From owner-chemistry@ccl.net Wed Jun  6 02:19:00 2007
From: "Mingyue Zheng myzheng././.gmail.com" <owner-chemistry/./server.ccl.net>
To: CCL
Subject: CCL: Papers on Quantum Chemical Topology
Message-Id: <-34422-070606020029-12498-aERxtpUKX4xYXe9TyM+ojQ/./server.ccl.net>
X-Original-From: "Mingyue Zheng" <myzheng*gmail.com>
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Sent to CCL by: "Mingyue Zheng" [myzheng-$-gmail.com]
------=_Part_14967_18064149.1181105807054
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The Wiley's book "Quantum Medicinal Chemistry" by Paolo Carloni and Frank
Alber may be what you want.

Good Luck!


2007/6/6, Mustafa Hussein mustafa.hussein86]|[yahoo.com <
owner-chemistry**ccl.net>:
>
>
> Sent to CCL by: "Mustafa  Hussein" [mustafa.hussein86!^!yahoo.com]
> Hi,
>
> I am preparing a review article on the theory of Atoms in Molecules and
> Quantum Chemical Topology (QCT). I need some papers on the application of
> QCT to biomacromolecular properties.
>
> Any help is appreciated.
>
> Thanks,
>
> Mustafa>
>
>
>


-- 
--------------------------------------------------------------------------------
Dr. Mingyue Zheng
Research Associate, Drug Discovery and Design Center (DDDC)
Box 1201, Shanghai Institute of Materia Medica.
555 Rd. Zuchongzhi, Shanghai, China
Tel:      86-021-50806600-1201
Web:   http://dddc.ac.cn
Email: myzheng**mail.shcnc.ac.cn

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<div>The&nbsp;Wiley&#39;s book &quot;Quantum Medicinal Chemistry&quot; by Paolo Carloni and Frank Alber&nbsp;may be what you want.</div>
<div>&nbsp;</div>
<div>Good&nbsp;Luck!<br><br>&nbsp;</div>
<div><span class="gmail_quote">2007/6/6, Mustafa Hussein mustafa.hussein86]|[<a href="http://yahoo.com">yahoo.com</a> &lt;<a href="mailto:owner-chemistry**ccl.net">owner-chemistry**ccl.net</a>&gt;:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br>Sent to CCL by: &quot;Mustafa&nbsp;&nbsp;Hussein&quot; [mustafa.hussein86!^!yahoo.com]<br>Hi,<br><br>I am preparing a review article on the theory of Atoms in Molecules and Quantum Chemical Topology (QCT). I need some papers on the application of QCT to biomacromolecular properties.
<br><br>Any help is appreciated.<br><br>Thanks,<br><br>Mustafa<br><br><br><br<br<br<br<br><br>E-mail to subscribers: <a href="mailto:CHEMISTRY**ccl.net">CHEMISTRY**ccl.net</a> or use:
<br>&nbsp;&nbsp;&nbsp;&nbsp; <a href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br><br>E-mail to administrators: <a href="mailto:CHEMISTRY-REQUEST**ccl.net">CHEMISTRY-REQUEST**ccl.net</a>
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</a><br><br>Before posting, check wait time at: <a href="http://www.ccl.net">http://www.ccl.net</a><br><br>Job: <a href="http://www.ccl.net/jobs">http://www.ccl.net/jobs</a><br>Conferences: <a href="http://server.ccl.net/chemistry/announcements/conferences/">
http://server.ccl.net/chemistry/announcements/conferences/</a><br><br>Search Messages: <a href="http://www.ccl.net/htdig">http://www.ccl.net/htdig</a>&nbsp;&nbsp;(login: ccl, Password: search)<br><br<br>&nbsp;&nbsp;&nbsp;&nbsp; <a href="http://www.ccl.net/spammers.txt">http://www.ccl.net/spammers.txt</a><br><br>RTFI: <a href="http://www.ccl.net/chemistry/aboutccl/instructions/">http://www.ccl.net/chemistry/aboutccl/instructions/
</a><br><br<br><br><br><br></blockquote></div><br><br clear="all"><br>-- <br>--------------------------------------------------------------------------------
<br>Dr. Mingyue Zheng<br>Research Associate, Drug Discovery and Design Center (DDDC)<br>Box 1201, Shanghai Institute of Materia Medica.<br>555 Rd. Zuchongzhi, Shanghai, China<br>Tel:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;86-021-50806600-1201<br>Web:&nbsp;&nbsp; <a href="http://dddc.ac.cn">
http://dddc.ac.cn</a><br>Email: <a href="mailto:myzheng**mail.shcnc.ac.cn">myzheng**mail.shcnc.ac.cn</a> 

------=_Part_14967_18064149.1181105807054--


From owner-chemistry@ccl.net Wed Jun  6 09:08:00 2007
From: "Curt Breneman brenec..rpi.edu" <owner-chemistry_._server.ccl.net>
To: CCL
Subject: CCL: Papers on Quantum Chemical Topology
Message-Id: <-34423-070606085717-17934-wMoI+bS1h8nuKO/AAWVkmg_._server.ccl.net>
X-Original-From: Curt Breneman <brenec!A!rpi.edu>
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Sent to CCL by: Curt Breneman [brenec : rpi.edu]
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Dear Mustafa,

You may also wish to look at some chapters in Cherif Matta and Russell 
Boyd's  book:


    The Quantum Theory of Atoms in Molecules
    <http://www3.interscience.wiley.com/cgi-bin/bookhome/114207328/>

Published Online: 26 Apr 2007

Editor(s): Prof. Chérif F. Matta, Prof. Russell J. Boyd

Print ISBN: 9783527307487    Online ISBN: 9783527610709

Copyright © 2007 Wiley-VCH Verlag GmbH & Co. KGaA

See: 
http://www3.interscience.wiley.com/cgi-bin/summary/114228620/SUMMARY?CRETRY=1&SRETRY=0

Sincerely,

Curt Breneman
RPI Chemistry
Director, RECCR Cheminformatics Center



Mingyue Zheng myzheng.[].gmail.com wrote:

> The Wiley's book "Quantum Medicinal Chemistry" by Paolo Carloni and 
> Frank Alber may be what you want.
>  
> Good Luck!
>
>  
> 2007/6/6, Mustafa Hussein mustafa.hussein86]|[yahoo.com 
> <http://yahoo.com> <owner-chemistry a ccl.net 
> <mailto:owner-chemistry%20a%20ccl.net>>:
>
>
>     Sent to CCL by: "Mustafa  Hussein" [mustafa.hussein86!^!yahoo.com]
>     Hi,
>
>     I am preparing a review article on the theory of Atoms in
>     Molecules and Quantum Chemical Topology (QCT). I need some papers
>     on the application of QCT to biomacromolecular properties.
>
>     Any help is appreciated.
>
>     Thanks,
>
>     Mustafa
>
>
>
>
>
>
>
>
>     E-mail to subscribers: CHEMISTRY a ccl.net
>     <mailto:CHEMISTRY%20a%20ccl.net> or use:>
>     E-mail to administrators: CHEMISTRY-REQUEST a ccl.net
>     <mailto:CHEMISTRY-REQUEST%20a%20ccl.net> or use>     <http://www.ccl.net/chemistry/sub_unsub.shtml>     Conferences:
>     http://server.ccl.net/chemistry/announcements/conferences/
>
>     Search Messages: http://www.ccl.net/htdig  (login: ccl, Password:
>     search)>     <http://www.ccl.net/chemistry/aboutccl/instructions/>
>
>
>
>
>
>
>
>
> -- 
> -------------------------------------------------------------------------------- 
>
> Dr. Mingyue Zheng
> Research Associate, Drug Discovery and Design Center (DDDC)
> Box 1201, Shanghai Institute of Materia Medica.
> 555 Rd. Zuchongzhi, Shanghai, China
> Tel:      86-021-50806600-1201
> Web:   http://dddc.ac.cn
> Email: myzheng a mail.shcnc.ac.cn <mailto:myzheng%20a%20mail.shcnc.ac.cn> 


--------------070108080408020308060304
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Dear Mustafa,<br>
<br>
You may also wish to look at some chapters in Cherif Matta and Russell
Boyd's&nbsp; book:
<h2><a
 href="http://www3.interscience.wiley.com/cgi-bin/bookhome/114207328/">The
Quantum Theory of Atoms in Molecules</a></h2>
<p><strong>Published Online: </strong>26 Apr 2007</p>
<p><strong>Editor(s): </strong>Prof. Ch&eacute;rif F. Matta, Prof. Russell J.
Boyd</p>
<p><strong>Print ISBN:</strong> 9783527307487&nbsp;&nbsp;&nbsp; <strong>Online ISBN:</strong>
9783527610709</p>
<p>Copyright &copy; 2007 Wiley-VCH Verlag GmbH &amp; Co. KGaA<br>
</p>
<p>See:
<a class="moz-txt-link-freetext" href="http://www3.interscience.wiley.com/cgi-bin/summary/114228620/SUMMARY?CRETRY=1&SRETRY=0">http://www3.interscience.wiley.com/cgi-bin/summary/114228620/SUMMARY?CRETRY=1&amp;SRETRY=0</a><br>
</p>
<p>Sincerely,<br>
</p>
<p>Curt Breneman<br>
RPI Chemistry<br>
Director, RECCR Cheminformatics Center<br>
<br>
</p>
<br>
<br>
Mingyue Zheng <a class="moz-txt-link-abbreviated" href="mailto:myzheng.[].gmail.com">myzheng.[].gmail.com</a> wrote:<br>
<blockquote type="cite"
 cite="mid-id%233d8-34422-070606020029-12498-4RlLy+AQbCub5wbwZT6Myw[]server.ccl.net">
  <div>The&nbsp;Wiley's book "Quantum Medicinal Chemistry" by Paolo Carloni
and Frank Alber&nbsp;may be what you want.</div>
  <div>&nbsp;</div>
  <div>Good&nbsp;Luck!<br>
  <br>
&nbsp;</div>
  <div><span class="gmail_quote">2007/6/6, Mustafa Hussein
mustafa.hussein86]|[<a href="http://yahoo.com">yahoo.com</a> &lt;<a
 href="mailto:owner-chemistry%20a%20ccl.net">owner-chemistry a ccl.net</a>&gt;:</span>
  <blockquote class="gmail_quote"
 style="border-left: 1px solid rgb(204, 204, 204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;"><br>
Sent to CCL by: "Mustafa&nbsp;&nbsp;Hussein" [mustafa.hussein86!^!yahoo.com]<br>
Hi,<br>
    <br>
I am preparing a review article on the theory of Atoms in Molecules and
Quantum Chemical Topology (QCT). I need some papers on the application
of QCT to biomacromolecular properties.
    <br>
    <br>
Any help is appreciated.<br>
    <br>
Thanks,<br>
    <br>
Mustafa<br>
    <br>
    <br>
    <br ="">
    <br ="">
    <br ="">
    <br ="">
    <br>
    <br>
E-mail to subscribers: <a href="mailto:CHEMISTRY%20a%20ccl.net">CHEMISTRY
a ccl.net</a> or use:
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&nbsp;&nbsp;&nbsp;&nbsp; <a href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br>
    <br>
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 href="mailto:CHEMISTRY-REQUEST%20a%20ccl.net">CHEMISTRY-REQUEST a
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Before posting, check wait time at: <a href="http://www.ccl.net">http://www.ccl.net</a><br>
    <br>
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  </blockquote>
  </div>
  <br>
  <br clear="all">
  <br>
-- <br>
--------------------------------------------------------------------------------
  <br>
Dr. Mingyue Zheng<br>
Research Associate, Drug Discovery and Design Center (DDDC)<br>
Box 1201, Shanghai Institute of Materia Medica.<br>
555 Rd. Zuchongzhi, Shanghai, China<br>
Tel:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;86-021-50806600-1201<br>
Web:&nbsp;&nbsp; <a href="http://dddc.ac.cn">
http://dddc.ac.cn</a><br>
Email: <a href="mailto:myzheng%20a%20mail.shcnc.ac.cn">myzheng a
mail.shcnc.ac.cn</a> </blockquote>
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--------------070108080408020308060304--


From owner-chemistry@ccl.net Wed Jun  6 10:34:00 2007
From: "Sergio Emanuel Galembeck segalemb++usp.br" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL: Papers on Quantum Chemical Topology
Message-Id: <-34424-070606094819-6706-eweoPQ4mxV9h+Dmg60VHBA(0)server.ccl.net>
X-Original-From: Sergio Emanuel Galembeck <segalemb[]usp.br>
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Sent to CCL by: Sergio Emanuel Galembeck [segalemb.(~).usp.br]
Dear Mustafa,

     I recomend that you search some papers of Cherif Matta and
of Paul Popelier. Also, take a look in:

    - Freitas, RF; Galembeck, SE, Chem. Phys. Lett., 2006, 423, 131-137.
    - Freitas, RF; Galembeck, SE, J. Phys. Chem. B, 2006, 110, 21287-21298.

          Hope this help you,

                      Sergio

Citando "Mustafa Hussein mustafa.hussein86]|[yahoo.com"  
<owner-chemistry(~)ccl.net>:

>
> Sent to CCL by: "Mustafa  Hussein" [mustafa.hussein86!^!yahoo.com]
> Hi,
>
> I am preparing a review article on the theory of Atoms in Molecules   
> and Quantum Chemical Topology (QCT). I need some papers on the   
> application of QCT to biomacromolecular properties.
>
> Any help is appreciated.
>
> Thanks,
>
> Mustafa>
>
>
>


From owner-chemistry@ccl.net Wed Jun  6 12:45:01 2007
From: "david.giesen]-[kodak.com" <owner-chemistry|*|server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian/PCM/chemical shifts
Message-Id: <-34425-070606103907-23115-7wWqb9xkktPyXWqf4AqiQw|*|server.ccl.net>
X-Original-From: david.giesen---kodak.com
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Sent to CCL by: david.giesen:_:kodak.com
Grigoriy -

You may find the data and discussion in the paper below to be useful.  It 
demonstrates that most QM methods (HF/DFT/MP2) even with small basis sets 
give NMR shifts that correlate very well with experiment.  Correction 
factors are given in the paper for many methods that should allow you to 
get good quantitative agreement with experiment.  Your chosen method 
(B3LYP/6-311G**) is unfortunately not included, but many similar methods 
are.

Using the method in this paper, very fast B3LYP/MIDI! calculations give 
13C NMR shift results that agree as well or better with experiment than 
many more computationally expensive calculations.

Giesen and Zumbulyadis, Phys. Chem. Chem. Phys., 2002, 4, 5498-5507

Dave Giesen

PS - Unfortunately, the labels on Table 2 didn't make it into the final 
copy - the columns indicate the geometry optimization method and the rows 
indicate the method used to calculate the chemical shift.




"Grigoriy Zhurko reg_zhurko ~~ chemcraftprog.com" 
<owner-chemistry||ccl.net> 
Sent by: owner-chemistry||ccl.net
06/04/2007 11:58 PM
Please respond to
"CCL Subscribers" <chemistry||ccl.net>


To
"Giesen, David J " <david.giesen||kodak.com>
cc

Subject
CCL: Gaussian/PCM/chemical shifts







Sent to CCL by: Grigoriy Zhurko [reg_zhurko]![chemcraftprog.com]
  I suppose, using the calculated TMS carbon shielding is not correct 
enough, because the TMS standard used in the experiment is not in the gas 
phase. I tried to calculate the TMS shielding at same level of theory as 
investigated molecules, but their chemical shifts with it were still 
overestimated.


> Dear Grigoriy Zhurko,

> in [1] we discuss the importance of the TMS 13C reference values.
> Please find a paragraph which might be relevant to your message
> cited below:

> [..]
> Particular attention should be paid to the case of 
> TMS. For this reference compound in proton and 
> carbon-13 NMR, two structures of Td symmetry exist, 
> as illustrated in ¨gure 1. The one in ¨gure 1 (a) is the 
> global minimum, and the structure of ¨gure 1 (b) is a 
> fourth-order saddle point. The energy of the global 
> minimum (¨gure 1 (a)) , taken from the B3LYP calcula- 
> tion, is 27. 3 kJ molÁ1 lower than the one for structure 
> (b). The corresponding absolute shielding value for 13 C 
> is 200.3 ppm. We chose this value as the reference chemi- 
> cal shift as it corresponds to a true minimum structure. 
> Cheeseman et al. [49] report a 13 C chemical shielding of 
> 195.1 ppm for TMS, whereas our calculation for the 
> non-minimum structure of ¨gure 1 (b) reproduced a 
> value of 195.4 ppm.
> [..]

> There is a little more discussion in the paper.
> Regards,
> Marc Baaden

> [1]  M. Baaden, P. Granger and A. Strich; "Dependence of isotropic
>      shift averages and nuclear shielding tensors on the internal
>      rotation of the functional group X about the C-X bond in seven
>      simple vinylic derivatives H2C=CH-X.", Mol. Phys., 98, 2000,
>      329-342.


>>>> "Grigoriy Zhurko reg_zhurko(!)chemcraftprog.com" said:
 >>> 
 >>> Sent to CCL by: Grigoriy Zhurko [reg_zhurko]*[chemcraftprog.com]
 >>>   This problem is interesting for me too. I have found that computed 
gas-ph
>      ase 13C chemical shifts (GIAO B3LYP/6-311G(D,P)) correlate very 
well with
>      the experiment (in CCl4), but the computed values of chemical 
shifts are s
>      ignificantly overestimated. Maybe the problem is in the reference 
value fo
>      r converting isotropic shielding into chemical shifts (e.g. with 
TMS). Wha
>      t value of the TMS shielding on carbon should be used?


  Sincerely,
  Grigoriy Zhurko.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 Wed Jun  6 15:01:00 2007
From: "barry.hardy.===.tiscali.ch" <owner-chemistry===server.ccl.net>
To: CCL
Subject: CCL: Drug Discovery Workshop, Oxford, September 10-14
Message-Id: <-34426-070606124249-27689-hfN7HZ/8nwubscc8pMREtA===server.ccl.net>
X-Original-From: <barry.hardy-$-tiscali.ch>
Content-Disposition: inline
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Date: Wed, 06 Jun 2007 18:42:34 +0200
MIME-Version: 1.0


Sent to CCL by: [barry.hardy*tiscali.ch]
I am pleased to announce that we will be holding the hands-on eCheminfo
Drug Discovery Workshop week a second time this year in Oxford the week
of 10-14 September. First option on places will go to the waiting list from
the June workshop but there nevertheless still are additional places available.
If interested in attending, please see links below for further information.

best regards
Barry Hardy
Community of Practice Manager
Douglas Connect
Switzerland
Tel: +41 61 851 0170

Latest Advances in Drug Discovery Design & Planning Methods
a Hands-on 5 Day eCheminfo Advanced Training Workshop Week

25-29 June 2007 (registration closed) AND 10-14 September 2007

Chemistry Research Laboratory, Oxford University, Oxford, UK

Brochure: http://www.douglasconnect.com/files/eChemProgramOxford07-Sept-v1web.PDF
Abstracts and Bios on Website: http://echeminfo.colayer.net/COMTY_training
Photos from Class of 2006: http://www.echeminfo.com/COMTY_oxfordphotos06
Feedback from Class of 2006: http://www.echeminfo.com/COMTY_oxfordfeedback06


From owner-chemistry@ccl.net Wed Jun  6 16:14:00 2007
From: "Yousef Sharifi ysharifi]-[gmail.com" <owner-chemistry.:.server.ccl.net>
To: CCL
Subject: CCL: 0 0 0 1 surface
Message-Id: <-34427-070606160744-27428-i0w3KkeuTUPZQ3XzF8ERow.:.server.ccl.net>
X-Original-From: "Yousef  Sharifi" <ysharifi|gmail.com>
Date: Wed, 6 Jun 2007 16:07:40 -0400


Sent to CCL by: "Yousef  Sharifi" [ysharifi[*]gmail.com]
I need a software to clevae [0 0 0 1] surface, any suggestion?


From owner-chemistry@ccl.net Wed Jun  6 16:49:00 2007
From: "Yousef Sharifi ysharifi#,#gmail.com" <owner-chemistry(!)server.ccl.net>
To: CCL
Subject: CCL: Periodic system to non-periodic
Message-Id: <-34428-070606161033-27743-FkCz/tYjyjhwyw8TFGyrIg(!)server.ccl.net>
X-Original-From: "Yousef  Sharifi" <ysharifi-.-gmail.com>
Date: Wed, 6 Jun 2007 16:10:30 -0400


Sent to CCL by: "Yousef  Sharifi" [ysharifi{:}gmail.com]
When you convert a periodic structure to a non periodic structure is it necessary to add hydrogen atoms to the structure? if yes, consider GaAs[001] surface, Do I need to add hydrogen atoms to Ga or As? if yes how many atoms? Is there any rule for it?

Thanks


From owner-chemistry@ccl.net Wed Jun  6 17:24:00 2007
From: "Mauricio Esguerra esguerra++rci.rutgers.edu" <owner-chemistry-*-server.ccl.net>
To: CCL
Subject: CCL: Papers on Quantum Chemical Topology
Message-Id: <-34429-070606124402-27886-fbHvn1kyfXel/BuO7rteQg-*-server.ccl.net>
X-Original-From: Mauricio Esguerra <esguerra|*|rci.rutgers.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Date: Wed, 6 Jun 2007 11:38:06 -0400 (EDT)
MIME-Version: 1.0


Sent to CCL by: Mauricio Esguerra [esguerra:_:rci.rutgers.edu]

I would recommend Mezey's work.
For example:

A topological analysis of molecular shape and structure
Zbigniew Zimpel, Paul G. Mezey
International Journal of Quantum Chemistry, Vol. 59, 379-390 (1996)


Good Luck,

Mauricio

P.S. Remember that:

Let X be any set and let T be a family of subsets of X. Then T is a 
topology on X if

    1. Both the empty set and X are elements of T.
    2. Any union of elements of T is an element of T.
    3. Any intersection of finitely many elements of T is an element of T.

If T is a topology on X, then X together with T is called a topological 
space.



On Wed, 6 Jun 2007, Sergio Emanuel Galembeck segalemb++usp.br wrote:

>
> Sent to CCL by: Sergio Emanuel Galembeck [segalemb. _ .usp.br]
> Dear Mustafa,
>
>   I recomend that you search some papers of Cherif Matta and
> of Paul Popelier. Also, take a look in:
>
>  - Freitas, RF; Galembeck, SE, Chem. Phys. Lett., 2006, 423, 131-137.
>  - Freitas, RF; Galembeck, SE, J. Phys. Chem. B, 2006, 110, 21287-21298.
>
>        Hope this help you,
>
>                    Sergio
>
> Citando "Mustafa Hussein mustafa.hussein86]|[yahoo.com" 
> <owner-chemistry()ccl.net>:
>
>> 
>> Sent to CCL by: "Mustafa  Hussein" [mustafa.hussein86!^!yahoo.com]
>> Hi,
>> 
>> I am preparing a review article on the theory of Atoms in Molecules  and 
>> Quantum Chemical Topology (QCT). I need some papers on the  application of 
>> QCT to biomacromolecular properties.
>> 
>> Any help is appreciated.
>> 
>> Thanks,
>> 
>> Mustafahttp://www.ccl.net/chemistry/sub_unsub.shtml>
> Job: http://www.ccl.net/jobsConferences: 
> http://server.ccl.net/chemistry/announcements/conferences/>
>
>


From owner-chemistry@ccl.net Wed Jun  6 20:51:00 2007
From: "M K Creber mary.creber||rmc.ca" <owner-chemistry%%server.ccl.net>
To: CCL
Subject: CCL: Using Metals with AutoDockTools
Message-Id: <-34430-070606160940-27633-SNVYbEydnRdCr0LeodD5Wg%%server.ccl.net>
X-Original-From: "M K Creber" <mary.creber/./rmc.ca>
Date: Wed, 6 Jun 2007 16:09:36 -0400


Sent to CCL by: "M K Creber" [mary.creber|,|rmc.ca]
I am a new user to AutoDock (version 3.0.5), currently attempting to use the GUI AutoDockTools to set up, launch and analyze AutoDockruns.  My macromolecule of interest, MMP-2 (Gelatinase-a) contains 2 Zinc molecules.  The program prompts me to input the ionic radius and potential energy well depth for Zn to create the .pdbqs file, but when I run autogrid I get the following error message:

autogrid3: WARNING! Atom type error, can't find type for "Zn" in typelist "CNOSHXM"

Does anyone with AD/ADT experience have any suggestions for where I might be going wrong or where to edit in the file to get it to recognize Zn as a type "M"  (metal)?

Thank you in advance,

MK Creber
Royal Military College of Canada