
From: "Shobe, David dshobe!A!sud-chemieinc.com" <owner-chemistry]=[server.ccl.net>
To: CCL
Subject: CCL: how to choose the bioactive conformation for CoMFA?
Message-Id: <-31289-060323091710-20811-Nw3lMYBxZGm/XS/b86tN0g]=[server.ccl.net>
X-Original-From: "Shobe, David" <dshobe---sud-chemieinc.com>
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Date: Thu, 23 Mar 2006 15:17:06 +0100
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Sent to CCL by: "Shobe, David" [dshobe||sud-chemieinc.com]
C Sakthivel wrote: 
> How do I choose the bioactive conformation of a perticular compound if 
> such type of compounds were not investigated earlier?

I'd be surprised if there were a general method for this...it all depends on which proteins it's supposed to interact with (the bioactive conformation would be whichever conformation fits the protein better), and it doesn't sound like you have that information.


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

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





-----Original Message-----
> From: owner-chemistry__ccl.net [mailto:owner-chemistry__ccl.net] 
Sent: Wednesday, March 22, 2006 6:48 PM
To: Shobe, David
Subject: CCL: how to choose the bioactive conformation for CoMFA?

Sent to CCL by: Sakthivel C [skvchem[]yahoo.com] --0-882663183-1143036218=:29550
Content-Type: text/plain; charset=iso-8859-1
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Dear CCLers,
  I'm working on 3D QSAR studies of some ancancer drugs that are developed in our lab.  Former members of our group synthesized & studied the ancancer activity for those compounds.  I want to use the activity data for my 3D QSAR studies (CoMFA & CoMSIA) and identify some new compounds in same series.  I learnt that choosing a wrong bioactive conformer would lead to worng results.  
  So, my question is
  How do I choose the bioactive conformation of a perticular compound if such type of compounds were not investigated earlier?
   
  Can any one suggest me?
   
  Looking forward to hear from you.
   
  Sincerely,
   
  C Sakthivel
  Bharathidasan University
  India


C. SAKTHIVEL
Research Scholar
School of Chemistry
Bharathidsan University
Tiruchirappalli 620 024
TN, India
E-mail: skvchem~!~yahoo.com
            skv_chem~!~yahoo.co.in 



		
---------------------------------
 Yahoo! Mail
 Use Photomail to share photos without annoying attachments.
--0-882663183-1143036218=:29550
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<div>Dear CCLers,</div>  <div>I'm working on 3D QSAR studies of some ancancer drugs that are developed in our lab.&nbsp; Former members of our group synthesized &amp; studied the ancancer activity for those compounds.&nbsp; I want to use the activity data for my 3D QSAR studies (CoMFA &amp; CoMSIA)&nbsp;and identify some new compounds in same series.&nbsp; I learnt that choosing a wrong bioactive conformer would lead to worng results.&nbsp; </div>  <div>So, my question is </div>  <div><STRONG>How do I choose the bioactive conformation of a perticular compound if&nbsp;such type of compounds were not investigated earlier?</STRONG></div>  <div>&nbsp;</div>  <div>Can any one suggest me?</div>  <div>&nbsp;</div>  <div>Looking forward to hear from you.</div>  <div>&nbsp;</div>  <div>Sincerely,</div>  <div>&nbsp;</div>  <div>C Sakthivel</div>  <div>Bharathidasan University</div>  <div>India</div><BR><BR><DIV> <DIV> <DIV><FONT face=arial color=#00007f><STRONG>C. SAKTHIVEL</STRONG></FONT></DIV> <DIV><FONT face=arial color=#ff007f>Research Scholar</FONT></DIV> <DIV><FONT face=arial color=#ff007f>School of Chemistry</FONT></DIV> <DIV><FONT face=arial color=#ff007f>Bharathidsan University</FONT></DIV> <DIV><FONT face=arial color=#ff007f>Tiruchirappalli 620 024</FONT></DIV> <DIV><FONT face=arial color=#ff007f>TN, India</FONT></DIV> <DIV><FONT color=#00007f><FONT face=arial>E-mail: </FONT><A href="mailto:skvchem~!~yahoo.com"><FONT face=arial>skvchem~!~yahoo.com</FONT></A></FONT></DIV>
<DIV><FONT color=#00007f><FONT face=arial>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </FONT><A href="mailto:skv_chem~!~yahoo.co.in"><FONT face=arial>skv_chem~!~yahoo.co.in</FONT></A><FONT face=arial> </FONT></FONT></DIV></DIV></DIV><p>
		<hr size=1> Yahoo! Mail<br>
<a href="http://pa.yahoo.com/*http://us.rd.yahoo.com/evt=38867/*http://photomail.mail.yahoo.com">Use Photomail</a> to share photos without annoying attachments.
--0-882663183-1143036218=:29550--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. 
Thank you.


From owner-chemistry@ccl.net Thu Mar 23 10:58:01 2006
From: "Axel Mathieu AMathieu++tranzyme.com" <owner-chemistry[#]server.ccl.net>
To: CCL
Subject: CCL: Docking to Cyps
Message-Id: <-31290-060323101104-16525-MTkjJNU8Q9bONDTWrN6TPA[#]server.ccl.net>
X-Original-From: "Axel Mathieu" <AMathieu]*[tranzyme.com>
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Sent to CCL by: "Axel Mathieu" [AMathieu===tranzyme.com]
This is a multi-part message in MIME format.

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=20
Greetings again to the community,
Following the recent publication of the human P450c2D6 X-Ray crystal  -
J Biol Chem. 2006 Mar 17;281(11):7614-22, we are considering embarking
on docking studies of our pharmacological candidates to a series of
human P450's to aid us in the design of molecules with enhanced P450
profiles. PK profiling is very important in drug design, I'm not
teaching anything new here, and several human P450 X-Ray structures have
been published now. Homology modeling of these has been going on for
years but what I'm interested in are studies with the X-Ray structures.
=20
I was thus wondering if some people would like to have a (short)
discussion of the relevance of this docking given the known flexibility
of these proteins and in some cases, the presence of large labile active
sites (such as for Cyp3A4). I'm really interested in personal experience
if you're willing to boast a bit ;o), docking methods used, validity of
the results, etc, anything that comes to mind. I understand that we are
in a world of confidential results and I accept if no one is willing to
share. Simple suggestions and pointers to good papers on this subject
are also quite acceptable and absolute details are not necessary.
=20
We can definitely take this discussion off the CCL newsgroup, if
desired.
Thanks,
APM
=20

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<body lang=3DEN-US link=3Dblue vlink=3Dpurple =
style=3D'tab-interval:36.0pt'>

<div class=3DSection1>

<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'>Greetings again to the =
community,<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'>Following the recent publication of the human =
P450c2D6 X-Ray
crystal <span style=3D'mso-spacerun:yes'>&nbsp;</span>- J <span =
class=3DSpellE>Biol</span>
Chem.</span> 2006 Mar 17;281(11):7614-22, we are considering embarking =
on docking
studies of our pharmacological candidates to a series of human =
P450&#8217;s to
aid us in the design of molecules with enhanced P450 profiles. PK =
profiling is
very important in drug design, I&#8217;m not teaching anything new here, =
and
several human P450 X-Ray structures have been published now. Homology =
modeling
of these has been going on for years but what I&#8217;m interested in =
are
studies with the X-Ray structures.<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'>I was thus wondering if some people would like to =
have a (short)
discussion of the relevance of this docking given the known flexibility =
of
these proteins and in some cases, the presence of large labile active =
sites
(such as for Cyp3A4). I&#8217;m really interested in personal experience =
if you&#8217;re
willing to boast a bit ;o), docking methods used, validity of the =
results, etc,
anything that comes to mind. I understand that we are in a world of
confidential results and I accept if no one is willing to share. Simple
suggestions and pointers to good papers on this subject are also quite
acceptable and absolute details are not =
necessary.<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 can definitely take this discussion off the CCL =
newsgroup,
if desired.<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'>Thanks,<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'>APM<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>

</div>

</body>

</html>

------_=_NextPart_001_01C64E8C.26F7FE54--


From owner-chemistry@ccl.net Thu Mar 23 11:32:00 2006
From: "s204ira-,-mail.chem.itb.ac.id" <owner-chemistry=-=server.ccl.net>
To: CCL
Subject: CCL: how to make psfgen input for estrogen receptor
Message-Id: <-31291-060321140215-6883-J+nfq/vOWC9qpbSXXB8DZA=-=server.ccl.net>
X-Original-From: s204ira(0)mail.chem.itb.ac.id
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;charset=iso-8859-1
Date: Tue, 21 Mar 2006 18:00:17 +0700 (WIT)
MIME-Version: 1.0


Sent to CCL by: s204ira:-:mail.chem.itb.ac.id

I am trying to dock estrogen receptor (1x7j.pdb) with isoflavon. Before
docking, i want to minimize the energy of estrogen receptor with NAMD.
When I try to minimize the energy with NAMD, I have problem with psfgen
input. The input is :

topology top_all27_prot_lipid.inp
pdbalias residue HIS HSE
segment prot {
	pdb 1x7j_prot.pdb
	first NTER
	last CTER
}
pdbalias atom ILE CD1 CD
coordpdb 1x7j_prot.pdb prot
pdbalias residue HOH TIP3
segment wat {
	pdb 1x7j_solv.pdb
	auto none
	first none
	last none
}
pdbalias atom TIP3 O OH2
coordpdb 1x7j_solv.pdb wat
guesscoord
writepsf 1x7jnew.psf
writepdb 1x7jnew.pdb

error message that i receive is:

error duplicate residue 263
...
error duplicate residue 436

I found no solution to this problem.
could anyone help me to solve this problem?!
I really appreciate for your help.

--ira


From owner-chemistry@ccl.net Thu Mar 23 12:07:02 2006
From: "Axel Mathieu AMathieu|a|tranzyme.com" <owner-chemistry%x%server.ccl.net>
To: CCL
Subject: CCL: Time for a Current Protocols in Computational Chemistry?
Message-Id: <-31292-060323094857-1495-XS9ZZdKgX045BGT2mR9KbA%x%server.ccl.net>
X-Original-From: "Axel Mathieu" <AMathieu^-^tranzyme.com>
Content-class: urn:content-classes:message
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;
	charset="us-ascii"
Date: Thu, 23 Mar 2006 09:49:59 -0500
MIME-Version: 1.0


Sent to CCL by: "Axel Mathieu" [AMathieu-.-tranzyme.com]

Greetings everyone,

I tend to agree with Dr. Steinmetz. Although, I do believe that there is
use for such documentation for a computational chemist who is interested
in exploring an area he/she has not utilized in the past. However, it
can only serve as a starting point; I'm not certain that this format
will be any better than a good textbook (for which there are a good few
already!).

I'm always amazed when a scientist approaches me with new projects
thinking that I just have to push on a few buttons to get the result
THEY want, a result they want quickly obviously - I admit that this does
not happen so often anymore though. The truth is that we always get a
result in computational chemistry/molecular modeling - the quality of
the result is totally another matter and depends entirely on the
method/parameters used to obtain the desired information. I do not
believe they detail every "parameter" in Current Protocols (remembering
my biochemistry days). Doing so would just produce another textbook.

I'm afraid that a "Current Protocol" will only augment the garbage-in
garbage-out phenomenon as more and more labs find it more accessible
(price, ease of use). Let's face it, molecular modeling/computational
chemistry is a good hype creator - always looking for that silver
bullet. In my opinion, the better solution is to get a good theoretical
and practical textbook if you're serous about molecular
modeling/computational chemistry. There's the theory and then there's
what can realistically be done on a daily/weekly basis.

APM

-----Original Message-----
> From: owner-chemistry%ccl.net [mailto:owner-chemistry%ccl.net] 
Sent: 21 mars, 2006 19:25
To: Axel Mathieu
Subject: CCL: Time for a Current Protocols in Computational Chemistry?

Sent to CCL by: "Wayne Steinmetz" [WES04747/./pomona.edu]
Yes and no.

I became aware of Current Protocols when I modified our NMR spectrometer
to perform MRI imaging.  I have downloaded helpful material from the
Current Protocol site devoted to MRI.  I looked at the sample protocol
at the Bioinformatics site.  I found it much too mechanical. Click here
and click there and the process works.  Ha!  Serious computational
chemists don't work that way.  A protocol written in that fashion would
be useless at best and probably dangerous.

However, following the MRI example, a discussion of the procedure in the
style of Organic Syntheses would be helpful.  A useful protocol would at
each step discuss the rationale for the step and point out the traps.
In other words, explain what works (and why) and what doesn't work (and
why). 

Wayne E. Steinmetz
Carnegie Professor of Chemistry
Woodbadge Course Director
Chemistry Department
Pomona College
645 North College Avenue
Claremont, California 91711-6338
USA
phone: 1-909-621-8447
FAX: 1-909-607-7726
Email: wsteinmetz#%#pomona.edu
WWW: pages.pomona.edu/~wsteinmetz
 

-----Original Message-----
> From: owner-chemistry#%#ccl.net [mailto:owner-chemistry#%#ccl.net] 
Sent: Monday, March 20, 2006 3:48 PM
To: Wayne Steinmetz
Subject: CCL: Time for a Current Protocols in Computational Chemistry?

Sent to CCL by: "Andrew D. Fant" [fant=pobox.com]
Afternoon all,
   For the past couple of weeks, I have been kicking around an idea and
I would
like some feedback from the larger community.

   Those here who deal with wet biology and biochemistry or
bioinformatics have
probably come in contact with the Current Protocols series.  For those
who
aren't familiar with it, Current Protocols is a set of loose-leaf
reference
volumes ( or their electronic equivalent) that provide a standard method
for
common lab operations and enough of the theory behind it.  They have a
volume
for bioinformatics as well, with articles such as "Multiple Sequence
Alignment
using ClustalW and ClustalX". The website, for those who are interested
is
http://www.currentprotocols.com .

    My question/proposal is simple.  Has the time come for the
computational
chemistry community to have a similar resource available?  I don't
necessarily
think that this need be a volume in the aforementioned series, but
someplace
that someone needing to perform a calculation that they aren't familiar
with can
go to get a sense of what others would consider the "right" way to do
it.

So, what say ye?  Would this be considered useful, and, more to the
point, are
there any practitioners out there who are interested in talking in more
depth
about what form and content this project could take on?

Thanks,
	Andy

-- 
Andrew Fant    | And when the night is cloudy    | This space to let
Molecular Geek | There is still a light          |----------------------
fant#,#pobox.com | That shines on me               | Disclaimer:  I
don't
Boston, MA     | Shine until tomorrow, Let it be | even speak for
myselfhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/
chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt----------------
---------------------------------------------


This message has been scanned by Postini anti-virus software.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

From owner-chemistry@ccl.net Thu Mar 23 12:42:00 2006
From: "SANDEEP KUMAR skumar23---jhem.jhu.edu" <owner-chemistry[A]server.ccl.net>
To: CCL
Subject: CCL: reveal your affiliation
Message-Id: <-31293-060323105206-9405-iw4K6o9Fx6wW5usy2sP+zA[A]server.ccl.net>
X-Original-From: SANDEEP KUMAR <skumar23=jhem.jhu.edu>
Content-Disposition: inline
Content-Language: en
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=us-ascii
Date: Thu, 23 Mar 2006 09:49:28 -0500
MIME-Version: 1.0


Sent to CCL by: SANDEEP KUMAR [skumar23|-|jhem.jhu.edu]
Hi: 

Several hundred years ago, an Indian saint had said something which when translated in English would roughly read something like this:  Ask the learned for wisdom, not the affiliation. 

I value CCL because it is open to all and often involves interesting discussions. For example, the recent one I really liked was on the review of forcefields for small molecules and macromolecules.  I did not matter if the contributors had the email address of  Yahoo, Hotmail or an organization. I agree with John that this a slippery path which CCL should avoid.  As for spam, I guess CCL administrator is already doing a wonderful job!

Sincerely, 
Sandeep
-------------------------------------------------------------------
Dr. Sandeep Kumar, 
Associate Research Scientist, 
Johns Hopkins University Department of Biology, 
106 Mudd Hall, 3400 N. Charles Street, 
Baltimore, MD 21218,  USA. 
Phone: 410-516-8433,
Email: kumarsan]_[jhu.edu.
URL:  http://myprofile.cos.com/Kumarsan.
or      https://jshare.johnshopkins.edu/skumar23/public_html/


----- Original Message -----
> From: "john furr john.furr . gmail.com" <owner-chemistry]_[ccl.net>
Date: Thursday, March 23, 2006 9:18 am
Subject: CCL: reveal your affiliation

> Sent to CCL by: "john furr" [john.furr++gmail.com]
> ------=_Part_4213_12649164.1143121458741
> Content-Type: text/plain; charset=ISO-8859-1
> Content-Transfer-Encoding: quoted-printable
> Content-Disposition: inline
> 
> "However, it would make the postings more credible if people who have
> yahoo,"
> 
> A persons credibility should not be judged by their affiliation.  
> As soon a=
> s
> we head down that path then science becomes inherently biased.  
> Good scienc=
> e
> (especially computational science) can be done by any person with a 
> desireto learn and experiment.  You certainly don't need to have a 
> position at on=
> e
> of the worlds Ivy League Universities to do quality science.  Nor 
> do you
> need to be employed in one of the major pharmas.  A person should 
> simply be
> judged based on the insights they bring to the discussion.  I do 
> understandthat you weren't implying any of these things with your 
> original request.
> However, I feel it could be a very slippery slope to head down.  
> Also as
> noted before many people may not be allowed to post their affiliation.
> 
> John
> http://www.dynamol.com
> 
> On 3/22/06, Andrew D. Fant fant:-:pobox.com <owner-
> chemistry^_^ccl.net >
> wrote:
> >
> > Sent to CCL by: "Andrew D. Fant" [ fant-x-pobox.com]
> > Boyd, D. boyd%chem.iupui.edu wrote:
> > > Sent to CCL by: "Boyd, D." [boyd]![chem.iupui.edu]
> > > Colleagues,
> > > I recommend/request that people who post on CCL include their
> > affiliation.
> > > I realize that because of spammers people do not want to reveal 
> their> full particulars.
> > > However, it would make the postings more credible if people who 
> have> yahoo,
> > > hotmail, etc. email addresses, include the university or 
> company they
> > are
> > > associated with.
> >
> > Many people are employed in situations where they are not allowed to
> > speak/post
> > in a public setting with reference to their employment status 
> without> clearing
> > it with their public relations or corporate communications
> > departments.  This is
> > to make management feel secure that nobody is representing 
> themselves in
> > any way
> > as an official spokesperson for the institution.   I don't think 
> that we
> > need
> > affiliation information to judge the merits of a posting/email in 
> any> case.  If
> > someone makes a statement that sounds outlandish, the claims 
> should be
> > examined
> > and validated by the same standards whether it comes from 
> wwcc.cc.wy.us,> tripos.com, phar.cam.ac.uk, or ru.yahoo.com.  
> Likewise, I would hope my
> > opinions
> > here are considered on their merits and my past participation, 
> rather the=
> n
> >
> > whether my circumstances require me to be discreet about my current
> > affiliation.
> >
> > Andy
> >
> > Andrew Fant    | And when the night is cloudy    | This space to let
> > Molecular Geek | There is still a light          |----------------
> ------
> > fant+*+pobox.com | That shines on me               | Disclaimer:  
> I don't
> > Boston, MA     | Shine until tomorrow, Let it be | even speak for 
> myself>
> >
> >
> > -=3D This is automatically added to each message by the mailing 
> script =
> =3D->
> > Search Messages: http://www.ccl.net/htdig   (login: ccl, 
> Password: search=
> )>
> >
> >
> >
> 
> ------=_Part_4213_12649164.1143121458741
> Content-Type: text/html; charset=ISO-8859-1
> Content-Transfer-Encoding: quoted-printable
> Content-Disposition: inline
> 
> &quot;However, it would make the postings more credible if people 
> who have =
> yahoo,&quot;<br>
> <br>
> A persons credibility should not be judged by their affiliation. 
> As soon as we head down that path then science becomes inherently
> biased.  Good science (especially computational science) can be
> done by any person with a desire to learn and experiment.  You
> certainly don't need to have a position at one of the worlds Ivy 
> LeagueUniversities to do quality science.  Nor do you need to be
> employed in one of the major pharmas.  A person should simply be
> judged based on the insights they bring to the discussion.  I do
> understand that you weren't implying any of these things with your
> original request.  However, I feel it could be a very slippery
> slope to head down.  Also as noted before many people may not be
> allowed to post their affiliation.  <br>
> <br>
> John<br>
> http://www.dynamol.com">http://www.dynamol.com<br><br><div><=
> span class=3D"gmail_quote">On 3/22/06, <b 
> class=3D"gmail_sendername">Andrew= D. Fant fant:-:http://pobox.com" 
> target=3D"_blank" onclick=3D"r=
> eturn top.js.OpenExtLink(window,event,this)">
> pobox.com</b> <owner-chemistry^_^ccl.net" target=3D"=
> _blank" onclick=3D"return 
> top.js.OpenExtLink(window,event,this)">owner-chem=
> istry^_^ccl.net
> &gt; wrote:</span><blockquote class=3D"gmail_quote" style=3D"border-
> lef=t: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; 
> padding-left: 1=
> ex;">Sent to CCL by: &quot;Andrew D. Fant&quot; [http://fant-x-p=
> obox.com" target=3D"_blank" onclick=3D"return 
> top.js.OpenExtLink(window,eve=nt,this)">
> 
> fant-x-pobox.com]<br>Boyd, D. boyd%chem.iupui.edu wrote:<br>&gt; 
> Sent t=
> o CCL by: &quot;Boyd, D.&quot; [boyd]![http://chem.iupui.edu" ta=
> rget=3D"_blank" onclick=3D"return 
> top.js.OpenExtLink(window,event,this)">ch=em.iupui.edu
> ]<br>&gt; Colleagues,<br>&gt; I recommend/request that people who 
> post =
> on CCL include their affiliation.
> <br>&gt; I realize that because of spammers people do not want to 
> reveal th=
> eir full particulars.<br>&gt; However, it would make the postings 
> more cred=
> ible if people who have yahoo,<br>&gt; hotmail, etc. email 
> addresses, inclu=
> de the university or company they are
> <br>&gt; associated with.<br><br>Many people are employed in 
> situations whe=
> re they are not allowed to speak/post<br>in a public setting with 
> reference= to their employment status without clearing<br>it with 
> their public relati=
> ons or corporate communications departments.  This is
> <br>to make management feel secure that nobody is representing 
> themselves i=
> n any way<br>as an official spokesperson for the institution.   I=
> don't think that we need<br>affiliation information to judge the 
> merits of=
> a posting/email in any case.  If
> <br>someone makes a statement that sounds outlandish, the claims 
> should be =
> examined<br>and validated by the same standards whether it comes 
> from ef=3D"http://wwcc.cc.wy.us" target=3D"_blank" 
> onclick=3D"return top.js.Open=
> ExtLink(window,event,this)">
> wwcc.cc.wy.us,<br>http://tripos.com" target=3D"_blank" oncli=
> ck=3D"return top.js.OpenExtLink(window,event,this)">
> tripos.com, http://phar.cam.ac.uk" target=3D"_blank" onclick=
> =3D"return top.js.OpenExtLink(window,event,this)">phar.cam.ac.uk, 
> or <a=
> href=3D"http://ru.yahoo.com" target=3D"_blank" onclick=3D"return 
> top.js.Op=enExtLink(window,event,this)">
> ru.yahoo.com.  Likewise, I would hope my opinions<br>here are=
> considered on their merits and my past participation, rather then
> <br>whether my circumstances require me to be discreet about my 
> current aff=
> iliation.<br><br>Andy<br><br>Andrew Fant    | And when =
> the night is cloudy    | This space to let<br>Molecular=
> Geek | There is still a light       &nb=
> sp;  |----------------------
> <br>fant+*+pobox.com
> | That shines on
> me            &=
> nbsp; 
> | Disclaimer:  I don't<br>Boston, MA     | Sh=
> ine until tomorrow, Let it be | even speak for 
> myself<br><br><br><br>-=3D T=
> his is automatically added to each message by the mailing script 
> =3D-<br>To=
> recover the email address of the author of the message, please change
> <br<br>l=
> ook up the X-Original-From: line in the mail header.<br><br>E-mail 
> to subsc=
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> CHEMISTRY^_^ccl.net or use:
> <br>      http://www.ccl.net/cgi-b=
> in/ccl/send_ccl_message" target=3D"_blank" onclick=3D"return 
> top.js.OpenExt=Link(window,event,this)">http://www.ccl.net/cgi-
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> CHEMISTRY-REQUEST^_^ccl.net" target=3D"_blank" onclick=3D"r=
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> l.net/cgi-bin/ccl/send_ccl_message" target=3D"_blank" 
> onclick=3D"return top=
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> bin/ccl/send_ccl=_message<br><br<br>      http://www.ccl.net/chemi=
> stry/sub_unsub.shtml" target=3D"_blank" onclick=3D"return 
> top.js.OpenExtLin=k(window,event,this)"<br><br>Before posting, che=
> ck wait time at: http://www.ccl.net" target=3D"_blank" onclick=
> =3D"return 
> top.js.OpenExtLink(window,event,this)">http://www.ccl.net<br=><br>
> Job: http://www.ccl.net/jobs" target=3D"_blank" onclick=3D"retur=
> n top.js.OpenExtLink(window,event,this)">http://www.ccl.net/jobs<br>
> Conferences: http://server.ccl.net/chemistry/announcements/confe=
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> top.js.OpenExtLink(window,even=t,this)">http://server.ccl.net/chemistry/announcements/conferences/<br>=
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> Search Messages: http://www.ccl.net/htdig" target=3D"_blank" onc=
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> top.js.OpenExtLink(window,event,this)">http://www.ccl.net/ht=dig
>  (login: ccl, Password: search)<br><br>If your mail bounces =
> > from CCL with 5.7.1 error, check:<br>      <a=
> href=3D"http://www.ccl.net/spammers.txt" target=3D"_blank" 
> onclick=3D"retu=rn 
> top.js.OpenExtLink(window,event,this)"<br><br>RTFI: http://www.ccl.=
> net/chemistry/aboutccl/instructions/" target=3D"_blank" 
> onclick=3D"return t=
> op.js.OpenExtLink(window,event,this)">
> http://www.ccl.net/chemistry/aboutccl/instructions/<br><br>-+-+-+-+-
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> 
> 
> -= This is automatically added to each message by the mailing 
> script =-
> To recover the email address of the author of the message, please 
> changethe strange characters on the top line to the ]_[ sign. You can 
> also> Conferences: 
> http://server.ccl.net/chemistry/announcements/conferences/
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> 
> 
>


From owner-chemistry@ccl.net Thu Mar 23 13:17:02 2006
From: "Pablo F. Salazar Pablo.Salazar^_^chemail.tamu.edu" <owner-chemistry!A!server.ccl.net>
To: CCL
Subject: CCL: ECP of heavy atoms
Message-Id: <-31294-060323105814-11682-MUSJbnAg4UHEfbYlDQ+Cjw!A!server.ccl.net>
X-Original-From: "Pablo F. Salazar" <Pablo.Salazar^_^chemail.tamu.edu>
Content-Transfer-Encoding: 8bit
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Date: Thu, 23 Mar 2006 09:58:09 -0600
MIME-Version: 1.0


Sent to CCL by: "Pablo F. Salazar" [Pablo.Salazar[A]chemail.tamu.edu]
Dear Zhijian WU,
thanks for your answer.
How to add functions to the extra functions to the basis set is not my 
question.
My question is whether the ECP needs to be modified due to the changes in the basis set.
thanks

Pablo F Salazar
Deparment Chemical Engineering
3122 TAMU
College Station, TX 77843-3122
Phone and Fax 979-862-1329>


-----Original Message-----
> From: "zjwu zjwu(0)imr.edu" <owner-chemistry _ ccl.net>
To: "Salazar, Pablo Felix " <pablo.salazar _ chemail.tamu.edu>
Date: Wed, 22 Mar 2006 22:48:35 -0500
Subject: CCL: ECP of heavy atoms

Sent to CCL by: "zjwu" [zjwu---imr.edu]
Hi,Pablo,

A months ago, I have asked the same question and make a summary to the CCL list. The following example is input file for adding f functions.


#p b3lyp/gen gfinput pseudo=read opt scf(maxcycle=1024)

Title Card Required

0 5
C
W 1 R

R 2.0

C 0
6-311++g(df)
****
W 0
LANL2DZ
F   1 1.00
  .8230000000D+00   .1000000000D+01
****

W 0
LANL2DZ


Cheers!

Zhijian WU
  
======= At 2006-03-23, 12:10:43 you wrote: =======

>Sent to CCL by: "Pablo F. Salazar" [Pablo.Salazar(~)chemail.tamu.edu]
>Dear All,
>I am trying to add polarizations functions (f, g, h) in the basis set of 
>heavy metals using LANL2DZ. But by doing this, Do I need to modify the 
>Effective Core Potential? How?
>Any adivice is highly appreciated
>Thanks
>
>Pablo F Salazar
>Deparment Chemical Engineering
>3122 TAMU
>College Station, TX 77843-3122
>Phone and Fax 979-862-1329>
>
>
>

= = = = = = = = = = = = = = = = = = = =
			
zjwu
zjwu(0)imr.edu
2006-03-23http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

From owner-chemistry@ccl.net Thu Mar 23 13:52:01 2006
From: "Andrew D. Fant fant(~)pobox.com" <owner-chemistry%server.ccl.net>
To: CCL
Subject: CCL: how to choose the bioactive conformation for CoMFA?
Message-Id: <-31295-060323124528-20673-hn6Mm5GcMEgzcs3TqPSQBQ%server.ccl.net>
X-Original-From: "Andrew D. Fant" <fant:_:pobox.com>
Content-Transfer-Encoding: 7bit
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Date: Thu, 23 Mar 2006 11:42:07 -0500
MIME-Version: 1.0


Sent to CCL by: "Andrew D. Fant" [fant++pobox.com]
Shobe, David dshobe!A!sud-chemieinc.com wrote:
> Sent to CCL by: "Shobe, David" [dshobe||sud-chemieinc.com]
> C Sakthivel wrote: 
> 
>>How do I choose the bioactive conformation of a perticular compound if 
>>such type of compounds were not investigated earlier?
> 
> 
> I'd be surprised if there were a general method for this...it all depends on which proteins it's supposed to interact with (the bioactive conformation would be whichever conformation fits the protein better), and it doesn't sound like you have that information.
> 
At the risk of sounding flippant, your best bet is to make friends with your
local crystallographer or macromolecular NMR specialist.  If your compounds are
flexible, there's no real substitute (IMHO) for "seeing" the active site,
preferably with something bound to it.

If you have no idea of what the binding site looks like, you can use the
activity from the older series of compounds with Catalyst to generate a
hypothesis for the conformations the previous members might take that would be
consistent with the observed activity data (hopefully you do have some compounds
in the series that are totally inactive).  If you are certain that your new
compound binds at the same site as the older series, you can then align your new
compound to the structures of the previous series and see if that conformation
is even plausible.  There are no promises that this will work, but it at least
gives you a starting point (hey, that's why they call it research) and you are
no further behind than if you just picked a conformation at random and went to
it.  (I guess this is a good illustration of why rigid scaffolds are a good
thing in the early phases of ligand-based design :-)

Just my CAD 0.026,
		Andy

-- 
Andrew Fant    | And when the night is cloudy    | This space to let
Molecular Geek | There is still a light          |----------------------
fant%%pobox.com | That shines on me               | Disclaimer:  I don't
Boston, MA     | Shine until tomorrow, Let it be | even speak for myself


From owner-chemistry@ccl.net Thu Mar 23 15:02:04 2006
From: "Ivanciuc, Ovidiu I. oiivanci,+,utmb.edu" <owner-chemistry---server.ccl.net>
To: CCL
Subject: CCL: CoEPrA: Test exercise - Regression
Message-Id: <-31296-060323140703-8941-WwbBdCEaMv9GMhn4LdsT2Q---server.ccl.net>
X-Original-From: "Ivanciuc, Ovidiu I." <oiivanci#,#utmb.edu>
Content-class: urn:content-classes:message
Content-Transfer-Encoding: 8bit
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	charset="Windows-1252"
Date: Thu, 23 Mar 2006 13:06:56 -0600
MIME-Version: 1.0


Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci[-]utmb.edu]
CoEPrA: Test exercise - Regression

A QSAR exercise is available for download from the
CoEPrA Web site, http://www.coepra.org/.

This is a test problem, intended to help CoEPrA participants
to streamline the prediction procedures.

 CoEPrA (Comparative Evaluation of Prediction Algorithms) is a modeling
 competition organized to provide an objective testing for various
 classification and regression algorithms via the process of blind prediction.

 The goal of the CoEPrA competition is to advance the algorithms and
 software for modeling chemical, biological, and medical data, with
 special emphasis on the prediction of physico-chemical properties
 and biological activities from molecular descriptors derived from
 the chemical structure.

 For details, see http://www.coepra.org/

Best regards,
Ovidiu


From owner-chemistry@ccl.net Thu Mar 23 15:37:00 2006
From: "Dominic Ryan dominic.ryan{}comcast.net" <owner-chemistry%%server.ccl.net>
To: CCL
Subject: CCL: how to choose the bioactive conformation for CoMFA?
Message-Id: <-31297-060323115852-19082-F1WiSuggyjI6krYwNtN1wg%%server.ccl.net>
X-Original-From: "Dominic Ryan" <dominic.ryan a comcast.net>
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Sent to CCL by: "Dominic Ryan" [dominic.ryan,+,comcast.net]
You are essentially asking about pharmacophore model perception, though in a
comfa-like approach.  This is a difficult area that has seen a resurgence of
activity.  It comes down to having enough constraining information from all
sources:

Have few but conformationally very constrained molecules. 

Have significant SAR covering several orders of magnitude, and some not too
flexible molecules.

Have knowledge of the binding site of the target and a good guess for
binding mode.

If you only have a few molecules you could try an arbitrary alignment of a
few and then test on others.  Bear in mind though, it is *very* easy to get
this wrong and to not know you are wrong.  (Untestable = bad science)

There are several commercial sources for pharmacophore model perception
methods. One of the newer ones is from Peter Willett / Val Gillet / Tripos,
but others are working away as well.  

If you only have one compound, no target information, and it is flexible, I
would say it is time to pick a different problem...

Dominic Ryan

Unaffiliated :-).

-----Original Message-----
> From: owner-chemistry[-]ccl.net [mailto:owner-chemistry[-]ccl.net] 
Sent: Thursday, March 23, 2006 10:32 AM
To: Ryan, M Dominic 
Subject: CCL: how to choose the bioactive conformation for CoMFA?

Sent to CCL by: "Shobe, David" [dshobe||sud-chemieinc.com]
C Sakthivel wrote: 
> How do I choose the bioactive conformation of a perticular compound if 
> such type of compounds were not investigated earlier?

I'd be surprised if there were a general method for this...it all depends on
which proteins it's supposed to interact with (the bioactive conformation
would be whichever conformation fits the protein better), and it doesn't
sound like you have that information.


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

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





-----Original Message-----
> From: owner-chemistry()ccl.net [mailto:owner-chemistry()ccl.net] 
Sent: Wednesday, March 22, 2006 6:48 PM
To: Shobe, David
Subject: CCL: how to choose the bioactive conformation for CoMFA?

Sent to CCL by: Sakthivel C [skvchem[]yahoo.com]
--0-882663183-1143036218=:29550
Content-Type: text/plain; charset=iso-8859-1
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Dear CCLers,
  I'm working on 3D QSAR studies of some ancancer drugs that are developed
in our lab.  Former members of our group synthesized & studied the ancancer
activity for those compounds.  I want to use the activity data for my 3D
QSAR studies (CoMFA & CoMSIA) and identify some new compounds in same
series.  I learnt that choosing a wrong bioactive conformer would lead to
worng results.  
  So, my question is
  How do I choose the bioactive conformation of a perticular compound if
such type of compounds were not investigated earlier?
   
  Can any one suggest me?
   
  Looking forward to hear from you.
   
  Sincerely,
   
  C Sakthivel
  Bharathidasan University
  India


C. SAKTHIVEL
Research Scholar
School of Chemistry
Bharathidsan University
Tiruchirappalli 620 024
TN, India
E-mail: skvchem~!~yahoo.com
            skv_chem~!~yahoo.co.in 



		
---------------------------------
 Yahoo! Mail
 Use Photomail to share photos without annoying attachments.
--0-882663183-1143036218=:29550
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<div>Dear CCLers,</div>  <div>I'm working on 3D QSAR studies of some
ancancer drugs that are developed in our lab.&nbsp; Former members of our
group synthesized &amp; studied the ancancer activity for those
compounds.&nbsp; I want to use the activity data for my 3D QSAR studies
(CoMFA &amp; CoMSIA)&nbsp;and identify some new compounds in same
series.&nbsp; I learnt that choosing a wrong bioactive conformer would lead
to worng results.&nbsp; </div>  <div>So, my question is </div>
<div><STRONG>How do I choose the bioactive conformation of a perticular
compound if&nbsp;such type of compounds were not investigated
earlier?</STRONG></div>  <div>&nbsp;</div>  <div>Can any one suggest
me?</div>  <div>&nbsp;</div>  <div>Looking forward to hear from you.</div>
<div>&nbsp;</div>  <div>Sincerely,</div>  <div>&nbsp;</div>  <div>C
Sakthivel</div>  <div>Bharathidasan University</div>
<div>India</div><BR><BR><DIV> <DIV> <DIV><FONT face=arial
color=#00007f><STRONG>C. SAKTHIVEL</STRONG></!
 FONT></DIV> <DIV><FONT face=arial color=#ff007f>Research
Scholar</FONT></DIV> <DIV><FONT face=arial color=#ff007f>School of
Chemistry</FONT></DIV> <DIV><FONT face=arial color=#ff007f>Bharathidsan
University</FONT></DIV> <DIV><FONT face=arial color=#ff007f>Tiruchirappalli
620 024</FONT></DIV> <DIV><FONT face=arial color=#ff007f>TN,
India</FONT></DIV> <DIV><FONT color=#00007f><FONT face=arial>E-mail:
</FONT><A href="mailto:skvchem~!~yahoo.com"><FONT
face=arial>skvchem~!~yahoo.com</FONT></A></FONT></DIV>
<DIV><FONT color=#00007f><FONT
face=arial>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp
; </FONT><A href="mailto:skv_chem~!~yahoo.co.in"><FONT
face=arial>skv_chem~!~yahoo.co.in</FONT></A><FONT face=arial>
</FONT></FONT></DIV></DIV></DIV><p>
		<hr size=1> Yahoo! Mail<br>
<a
href="http://pa.yahoo.com/*http://us.rd.yahoo.com/evt=38867/*http://photomai
l.mail.yahoo.com">Use Photomail</a> to share photos without annoying
attachments.
--0-882663183-1143036218=:29550--http://www.ccl.net/cgi-bin/ccl/send_ccl_mes
sagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.
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Thank you.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

From owner-chemistry@ccl.net Thu Mar 23 16:12:00 2006
From: "Deng, Jun jdeng . ppg.com" <owner-chemistry===server.ccl.net>
To: CCL
Subject: CCL: Bandwidth prediction
Message-Id: <-31298-060322115115-8442-d1HXiXH0+DYqRtaHFu8wjA===server.ccl.net>
X-Original-From: "Deng, Jun" <jdeng(!)ppg.com>
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Sent to CCL by: "Deng, Jun" [jdeng.:.ppg.com]


Dear college:

Do you have any suggestion on how to qualitatively estimate the bandwidth of absorption spectrum given a molecular structure?  Can factors affecting the bandwidth be calculated practically (for instance, molecule with 20 heavy atoms)?

Thanks in advance!

Jun Deng


From owner-chemistry@ccl.net Thu Mar 23 16:47:01 2006
From: "Phil Hultin hultin_-_cc.umanitoba.ca" <owner-chemistry[]server.ccl.net>
To: CCL
Subject: CCL: Affiliation
Message-Id: <-31299-060323145758-4645-8OAaa+dQT0difPikYxssVg[]server.ccl.net>
X-Original-From: "Phil Hultin" <hultin]*[cc.umanitoba.ca>
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Sent to CCL by: "Phil Hultin" [hultin(0)cc.umanitoba.ca]
This is a multi-part message in MIME format.

------=_NextPart_000_0038_01C64E7C.36513240
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While I agree with everyone who has posted their belief in the democracy of
ideas on CCL, I can see one argument in support of making one's affiliation
clear.  In many postings, statements are made assessing the capabilities and
quality of various packages of software or hardware.  It would be very
helpful to know that the people making these statements a) do not stand to
gain financially or in any other way from the adoption of the product(s) in
questions and b) do not stand to gain from any negative effects on other
possibly competing products.

 

When I read the first message about posting one's affiliation, my thoughts
were basically "Great, that way I will find it easier to distinguish the
infomercials from the real discussion" - only later did I see that a lot of
people thought that we would put more weight on a comment from someone at
University X than from College Y.

 

Dr. Philip G. Hultin

Associate Professor of Chemistry,

University of Manitoba

Winnipeg, MB

R3T 2N2

hultin-x-cc.umanitoba.ca

http://umanitoba.ca/chemistry/people/hultin

 


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<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>While I agree with everyone who has posted their =
belief in
the democracy of ideas on CCL, I can see one argument in support of =
making one&#8217;s
affiliation clear. &nbsp;In many postings, statements are made assessing =
the
capabilities and quality of various packages of software or hardware. =
&nbsp;It
would be very helpful to know that the people making these statements a) =
do not
stand to gain financially or in any other way from the adoption of the
product(s) in questions and b) do not stand to gain from any negative =
effects
on other possibly competing products.<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'>When I read the first message about posting =
one&#8217;s
affiliation, my thoughts were basically &#8220;Great, that way I will =
find it
easier to distinguish the infomercials from the real discussion&#8221; =
&#8211;
only later did I see that a lot of people thought that we would put more =
weight
on a comment from someone at University X than from College =
Y.<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'>Dr. Philip G. Hultin<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'>Associate Professor of =
Chemistry,<o:p></o:p></span></font></p>

<p class=3DMsoNormal><u1:place u2:st=3D"on"><u1:PlaceType =
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w:st=3D"on"><st1:PlaceType w:st=3D"on"><font size=3D2 face=3DArial><span
  =
style=3D'font-size:10.0pt;font-family:Arial'>University</span></font></st=
1:PlaceType><font
 size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'></u1:PlaceType>
 of <u1:PlaceName u2:st=3D"on"><st1:PlaceName =
w:st=3D"on">Manitoba</u1:PlaceName></st1:PlaceName></span></font></st1:pl=
ace></u1:place><font
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'><o:p></o:p></span></font></p=
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  Arial'>Winnipeg</span></font></st1:City><font size=3D2 =
face=3DArial><span
 style=3D'font-size:10.0pt;font-family:Arial'></u1:City>, <u1:State =
u2:st=3D"on"><st1:State
 =
w:st=3D"on">MB</u1:State></st1:State></span></font></st1:place></u1:place=
><font
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'><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'>R3T 2N2<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'><a =
href=3D"mailto:hultin-x-cc.umanitoba.ca">hultin-x-cc.umanitoba.ca</a><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'><a =
href=3D"http://umanitoba.ca/chemistry/people/hultin">http://umanitoba.ca/=
chemistry/people/hultin</a><o:p></o:p></span></font></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>

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From owner-chemistry@ccl.net Thu Mar 23 17:23:00 2006
From: "Chris Van Dyke vandyke*o*tripos.com" <owner-chemistry*server.ccl.net>
To: CCL
Subject: CCL: Tripos Training Workshops April-June 2006
Message-Id: <-31300-060323115237-14994-QiPHl6i8lRhV5I1ZitH1pQ*server.ccl.net>
X-Original-From: "Chris  Van Dyke" <vandyke%%tripos.com>
Date: Thu, 23 Mar 2006 11:52:35 -0500


Sent to CCL by: "Chris  Van Dyke" [vandyke^tripos.com]

Tripos is pleased to announce the following Training Workshops during the coming months:

LIGAND-BASED MODELING FOR NEW MODELERS
   St. Louis, MO, USA. April 25-26, 2006

RECEPTOR-LIGAND MODELING FOR NEW MODELERS
   Paris, France. May 16-17, 2006
   Edison, NJ, USA. June 06-07, 2006

DESIGNING ACTIVE LIGANDS WITH QSAR/COMFA
   St. Louis, MO, USA. April 27-28, 2006
	
MOLECULAR DIVERSITY ANALYSIS
   St. Louis, MO, USA. June 15-16, 2006

LIGAND DOCKING
   Edison, NJ, USA. June 08, 2006

VIRTUAL SCREENING
   Paris, France. May 18-19, 2006

COMBINATORIAL LIBRARY DESIGN
   St. Louis, MO, USA. June 13-14, 2006

For course descriptions, pricing information and registration, please visit http://www.tripos.com/training. You may send questions concerning these Training Workshops to training^tripos.com.


=============================
Chris Van Dyke, Ph.D.
Director, Scientific Training
Tripos, Inc.
=============================


From owner-chemistry@ccl.net Thu Mar 23 17:57:01 2006
From: "Sengen Sun sengensun||yahoo.com" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL: Highlights and significance of a new mechanistic theory
Message-Id: <-31301-060323161211-9405-sbVq2oP0VQuZWvNKiqt2PA:server.ccl.net>
X-Original-From: Sengen Sun <sengensun[-]yahoo.com>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=iso-8859-1
Date: Thu, 23 Mar 2006 13:12:07 -0800 (PST)
MIME-Version: 1.0


Sent to CCL by: Sengen Sun [sengensun*|*yahoo.com]

--- "Boyles, David A." <David.Boyles(-)sdsmt.edu> wrote:

> Sengen:
> 
> Would we be correct in summarizing your paper were
> we to state that "electron flow is induced by
> electron repulsion which is in turn induced upon
> molecular collision"?
> 

This statement has a tiny problem. The closed-shell
electron flow is governed by ALL electrostatic forces.
But for neutral molecules such as those in the parent
D-A, a collision starts with e-e repulsion, which
predominantly contributes to the potential energy
increase in a collision. The N-N repulsion exists
but is relatively less significant in the early
collision. It is common practice to say
electron-pushing mechanism in org chem, which does not
mean that N-N repulsion and e-N attraction don't
exist. 

> Is this the "electron migration of CC's that has
> never been documented in the literature" as you have
> stated on slide 23(?) of your Powerpoint
>presentation?
> 
> Thanks,
> 
> David
 
Anyway, you are right here, but not enough! None of
the closed-shell mechanism of any CCs had been ever
established at a theoretical level. That is, there
had never been concrete computational numbers to
support the electron-pushing mechanism for any CCs. 

What we had is nothing but confusion on mechanism of
CCs. As I said, we chemists lost our direction along
the rings in general, theoretically or by the
intuition of experimentalists. The three examples I
already discussed:

1. Hoffmann does not know the direction in his JACS
paper mentioned early on.
2. The parent D-A reaction had been a controversy ever
since. The electron-pushing mechanism had never been
accepted by (almost all?) high profile theoretical
chemists. That is why a concerted spin-recoupling was
published (JACS 1998, 120, 3975), but as a mistake!
3. For the simple 1,3-dipolar cycloaddition shown on
Slide 16 (references therein) of my ppt file, all the
three possible mechanisms were proposed by four
different groups. Although Karadakov, et al. argued
for a correct one to me, but their data really do not
mean what they claimed!

Now, I have established concrete computational data to
support the electron-pushing mechanism as exemplified
on slides 19 and 21 of my ppt file. 

I do wish to have opportunities to discuss my
competitive scientific arguments in the main stream of
the scientific community. I don't know when such a day
can come, but have a feeling of being rejected and
ignored. I made my hard effort for so many years. Once
a puzzle is solved, everything is easy. That is what
science is about. I feel guilty from time to time by
engaging in the Internet polemics. But I really did
not have a better option to reward myself. Is it the
time for me to give up? I welcome any public or
personal advice.

Thanks to Dr. David Boyles for your contribution to
the discussion.

Regards,

Sengen


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


From owner-chemistry@ccl.net Thu Mar 23 18:32:01 2006
From: "Gon alo Justino goncalo.justino(0)zmail.pt" <owner-chemistry ~ server.ccl.net>
To: CCL
Subject: CCL: reveal your affiliation
Message-Id: <-31302-060323103501-28993-EsNfr6an51/cN72tvjlIVA ~ server.ccl.net>
X-Original-From: "Gon  alo  Justino" <goncalo.justino~~zmail.pt>
Date: Thu, 23 Mar 2006 10:34:59 -0500


Sent to CCL by: "Gon  alo  Justino" [goncalo.justino.*|*.zmail.pt]

About the affiliation issue, I'm (un?)fortunate enough in the point that I'm not affiliated with any institution. True, I get some papers published that include an affiliation, but the area they belong to is in no way close to the issues discussed at ccl.net. True, I do have an email from that institution, but I always post to ccl from the ccl site and I always include my personal and private mail, for which I'm paying an annual fee so that my work doesn't get mixed with my "personal scientific affairs". All the work I do for that institution is purely lab/experimental/wet work, and all the computational/dry work is done on my pc, with the software I paid for from my own money. The only attempt to get my institution to contribute with some money failed redudantly. Maybe if I lived/worked in a country with money to spend on R&D I could be able to get everything done with the institution's money, and then I'd proudly advertise it by including the aff. in all messages. As I come from the west end of Europe, I do what I'm paid for and manage to do what I like at out-of-office hours.

I hope it is clear the motive why I don't and won't reveal/include my affiliation when I post to ccl.net.

Best wishes,
Gonalo

goncalo.justino[*]zmail.pt


From owner-chemistry@ccl.net Thu Mar 23 19:07:01 2006
From: "Kalju Kahn kalju#chem.ucsb.edu" <owner-chemistry[A]server.ccl.net>
To: CCL
Subject: CCL:G: Time for a Current Protocols in Computational =?us-ascii?q?Chemistry=3F_=28longer_discussion=29?=
Message-Id: <-31303-060323160315-4413-8bfiS8nOZVYQF0AvdkhSyA[A]server.ccl.net>
X-Original-From: Kalju Kahn <kalju^chem.ucsb.edu>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=utf-8
Date: Thu, 23 Mar 2006 12:13:41 -0800
MIME-Version: 1.0


Sent to CCL by: Kalju Kahn [kalju=-=chem.ucsb.edu]
Time For Current Protocols?

I thought I'll throw in my two cents here as I am somewhat familiar
with both molecular biology and computational chemistry.  Even
happened to teach both classes at the same quarter this year.  

Molecular biology, bioinformatics, and even protein analysis are
topics that lend itself well into recipe-type protocols.  The main
reason is that the chemical and physical properties of subjects in
such studies are fairly independent on the details of the  
composition of these molecules.  For example, the melting temperature
or electrophoretic mobility of DNA depends in a fairly simple and
well-understood manner of its nucleotide composition.  This allows one
to write a general protocol, for example on how to amplify DNA by PCR
(see sample protocol  at 
http://media.wiley.com/CurrentProtocols/047150338X/047150338X-sampleUn
it.pdf)

In essence, the same operations (add the same buffer, same
concentrations of template and primers, same amount of substrates,
bring volume always to the same level, and add the same amount of
polymerase enzyme last, then put it into a robotic thermocycler) can
be used to amplify or clone out, or even mutate pretty much arbitrary
DNA sequence.  The few system-specific things are the template DNA, a
pair of primers and appropriate annealing temperature. There are
recipies for figuring out how to purify the template from cells, how
to figure out appropriate primers, and estimate appropriate
temperature.  Of course, the specialists in the molecular biology will
point out that there are more to this ... may need to adjust the
annealing temperature from default for better purity, maybe tinker
with Mg concentration, things are little different with eukaryotic DNA
... However, for the novice the standard protocol will provide an
excellent starting point to amplify a piece of DNA regardless of what
it codes for.  The same basic protocol works if you plan to clone the
whole gene for hexokinase, make a mutation in the 42-residue Alzheimer
peptide, or identify a suspect based on the DNA sample!

The same goes for bioinformatics.  The steps are roughly the same if I
want to find out conserved residues in HIV protease, hemoglobin, or
ribosomal RNA.  Yes, one needs to realize that vertebrate databases
are more useful than bacterial databases for hemoglobin genes but
besides few obvious selections, the process is the same.  Again,
specialist would scorn and point out that appropriate gap penalty and
BLOSUM matrix should be selected for a particular case for optimal
results.  However, a novice can use a standard protocol with default
settings and still get very meaningful results.  Similar situation
applies for other common bioinformatics tasks, such as finding
evolutionary relationships, predict secondary structures, and for
predicting clevage by restriction endonucleases or proteases. 

Now, lets' see what in computational chemistry lends to such recipies.
 I think that some things do.  Consider for example, a conformational
analysis of molecules, say smaller than 600 Da (typical drugs).  Maybe
one could write a general recipy on how to carry out conformational
analysis: 
   obtain the structure of the molecule in an arbitrary initial
conformation
   identify rotatable bonds (ignore rotations that lead to same
structures, e.g. CH3)
   pick a method to generate new conformations (choose between
systematic or random search depending on the number of rotatable
bonds)
   pick a method to evaluate energy (choose a force field that is
known to work for this class of compounds)
   pick a method to minimize the guess structures (choose between
gradient and Hessian based methods, select convergence criteria)
   pick a treshold if you do not care about very-high-energy
conformers (recall that bioactive conformers bound to target proteins
in water could be several kcal/mol above the gas phase minimum)
  generate new conformations, minimize these, eliminate duplicate
structures, sort the remaining according to energy
  perform vibrational analysis to confirm the structures are minima
and not saddle points
  visually examine each to make sure they are really unique 

Now, what good does this recipy do for us?  First, the material above
is already explained at this level in some textbooks.   Can a novice
follow this recipe?  What if he'll wonder how do you define rotatable
bonds?  In CHARMM?  In AMBER? In BOSS? In SYBYL? In MacroModel? In
HyperChem? What about Gaussian?  Would we write a current protocols
for each of the common programs?  No, this would just duplicate the
program manuals.  Would we write a current protocol for a particular
program? No, this is not fair.  

To summarize the first point, even simple techniques in computational
chemistry are too dependent on a particular software and this prevents
the description of universally applicable protocols.  Current
textbooks and online tutorials cover the basic principles of methods
quite well.

If you are still with me ... There are plenty of things in
computational chemistry that do not lend itself into stanard
protocols.  Ever tried CAS or RAS, or MRCI?  But even simpler and more
common things are problematic.  Take transition states.  The best
methodology for finding a reasonably correct transition state for
isomerization of HCN is rather different for finding a TS for SN2
reaction between acetate and ethyl bromide, and yet another approach
may be required to find a correct TS for rotation in CH3-O-O-CH3.  
The search method, the electron correlation method, the practical
basis sets are different here.  In this case, QST2 is a good choice
for the SN2 reaction but not for HCN isomerization, and who know what
kind of electron correlation method gets the CH3-O-O-CH3 torsionl
motion right.  Furthermore, the protocols run at risk of becoming
obsolete quickly.  Remember the days when HF/6-31G(d) was the method
of choice to optimize everything?

To summarize the second point, most techniques in computational
chemistry have a limited range of practical applicability.  Or other
way around, most tasks in computational chemistry do not have one
standard solution.  A good practitioner in the art of computational
chemistry knows what methods to apply to what problems.  However, this
knowledge cannot be efficiently presented in the format of a
“current protocol”. 

I thus feel that we are not at the point of benefiting significantly
> from “current protocols”.  We could benefit for some problems if a
common, free, multiplatform front end to most computational chemistry
programs emerges such that the program-specific input and keywords can
be hidden from the novice.  (In bioinformatics, Biology Workbench at
SDSC is a good example).  I believe that molecular-mechanics-based
methods like conformational analysis, molecular dynamics, Monte Carlo,
and free energy calculations are good first candidates for such
protocols.  For problems that require quantum mechanics, we have to
wait until methods universally regarded as accurate are practically
applicable to a wide range of problems. 

That's all :)
Kalju
-------------------
> Sent to CCL by: "Andrew D. Fant" [fant=pobox.com]
> Afternoon all,
>    For the past couple of weeks, I have been kicking around an idea
and I would
> like some feedback from the larger community.
> 
>    Those here who deal with wet biology and biochemistry or
bioinformatics have
> probably come in contact with the Current Protocols series.  For
those who
> aren't familiar with it, Current Protocols is a set of loose-leaf
reference
> volumes ( or their electronic equivalent) that provide a standard
method for
> common lab operations and enough of the theory behind it.  They have
a volume
> for bioinformatics as well, with articles such as "Multiple Sequence
Alignment
> using ClustalW and ClustalX". The website, for those who are
interested is
> http://www.currentprotocols.com .
> 
>     My question/proposal is simple.  Has the time come for the
computational
> chemistry community to have a similar resource available?  I don't
necessarily
> think that this need be a volume in the aforementioned series, but
someplace
> that someone needing to perform a calculation that they aren't
familiar with can
> go to get a sense of what others would consider the "right" way to
do it.
> 
> So, what say ye?  Would this be considered useful, and, more to the
point, are
> there any practitioners out there who are interested in talking in
more depth
> about what form and content this project could take on?
> 
> Thanks,
> 	Andy
> 
> -- 
> Andrew Fant    | And when the night is cloudy    | This space to let
> Molecular Geek | There is still a light         
|----------------------
> fant#,#pobox.com | That shines on me               | Disclaimer:  I
don't
> Boston, MA     | Shine until tomorrow, Let it be | even speak for
myself

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Kalju Kahn
Department of Chemistry and Biochemistry
University of California, Santa Barbara


From owner-chemistry@ccl.net Thu Mar 23 19:43:01 2006
From: "Rick Venable rvenable|-|pollux.cber.nih.gov" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL: how to make psfgen input for estrogen receptor
Message-Id: <-31304-060323154651-29313-vRHBZVa3mYxwP2W6nQ/l7Q,+,server.ccl.net>
X-Original-From: Rick Venable <rvenable]~[pollux.cber.nih.gov>
Content-Type: TEXT/PLAIN; charset=US-ASCII
Date: Thu, 23 Mar 2006 13:53:55 -0500
MIME-Version: 1.0


Sent to CCL by: Rick Venable [rvenable ~ pollux.cber.nih.gov]

	I suggest checking the PDB file-- there can be repeated
coordinates for atoms or residues for degenerate solutions to fitting
the electron density.  The "weight" data column should be e.g. 0.5
instead of 1.0 for this case.

-------------------------------------
Rick Venable           29/500
FDA/CBER/OVRR Biophysics Lab
1401 Rockville Pike    HFM-419
Rockville, MD  20852-1448  U.S.A.
(301) 496-1905  Rick_Venable AT nih*gov
ALT email:  rvenable AT speakeasy*org
-------------------------------------

On Thu, 23 Mar 2006, s204ira-,-mail.chem.itb.ac.id wrote:
> I am trying to dock estrogen receptor (1x7j.pdb) with isoflavon. Before
> docking, i want to minimize the energy of estrogen receptor with NAMD.
> When I try to minimize the energy with NAMD, I have problem with psfgen
> input. The input is :
>
> topology top_all27_prot_lipid.inp
> pdbalias residue HIS HSE
> segment prot {
> 	pdb 1x7j_prot.pdb
> 	first NTER
> 	last CTER
> }
> pdbalias atom ILE CD1 CD
> coordpdb 1x7j_prot.pdb prot
> pdbalias residue HOH TIP3
> segment wat {
> 	pdb 1x7j_solv.pdb
> 	auto none
> 	first none
> 	last none
> }
> pdbalias atom TIP3 O OH2
> coordpdb 1x7j_solv.pdb wat
> guesscoord
> writepsf 1x7jnew.psf
> writepdb 1x7jnew.pdb
>
> error message that i receive is:
>
> error duplicate residue 263
> ..
> error duplicate residue 436
>
> I found no solution to this problem.
> could anyone help me to solve this problem?!
> I really appreciate for your help.
>
> --ira


From owner-chemistry@ccl.net Thu Mar 23 20:18:00 2006
From: "Paul.M.Mathias|*|fluor.com" <owner-chemistry%a%server.ccl.net>
To: CCL
Subject: CCL: reveal your affiliation
Message-Id: <-31305-060323180617-24703-9y8lZ6cOS35/0Ivd9sMR8A%a%server.ccl.net>
X-Original-From: Paul.M.Mathias:fluor.com
Content-Type: multipart/alternative; 
    boundary="=_alternative 007AC6038825713A_="
Date: Thu, 23 Mar 2006 14:25:10 -0800
MIME-Version: 1.0


Sent to CCL by: Paul.M.Mathias,fluor.com
This is a multipart message in MIME format.
--=_alternative 007AC6038825713A_=
Content-Type: text/plain; charset="US-ASCII"

There is another point to be considered here, which is the apparent 
discrimination of the CCL against those with Hotmail, Yahoo, Gmail, etc. 
addresses.

I have been a subscriber to the CCL through various organizational email 
addresses for many years.  For a period I worked as an independent 
consultant and used Gmail as my business email.  I did not succeed in 
becoming a CCL subscriber using a Gmail address, in spite of several 
direct pleas to the CCL administrator.  As soon as I joined my present 
company, I applied to become a CCL member and was immediately accepted.

Is there a CCL policy that denies membership to those with Hotmail, Yahoo, 
Gmail, etc.  addresses, or, at least, deems them suspicious until proven 
otherwise?

Paul Mathias






"SANDEEP KUMAR skumar23---jhem.jhu.edu" <owner-chemistry-,-ccl.net>
Sent by: owner-chemistry-,-ccl.net
03/23/2006 10:37 AM
Please respond to "CCL Subscribers"
 
        To:     "Mathias, Paul M. " <paul.m.mathias-,-fluor.com>
        cc: 
        Subject:        CCL: reveal your affiliation
.


Sent to CCL by: SANDEEP KUMAR [skumar23|-|jhem.jhu.edu]
Hi: 

Several hundred years ago, an Indian saint had said something which when 
translated in English would roughly read something like this:  Ask the 
learned for wisdom, not the affiliation. 

I value CCL because it is open to all and often involves interesting 
discussions. For example, the recent one I really liked was on the review 
of forcefields for small molecules and macromolecules.  I did not matter 
if the contributors had the email address of  Yahoo, Hotmail or an 
organization. I agree with John that this a slippery path which CCL should 
avoid.  As for spam, I guess CCL administrator is already doing a 
wonderful job!

Sincerely, 
Sandeep
-------------------------------------------------------------------
Dr. Sandeep Kumar, 
Associate Research Scientist, 
Johns Hopkins University Department of Biology, 
106 Mudd Hall, 3400 N. Charles Street, 
Baltimore, MD 21218,  USA. 
Phone: 410-516-8433,
Email: kumarsan%%jhu.edu.
URL:  http://myprofile.cos.com/Kumarsan.
or      https://jshare.johnshopkins.edu/skumar23/public_html/


----- Original Message -----
> From: "john furr john.furr . gmail.com" <owner-chemistry%%ccl.net>
Date: Thursday, March 23, 2006 9:18 am
Subject: CCL: reveal your affiliation

> Sent to CCL by: "john furr" [john.furr++gmail.com]
> ------=_Part_4213_12649164.1143121458741
> Content-Type: text/plain; charset=ISO-8859-1
> Content-Transfer-Encoding: quoted-printable
> Content-Disposition: inline
> 
> "However, it would make the postings more credible if people who have
> yahoo,"
> 
> A persons credibility should not be judged by their affiliation. 
> As soon a=
> s
> we head down that path then science becomes inherently biased. 
> Good scienc=
> e
> (especially computational science) can be done by any person with a 
> desireto learn and experiment.  You certainly don't need to have a 
> position at on=
> e
> of the worlds Ivy League Universities to do quality science.  Nor 
> do you
> need to be employed in one of the major pharmas.  A person should 
> simply be
> judged based on the insights they bring to the discussion.  I do 
> understandthat you weren't implying any of these things with your 
> original request.
> However, I feel it could be a very slippery slope to head down. 
> Also as
> noted before many people may not be allowed to post their affiliation.
> 
> John
> http://www.dynamol.com
> 
> On 3/22/06, Andrew D. Fant fant:-:pobox.com <owner-
> chemistry^_^ccl.net >
> wrote:
> >
> > Sent to CCL by: "Andrew D. Fant" [ fant-x-pobox.com]
> > Boyd, D. boyd%chem.iupui.edu wrote:
> > > Sent to CCL by: "Boyd, D." [boyd]![chem.iupui.edu]
> > > Colleagues,
> > > I recommend/request that people who post on CCL include their
> > affiliation.
> > > I realize that because of spammers people do not want to reveal 
> their> full particulars.
> > > However, it would make the postings more credible if people who 
> have> yahoo,
> > > hotmail, etc. email addresses, include the university or 
> company they
> > are
> > > associated with.
> >
> > Many people are employed in situations where they are not allowed to
> > speak/post
> > in a public setting with reference to their employment status 
> without> clearing
> > it with their public relations or corporate communications
> > departments.  This is
> > to make management feel secure that nobody is representing 
> themselves in
> > any way
> > as an official spokesperson for the institution.   I don't think 
> that we
> > need
> > affiliation information to judge the merits of a posting/email in 
> any> case.  If
> > someone makes a statement that sounds outlandish, the claims 
> should be
> > examined
> > and validated by the same standards whether it comes from 
> wwcc.cc.wy.us,> tripos.com, phar.cam.ac.uk, or ru.yahoo.com. 
> Likewise, I would hope my
> > opinions
> > here are considered on their merits and my past participation, 
> rather the=
> n
> >
> > whether my circumstances require me to be discreet about my current
> > affiliation.
> >
> > Andy
> >
> > Andrew Fant    | And when the night is cloudy    | This space to let
> > Molecular Geek | There is still a light          |----------------
> ------
> > fant+*+pobox.com | That shines on me               | Disclaimer: 
> I don't
> > Boston, MA     | Shine until tomorrow, Let it be | even speak for 
> myself>
> >
> >
> > -=3D This is automatically added to each message by the mailing 
> script =
> =3D->
> > Search Messages: http://www.ccl.net/htdig   (login: ccl, 
> Password: search=
> )>
> >
> >
> >
> 
> ------=_Part_4213_12649164.1143121458741
> Content-Type: text/html; charset=ISO-8859-1
> Content-Transfer-Encoding: quoted-printable
> Content-Disposition: inline
> 
> &quot;However, it would make the postings more credible if people 
> who have =
> yahoo,&quot;<br>
> <br>
> A persons credibility should not be judged by their affiliation. 
> As soon as we head down that path then science becomes inherently
> biased.  Good science (especially computational science) can be
> done by any person with a desire to learn and experiment.  You
> certainly don't need to have a position at one of the worlds Ivy 
> LeagueUniversities to do quality science.  Nor do you need to be
> employed in one of the major pharmas.  A person should simply be
> judged based on the insights they bring to the discussion.  I do
> understand that you weren't implying any of these things with your
> original request.  However, I feel it could be a very slippery
> slope to head down.  Also as noted before many people may not be
> allowed to post their affiliation.  <br>
> <br>
> John<br>
> http://www.dynamol.com">http://www.dynamol.com<br><br><div><=
> span class=3D"gmail_quote">On 3/22/06, <b 
> class=3D"gmail_sendername">Andrew= D. Fant fant:-:http://pobox.com" 
> target=3D"_blank" onclick=3D"r=
> eturn top.js.OpenExtLink(window,event,this)">
> pobox.com</b> <owner-chemistry^_^ccl.net" target=3D"=
> _blank" onclick=3D"return 
> top.js.OpenExtLink(window,event,this)">owner-chem=
> istry^_^ccl.net
> &gt; wrote:</span><blockquote class=3D"gmail_quote" style=3D"border-
> lef=t: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; 
> padding-left: 1=
> ex;">Sent to CCL by: &quot;Andrew D. Fant&quot; [http://fant-x-p=
> obox.com" target=3D"_blank" onclick=3D"return 
> top.js.OpenExtLink(window,eve=nt,this)">
> 
> fant-x-pobox.com]<br>Boyd, D. boyd%chem.iupui.edu wrote:<br>&gt; 
> Sent t=
> o CCL by: &quot;Boyd, D.&quot; [boyd]![http://chem.iupui.edu" ta=
> rget=3D"_blank" onclick=3D"return 
> top.js.OpenExtLink(window,event,this)">ch=em.iupui.edu
> ]<br>&gt; Colleagues,<br>&gt; I recommend/request that people who 
> post =
> on CCL include their affiliation.
> <br>&gt; I realize that because of spammers people do not want to 
> reveal th=
> eir full particulars.<br>&gt; However, it would make the postings 
> more cred=
> ible if people who have yahoo,<br>&gt; hotmail, etc. email 
> addresses, inclu=
> de the university or company they are
> <br>&gt; associated with.<br><br>Many people are employed in 
> situations whe=
> re they are not allowed to speak/post<br>in a public setting with 
> reference= to their employment status without clearing<br>it with 
> their public relati=
> ons or corporate communications departments.  This is
> <br>to make management feel secure that nobody is representing 
> themselves i=
> n any way<br>as an official spokesperson for the institution.   I=
> don't think that we need<br>affiliation information to judge the 
> merits of=
> a posting/email in any case.  If
> <br>someone makes a statement that sounds outlandish, the claims 
> should be =
> examined<br>and validated by the same standards whether it comes 
> from ef=3D"http://wwcc.cc.wy.us" target=3D"_blank" 
> onclick=3D"return top.js.Open=
> ExtLink(window,event,this)">
> wwcc.cc.wy.us,<br>http://tripos.com" target=3D"_blank" oncli=
> ck=3D"return top.js.OpenExtLink(window,event,this)">
> tripos.com, http://phar.cam.ac.uk" target=3D"_blank" onclick=
> =3D"return top.js.OpenExtLink(window,event,this)">phar.cam.ac.uk, 
> or <a=
> href=3D"http://ru.yahoo.com" target=3D"_blank" onclick=3D"return 
> top.js.Op=enExtLink(window,event,this)">
> ru.yahoo.com.  Likewise, I would hope my opinions<br>here are=
> considered on their merits and my past participation, rather then
> <br>whether my circumstances require me to be discreet about my 
> current aff=
> iliation.<br><br>Andy<br><br>Andrew Fant    | And when =
> the night is cloudy    | This space to let<br>Molecular=
> Geek | There is still a light       &nb=
> sp;  |----------------------
> <br>fant+*+pobox.com
> | That shines on
> me            &=
> nbsp; 
> | Disclaimer:  I don't<br>Boston, MA     | Sh=
> ine until tomorrow, Let it be | even speak for 
> myself<br><br><br><br>-=3D T=
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Content-Type: text/html; charset="US-ASCII"


<br><font size=2 face="sans-serif">There is another point to be considered
here, which is the apparent discrimination of the CCL against those with
Hotmail, Yahoo, Gmail, etc. &nbsp;addresses.</font>
<br>
<br><font size=2 face="sans-serif">I have been a subscriber to the CCL
through various organizational email addresses for many years. &nbsp;For
a period I worked as an independent consultant and used Gmail as my business
email. &nbsp;I did not succeed in becoming a CCL subscriber using a Gmail
address, in spite of several direct pleas to the CCL administrator. &nbsp;As
soon as I joined my present company, I applied to become a CCL member and
was immediately accepted.</font>
<br>
<br><font size=2 face="sans-serif">Is there a CCL policy that denies membership
to those with Hotmail, Yahoo, Gmail, etc. &nbsp;addresses, or, at least,
deems them suspicious until proven otherwise?</font>
<br>
<br><font size=2 face="sans-serif">Paul Mathias</font>
<br>
<br>
<br>
<br>
<br>
<table width=100%>
<tr valign=top>
<td>
<td><font size=1 face="sans-serif"><b>&quot;SANDEEP KUMAR skumar23---jhem.jhu.edu&quot;
&lt;owner-chemistry-,-ccl.net&gt;</b></font>
<br><font size=1 face="sans-serif">Sent by: owner-chemistry-,-ccl.net</font>
<br><font size=1 face="sans-serif">03/23/2006 10:37 AM</font>
<br><font size=1 face="sans-serif">Please respond to &quot;CCL Subscribers&quot;</font>
<td><font size=1 face="Arial">&nbsp; &nbsp; &nbsp; &nbsp; </font>
<br><font size=1 face="sans-serif">&nbsp; &nbsp; &nbsp; &nbsp; To:
&nbsp; &nbsp; &nbsp; &nbsp;&quot;Mathias, Paul M. &quot;
&lt;paul.m.mathias-,-fluor.com&gt;</font>
<p><font size=1 face="sans-serif">&nbsp; &nbsp; &nbsp; &nbsp; cc:
&nbsp; &nbsp; &nbsp; &nbsp;</font>
<p><font size=1 face="sans-serif">&nbsp; &nbsp; &nbsp; &nbsp; Subject:
&nbsp; &nbsp; &nbsp; &nbsp;CCL: reveal your affiliation</font>
<div align=right>
<p><font size=3 color=white face="Arial">.</font></div></table>
<br>
<br>
<br><font size=2><tt>Sent to CCL by: SANDEEP KUMAR [skumar23|-|jhem.jhu.edu]<br>
Hi: <br>
<br>
Several hundred years ago, an Indian saint had said something which when
translated in English would roughly read something like this: &nbsp;Ask
the learned for wisdom, not the affiliation. <br>
<br>
I value CCL because it is open to all and often involves interesting discussions.
For example, the recent one I really liked was on the review of forcefields
for small molecules and macromolecules. &nbsp;I did not matter if the contributors
had the email address of &nbsp;Yahoo, Hotmail or an organization. I agree
with John that this a slippery path which CCL should avoid. &nbsp;As for
spam, I guess CCL administrator is already doing a wonderful job!<br>
<br>
Sincerely, <br>
Sandeep<br>
-------------------------------------------------------------------<br>
Dr. Sandeep Kumar, <br>
Associate Research Scientist, <br>
Johns Hopkins University Department of Biology, <br>
106 Mudd Hall, 3400 N. Charles Street, <br>
Baltimore, MD 21218, &nbsp;USA. <br>
Phone: 410-516-8433,<br>
Email: kumarsan%%jhu.edu.<br>
URL: &nbsp;http://myprofile.cos.com/Kumarsan.<br>
or &nbsp; &nbsp; &nbsp;https://jshare.johnshopkins.edu/skumar23/public_html/<br>
<br>
<br>
----- Original Message -----<br>
&gt; From: &quot;john furr john.furr . gmail.com&quot; &lt;owner-chemistry%%ccl.net&gt;<br>
Date: Thursday, March 23, 2006 9:18 am<br>
Subject: CCL: reveal your affiliation<br>
<br>
&gt; Sent to CCL by: &quot;john furr&quot; [john.furr++gmail.com]<br>
&gt; ------=_Part_4213_12649164.1143121458741<br>
&gt; Content-Type: text/plain; charset=ISO-8859-1<br>
&gt; Content-Transfer-Encoding: quoted-printable<br>
&gt; Content-Disposition: inline<br>
&gt; <br>
&gt; &quot;However, it would make the postings more credible if people
who have<br>
&gt; yahoo,&quot;<br>
&gt; <br>
&gt; A persons credibility should not be judged by their affiliation. &nbsp;<br>
&gt; As soon a=<br>
&gt; s<br>
&gt; we head down that path then science becomes inherently biased. &nbsp;<br>
&gt; Good scienc=<br>
&gt; e<br>
&gt; (especially computational science) can be done by any person with
a <br>
&gt; desireto learn and experiment. &nbsp;You certainly don't need to have
a <br>
&gt; position at on=<br>
&gt; e<br>
&gt; of the worlds Ivy League Universities to do quality science. &nbsp;Nor
<br>
&gt; do you<br>
&gt; need to be employed in one of the major pharmas. &nbsp;A person should
<br>
&gt; simply be<br>
&gt; judged based on the insights they bring to the discussion. &nbsp;I
do <br>
&gt; understandthat you weren't implying any of these things with your
<br>
&gt; original request.<br>
&gt; However, I feel it could be a very slippery slope to head down. &nbsp;<br>
&gt; Also as<br>
&gt; noted before many people may not be allowed to post their affiliation.<br>
&gt; <br>
&gt; John<br>
&gt; http://www.dynamol.com<br>
&gt; <br>
&gt; On 3/22/06, Andrew D. Fant fant:-:pobox.com &lt;owner-<br>
&gt; chemistry^_^ccl.net &gt;<br>
&gt; wrote:<br>
&gt; &gt;<br>
&gt; &gt; Sent to CCL by: &quot;Andrew D. Fant&quot; [ fant-x-pobox.com]<br>
&gt; &gt; Boyd, D. boyd%chem.iupui.edu wrote:<br>
&gt; &gt; &gt; Sent to CCL by: &quot;Boyd, D.&quot; [boyd]![chem.iupui.edu]<br>
&gt; &gt; &gt; Colleagues,<br>
&gt; &gt; &gt; I recommend/request that people who post on CCL include
their<br>
&gt; &gt; affiliation.<br>
&gt; &gt; &gt; I realize that because of spammers people do not want to
reveal <br>
&gt; their&gt; full particulars.<br>
&gt; &gt; &gt; However, it would make the postings more credible if people
who <br>
&gt; have&gt; yahoo,<br>
&gt; &gt; &gt; hotmail, etc. email addresses, include the university or
<br>
&gt; company they<br>
&gt; &gt; are<br>
&gt; &gt; &gt; associated with.<br>
&gt; &gt;<br>
&gt; &gt; Many people are employed in situations where they are not allowed
to<br>
&gt; &gt; speak/post<br>
&gt; &gt; in a public setting with reference to their employment status
<br>
&gt; without&gt; clearing<br>
&gt; &gt; it with their public relations or corporate communications<br>
&gt; &gt; departments. &nbsp;This is<br>
&gt; &gt; to make management feel secure that nobody is representing <br>
&gt; themselves in<br>
&gt; &gt; any way<br>
&gt; &gt; as an official spokesperson for the institution. &nbsp; I don't
think <br>
&gt; that we<br>
&gt; &gt; need<br>
&gt; &gt; affiliation information to judge the merits of a posting/email
in <br>
&gt; any&gt; case. &nbsp;If<br>
&gt; &gt; someone makes a statement that sounds outlandish, the claims
<br>
&gt; should be<br>
&gt; &gt; examined<br>
&gt; &gt; and validated by the same standards whether it comes from <br>
&gt; wwcc.cc.wy.us,&gt; tripos.com, phar.cam.ac.uk, or ru.yahoo.com. &nbsp;<br>
&gt; Likewise, I would hope my<br>
&gt; &gt; opinions<br>
&gt; &gt; here are considered on their merits and my past participation,
<br>
&gt; rather the=<br>
&gt; n<br>
&gt; &gt;<br>
&gt; &gt; whether my circumstances require me to be discreet about my current<br>
&gt; &gt; affiliation.<br>
&gt; &gt;<br>
&gt; &gt; Andy<br>
&gt; &gt;<br>
&gt; &gt; Andrew Fant &nbsp; &nbsp;| And when the night is cloudy &nbsp;
&nbsp;| This space to let<br>
&gt; &gt; Molecular Geek | There is still a light &nbsp; &nbsp; &nbsp;
&nbsp; &nbsp;|----------------<br>
&gt; ------<br>
&gt; &gt; fant+*+pobox.com | That shines on me &nbsp; &nbsp; &nbsp; &nbsp;
&nbsp; &nbsp; &nbsp; | Disclaimer: &nbsp;<br>
&gt; I don't<br>
&gt; &gt; Boston, MA &nbsp; &nbsp; | Shine until tomorrow, Let it be |
even speak for <br>
&gt; myself&gt;<br>
&gt; &gt;<br>
&gt; &gt;<br>
&gt; &gt; -=3D This is automatically added to each message by the mailing
<br>
&gt; script =<br>
&gt; =3D-&gt;<br>
&gt; &gt; Search Messages: http://www.ccl.net/htdig &nbsp; (login: ccl,
<br>
&gt; Password: search=<br>
&gt; )&gt;<br>
&gt; &gt;<br>
&gt; &gt;<br>
&gt; &gt;<br>
&gt; <br>
&gt; ------=_Part_4213_12649164.1143121458741<br>
&gt; Content-Type: text/html; charset=ISO-8859-1<br>
&gt; Content-Transfer-Encoding: quoted-printable<br>
&gt; Content-Disposition: inline<br>
&gt; <br>
&gt; &amp;quot;However, it would make the postings more credible if people
<br>
&gt; who have =<br>
&gt; yahoo,&amp;quot;&lt;br&gt;<br>
&gt; &lt;br&gt;<br>
&gt; A persons credibility should not be judged by their affiliation. <br>
&gt; As soon as we head down that path then science becomes inherently<br>
&gt; biased. &nbsp;Good science (especially computational science) can
be<br>
&gt; done by any person with a desire to learn and experiment. &nbsp;You<br>
&gt; certainly don't need to have a position at one of the worlds Ivy <br>
&gt; LeagueUniversities to do quality science. &nbsp;Nor do you need to
be<br>
&gt; employed in one of the major pharmas. &nbsp;A person should simply
be<br>
&gt; judged based on the insights they bring to the discussion. &nbsp;I
do<br>
&gt; understand that you weren't implying any of these things with your<br>
&gt; original request. &nbsp;However, I feel it could be a very slippery<br>
&gt; slope to head down. &nbsp;Also as noted before many people may not
be<br>
&gt; allowed to post their affiliation. &nbsp;&lt;br&gt;<br>
&gt; &lt;br&gt;<br>
&gt; John&lt;br&gt;<br>
&gt; http://www.dynamol.com&quot;&gt;http://www.dynamol.com&lt;br&gt;&lt;br&gt;&lt;div&gt;&lt;=<br>
&gt; span class=3D&quot;gmail_quote&quot;&gt;On 3/22/06, &lt;b <br>
&gt; class=3D&quot;gmail_sendername&quot;&gt;Andrew= D. Fant fant:-:http://pobox.com&quot;
<br>
&gt; target=3D&quot;_blank&quot; onclick=3D&quot;r=<br>
&gt; eturn top.js.OpenExtLink(window,event,this)&quot;&gt;<br>
&gt; pobox.com&lt;/b&gt; &lt;owner-chemistry^_^ccl.net&quot; target=3D&quot;=<br>
&gt; _blank&quot; onclick=3D&quot;return <br>
&gt; top.js.OpenExtLink(window,event,this)&quot;&gt;owner-chem=<br>
&gt; istry^_^ccl.net<br>
&gt; &amp;gt; wrote:&lt;/span&gt;&lt;blockquote class=3D&quot;gmail_quote&quot;
style=3D&quot;border-<br>
&gt; lef=t: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; <br>
&gt; padding-left: 1=<br>
&gt; ex;&quot;&gt;Sent to CCL by: &amp;quot;Andrew D. Fant&amp;quot; [http://fant-x-p=<br>
&gt; obox.com&quot; target=3D&quot;_blank&quot; onclick=3D&quot;return
<br>
&gt; top.js.OpenExtLink(window,eve=nt,this)&quot;&gt;<br>
&gt; <br>
&gt; fant-x-pobox.com]&lt;br&gt;Boyd, D. boyd%chem.iupui.edu wrote:&lt;br&gt;&amp;gt;
<br>
&gt; Sent t=<br>
&gt; o CCL by: &amp;quot;Boyd, D.&amp;quot; [boyd]![http://chem.iupui.edu&quot;
ta=<br>
&gt; rget=3D&quot;_blank&quot; onclick=3D&quot;return <br>
&gt; top.js.OpenExtLink(window,event,this)&quot;&gt;ch=em.iupui.edu<br>
&gt; ]&lt;br&gt;&amp;gt; Colleagues,&lt;br&gt;&amp;gt; I recommend/request
that people who <br>
&gt; post =<br>
&gt; on CCL include their affiliation.<br>
&gt; &lt;br&gt;&amp;gt; I realize that because of spammers people do not
want to <br>
&gt; reveal th=<br>
&gt; eir full particulars.&lt;br&gt;&amp;gt; However, it would make the
postings <br>
&gt; more cred=<br>
&gt; ible if people who have yahoo,&lt;br&gt;&amp;gt; hotmail, etc. email
<br>
&gt; addresses, inclu=<br>
&gt; de the university or company they are<br>
&gt; &lt;br&gt;&amp;gt; associated with.&lt;br&gt;&lt;br&gt;Many people
are employed in <br>
&gt; situations whe=<br>
&gt; re they are not allowed to speak/post&lt;br&gt;in a public setting
with <br>
&gt; reference= to their employment status without clearing&lt;br&gt;it
with <br>
&gt; their public relati=<br>
&gt; ons or corporate communications departments. &nbsp;This is<br>
&gt; &lt;br&gt;to make management feel secure that nobody is representing
<br>
&gt; themselves i=<br>
&gt; n any way&lt;br&gt;as an official spokesperson for the institution.
&nbsp; I=<br>
&gt; don't think that we need&lt;br&gt;affiliation information to judge
the <br>
&gt; merits of=<br>
&gt; a posting/email in any case. &nbsp;If<br>
&gt; &lt;br&gt;someone makes a statement that sounds outlandish, the claims
<br>
&gt; should be =<br>
&gt; examined&lt;br&gt;and validated by the same standards whether it comes
<br>
&gt; from ef=3D&quot;http://wwcc.cc.wy.us&quot; target=3D&quot;_blank&quot;
<br>
&gt; onclick=3D&quot;return top.js.Open=<br>
&gt; ExtLink(window,event,this)&quot;&gt;<br>
&gt; wwcc.cc.wy.us,&lt;br&gt;http://tripos.com&quot; target=3D&quot;_blank&quot;
oncli=<br>
&gt; ck=3D&quot;return top.js.OpenExtLink(window,event,this)&quot;&gt;<br>
&gt; tripos.com, http://phar.cam.ac.uk&quot; target=3D&quot;_blank&quot;
onclick=<br>
&gt; =3D&quot;return top.js.OpenExtLink(window,event,this)&quot;&gt;phar.cam.ac.uk,
<br>
&gt; or &lt;a=<br>
&gt; href=3D&quot;http://ru.yahoo.com&quot; target=3D&quot;_blank&quot;
onclick=3D&quot;return <br>
&gt; top.js.Op=enExtLink(window,event,this)&quot;&gt;<br>
&gt; ru.yahoo.com. &nbsp;Likewise, I would hope my opinions&lt;br&gt;here
are=<br>
&gt; considered on their merits and my past participation, rather then<br>
&gt; &lt;br&gt;whether my circumstances require me to be discreet about
my <br>
&gt; current aff=<br>
&gt; iliation.&lt;br&gt;&lt;br&gt;Andy&lt;br&gt;&lt;br&gt;Andrew Fant &nbsp;
&nbsp;| And when =<br>
&gt; the night is cloudy &nbsp; &nbsp;| This space to let&lt;br&gt;Molecular=<br>
&gt; Geek | There is still a light &nbsp; &nbsp; &nbsp; &amp;nb=<br>
&gt; sp; &nbsp;|----------------------<br>
&gt; &lt;br&gt;fant+*+pobox.com<br>
&gt; | That shines on<br>
&gt; me &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&amp;=<br>
&gt; nbsp; <br>
&gt; | Disclaimer: &nbsp;I don't&lt;br&gt;Boston, MA &nbsp; &nbsp; | Sh=<br>
&gt; ine until tomorrow, Let it be | even speak for <br>
&gt; myself&lt;br&gt;&lt;br&gt;&lt;br&gt;&lt;br&gt;-=3D T=<br>
&gt; his is automatically added to each message by the mailing script <br>
&gt; =3D-&lt;br&gt;To=<br>
&gt; recover the email address of the author of the message, please change<br>
&gt; &lt;br&lt;br&gt;l=<br>
&gt; ook up the X-Original-From: line in the mail header.&lt;br&gt;&lt;br&gt;E-mail
<br>
&gt; to subsc=<br>
&gt; ribers: CHEMISTRY^_^ccl.net&quot; target=3D&quot;_blank&quot; onclick=3D&quot;r=<br>
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&gt; &lt;br&gt; &nbsp; &nbsp; &nbsp;http://www.ccl.net/cgi-b=<br>
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--=_alternative 007AC6038825713A_=--


From owner-chemistry@ccl.net Thu Mar 23 21:47:00 2006
From: "Jan Labanowski janl{}speakeasy.net" <owner-chemistry*_*server.ccl.net>
To: CCL
Subject: CCL: reveal your affiliation
Message-Id: <-31306-060323214450-31287-gxeahQjuLmkszjMomR8L4A*_*server.ccl.net>
X-Original-From: "Jan Labanowski" <janl*|*speakeasy.net>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset="iso-8859-1"
Date: Fri, 24 Mar 2006 02:44:45 +0000
MIME-Version: 1.0


Sent to CCL by: "Jan Labanowski" [janl[a]speakeasy.net]

Paul Mathias writes:
> There is another point to be considered here, which is the apparent
> discrimination of the CCL against those with Hotmail, Yahoo, Gmail, etc.
> addresses.
>
> I have been a subscriber to the CCL through various organizational email
> addresses for many years.  For a period I worked as an independent
> consultant and used Gmail as my business email.  I did not succeed in
> becoming a CCL subscriber using a Gmail address, in spite of several
> direct pleas to the CCL administrator.  As soon as I joined my present
> company, I applied to become a CCL member and was immediately accepted.
>
> Is there a CCL policy that denies membership to those with Hotmail,
> Yahoo, Gmail, etc.  addresses, or, at least, deems them suspicious until
> proven otherwise?

Paul,
A FEW YEARS AGO, I was insisting that people subscribe from some
institutional address to protect the list against spam. At that time,
the Yahoos, Hotmails, AOLs, and the like were giving anonymous accounts
to people and did not do ANY POLICING OF SPAM coming from these accounts.
Once people took action, and started to block them, they got their act
together, though I still get a lot of spam from some of them.
This is long time gone. Moreover, I had completely redone the way CCL
is distributed, and keep my fingers crossed that it is safe for a while.
You do not get much spam (though what is spam is in the eye of beholder)
> from CCL, do you?

In addition, many tools for fighting spam become available that were not
available before. I use them, and probably should write about my
experience on this, since I seem to be doing pretty decent job.
Each day CCL gets about 6 thousands spam messages, and you do not
get most of it, do you?

I do not insist on institutional addresses anymore because:
1) Yes... with lawyers chasing on the Internet ambulance, many people
   do not subscribe from their institutional addresses. They are
   specifically asked not to or asked to work elsewhere.

2) What is an institutional address anymore? You can register a domain
   of your choice (except for .edu and few others TLDs) for 9 bucks/year
   on godaddy.com.

3) The spam filters and the requirement that EACH MESSAGE IS CONFIRMED
   makes it less likely that spam will reach CCL, though there is no
   way to guarantee it. The best minds are working on ways to beat
   our protections, and by necessity we are in a reactive mode and
   can defend ourselves only when we know the details of the attack.

So, in short... I do not check or care what address people use to
subscribe to CCL. If you have problem subscribing, you better
check your SPAMBOX for CCL confirmation requests or check your
SPAM filter setting. CCL does not care what is the email address
of the subscriber, as long as it is valid.

Note... CCL uses spam filters, and reject your mail if it is suspicious.
You can still use the Mail Sending web form to send email to CCL.
The common problem with your mail being rejected is that you have
a BAD OUTGOING SMTP SERVER set in your mail composing gizmo. For example,
you go with your laptop to StarBucks and send mail from the random
IP address that you get from the wireless DHCP server. This is NO GO
since spam filters reject the dynamic IP addresses routinely. You should
always send outgoing mail via the OFFICIAL SMTP server of your Internet
Service Provider. Read their instructions and comply if you want to have
your mail messages delivered rather than junked by spam filters.
Also, support these ISPs that care what gets out from their network.
If they do not care, their IP addresses end up on black lists and you
sending mail to junk boxes. If they look bad, you look bad...

Practical note: If you have problems with sending your mail to CCL,
check if your IP address and domain is present on the CCL blacklist.
The blacklist is available at:and IS VERY, VERY, LOOOONG, and updated quite often. If you find
your machine there, read the top of the file, and you will know
what to do...

Jan
Your shadow admin...