From owner-chemistry@ccl.net Sun Oct 23 11:59:00 2005
From: "Wendy Cornell wdcornell-#-yahoo.com" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL: ACS COMP Division Call for Papers -- Spring National Meeting in Atlanta
Message-Id: <-29693-051023113406-19618-ydYI9r1F1OvkpDM+uEj6Qg**server.ccl.net>
X-Original-From: Wendy Cornell <wdcornell-,-yahoo.com>
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Sent to CCL by: Wendy Cornell [wdcornell]_[yahoo.com]
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The Spring 2006 ACS national meeting will take place March 26-30, 2006 in Atlanta, GA.  The oasys.acs.org web site is open for abstract submission for the following COMP Division symposia.  
 
Deadline for abstract submission in COMP is November 15.

   CCG Student Excellence Awards
   Frontier Applications and Developments of Density Functional Theory:  A Symposium in Honor of Robert G. Parr's 85th Birthday
   G-Protein Coupled Receptor Structure, Modeling, and Ligand Design
   General Oral -- Drug Discovery
   General Oral -- Molecular Mechanics and Simulation
   General Oral -- Quantum Chemistry
   Poster Session
   Protein Kinases:  Computer Modeling and Experiment
   Structure Determination Using NMR and Computational Methods
   Thomas Kuhn Paradigm Shift Award Competition
   Virtual Screening Using Structure-Based and Ligand-Based Methods for Lead Identification
 
 

 


		
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<DIV>
<DIV>The Spring 2006 ACS national meeting will take place March 26-30, 2006&nbsp;in Atlanta, GA.&nbsp; The <U>oasys.acs.org</U> web site is open for abstract submission for the following COMP Division symposia.&nbsp; </DIV>
<DIV>&nbsp;</DIV>
<DIV>Deadline for abstract submission in COMP is November 15.</DIV>
<UL>
<LI>CCG Student Excellence Awards</LI>
<LI>Frontier Applications and Developments of Density Functional Theory:&nbsp; A Symposium in Honor of Robert G. Parr's 85th Birthday</LI>
<LI>G-Protein Coupled Receptor Structure, Modeling, and Ligand Design</LI>
<LI>General Oral -- Drug Discovery</LI>
<LI>General Oral -- Molecular Mechanics and Simulation</LI>
<LI>General Oral -- Quantum Chemistry</LI>
<LI>Poster Session</LI>
<LI>Protein Kinases:&nbsp; Computer Modeling and Experiment</LI>
<LI>Structure Determination Using NMR and Computational Methods</LI>
<LI>Thomas Kuhn Paradigm Shift Award Competition</LI>
<LI>Virtual Screening Using Structure-Based and Ligand-Based Methods for Lead Identification</LI></UL>
<DIV>&nbsp;</DIV>
<DIV>&nbsp;</DIV>
<DIV><BR>&nbsp;</DIV></DIV><p>
		<hr size=1> <a href="http://us.lrd.yahoo.com/_ylc=X3oDMTFqODRtdXQ4BF9TAzMyOTc1MDIEX3MDOTY2ODgxNjkEcG9zAzEEc2VjA21haWwtZm9vdGVyBHNsawNmYw--/SIG=110oav78o/**http%3a//farechase.yahoo.com/">Yahoo! FareChase - Search multiple travel sites in one click.</a>

 

 
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From owner-chemistry@ccl.net Sun Oct 23 13:18:00 2005
From: "Vlad Cojocaru Vlad.Cojocaru()eml-r.villa-bosch.de" <owner-chemistry/./server.ccl.net>
To: CCL
Subject: CCL: free software for LINUX to edit and sketch molecules
Message-Id: <-29694-051023122706-9915-xeBoO1irt65AmvfxKl0Zog/./server.ccl.net>
X-Original-From: Vlad Cojocaru <Vlad.Cojocaru!A!eml-r.villa-bosch.de>
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Date: Sun, 23 Oct 2005 18:02:29 +0200
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Sent to CCL by: Vlad Cojocaru [Vlad.Cojocaru*eml-r.villa-bosch.de]
Dear ccl-ers,
   Can somebody indicate me a good free program for LINUX that allows me to
sketch, edit molecules and then save them as mol2 or Z-matrix files (or
at least pdb file with CONNECT records). Sybyl can do this very well but
I am wondering if there is any free software that can also do this.
Thank you
vlad


-- 
Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Villa Bosch
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
e-mail: Vlad.Cojocaru^^eml-r.villa-bosch.de


From owner-chemistry@ccl.net Sun Oct 23 15:18:00 2005
From: "john furr john.furr]_[gmail.com" <owner-chemistry^_^server.ccl.net>
To: CCL
Subject: CCL: free software for LINUX to edit and sketch molecules
Message-Id: <-29695-051023151416-18056-OUT/MN3pEjiQzPdF+i/wdA^_^server.ccl.net>
X-Original-From: john furr <john.furr-.-gmail.com>
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Date: Sun, 23 Oct 2005 15:14:02 -0400
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Sent to CCL by: john furr [john.furr*o*gmail.com]
Dynamol has a 3D editor.  You can save as *.sdf and *.mol2 but not PDB.

John Furr
Dynamol Inc.
http://www.dynamol.com


On 10/23/05, Vlad Cojocaru Vlad.Cojocaru()eml-r.villa-bosch.de
<owner-chemistry*ccl.net> wrote:
>
> Sent to CCL by: Vlad Cojocaru [Vlad.Cojocaru*eml-r.villa-bosch.de]
> Dear ccl-ers,
>    Can somebody indicate me a good free program for LINUX that allows me to
> sketch, edit molecules and then save them as mol2 or Z-matrix files (or
> at least pdb file with CONNECT records). Sybyl can do this very well but
> I am wondering if there is any free software that can also do this.
> Thank you
> vlad
>
>
> --
> Dr. Vlad Cojocaru
> EML Research gGmbH
> Molecular and Cellular Modeling Group
> Villa Bosch
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg
> Germany
> Phone: +49-6221-533266
> Fax: +49-6221-533298
> e-mail: Vlad.Cojocaru=-=eml-r.villa-bosch.de>
>
>
>


From owner-chemistry@ccl.net Sun Oct 23 15:52:01 2005
From: "Evgeniy Gromov Evgeniy.Gromov{=}tc.pci.uni-heidelberg.de" <owner-chemistry_+_server.ccl.net>
To: CCL
Subject: CCL: free software for LINUX to edit and sketch molecules
Message-Id: <-29696-051023141428-11465-5GFurxzs5vQRM84ZKtpeZA_+_server.ccl.net>
X-Original-From: Evgeniy Gromov <Evgeniy.Gromov(-)tc.pci.uni-heidelberg.de>
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Sent to CCL by: Evgeniy Gromov [Evgeniy.Gromov#%#tc.pci.uni-heidelberg.de]
Molden can do this job quite well.

Evgeniy

Vlad Cojocaru Vlad.Cojocaru()eml-r.villa-bosch.de wrote:
> Sent to CCL by: Vlad Cojocaru [Vlad.Cojocaru*eml-r.villa-bosch.de]
> Dear ccl-ers,
>    Can somebody indicate me a good free program for LINUX that allows me to
> sketch, edit molecules and then save them as mol2 or Z-matrix files (or
> at least pdb file with CONNECT records). Sybyl can do this very well but
> I am wondering if there is any free software that can also do this.
> Thank you
> vlad
> 
> 


-- 
_______________________________________
Dr. Evgeniy Gromov
Theoretische Chemie
Physikalisch-Chemisches Institut
Im Neuenheimer Feld 229
D-69120 Heidelberg
Germany

Telefon: +49/(0)6221/545263
Fax: +49/(0)6221/545221
E-mail: evgeniy%tc.pci.uni-heidelberg.de
_______________________________________


From owner-chemistry@ccl.net Sun Oct 23 16:27:00 2005
From: "Gustavo Mercier gamercier[-]yahoo.com" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL: free software for LINUX to edit and sketch molecules
Message-Id: <-29697-051023152317-20666-8pafmzQp2IKcFf5S0evlKQ^server.ccl.net>
X-Original-From: Gustavo Mercier <gamercier- -yahoo.com>
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Sent to CCL by: Gustavo Mercier [gamercier|*|yahoo.com]
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Hi!
 
MarvinSketch can do this. You can download this from chemaxon site. I find it very intuitive. For the full feature you need to get a license, but for sketching and editing you don't. I will save in several mol formats and pdb with connect records. It will not save in Z-matrix format. Molden has a Z-matrix editor.
 
Bye!
GMercier

"Vlad Cojocaru Vlad.Cojocaru()eml-r.villa-bosch.de" <owner-chemistry=-=ccl.net> wrote:

Sent to CCL by: Vlad Cojocaru [Vlad.Cojocaru*eml-r.villa-bosch.de]
Dear ccl-ers,
Can somebody indicate me a good free program for LINUX that allows me to
sketch, edit molecules and then save them as mol2 or Z-matrix files (or
at least pdb file with CONNECT records). Sybyl can do this very well but
I am wondering if there is any free software that can also do this.
Thank you
vlad


-- 
Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Villa Bosch
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
e-mail: Vlad.Cojocaru=-=eml-r.villa-bosch.dehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--
Gustavo A. Mercier, Jr. MD,PhD
Baylor University Medical Center
Radiology
American Radiology Associates
712 N. Washington, Suite 101
Dallas, TX 75246
214-826-8822
214-826-9792 fax
gamercier=-=yahoo.com 

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<DIV>Hi!</DIV>
<DIV>&nbsp;</DIV>
<DIV>MarvinSketch can do this. You can download this from chemaxon site. I find it very intuitive. For the full feature you need to get a license, but for sketching and editing you don't. I will save in several mol formats and pdb with connect records. It will not save in Z-matrix format. Molden has a Z-matrix editor.</DIV>
<DIV>&nbsp;</DIV>
<DIV>Bye!</DIV>
<DIV>GMercier<BR><BR><B><I>"Vlad Cojocaru Vlad.Cojocaru()eml-r.villa-bosch.de" &lt;owner-chemistry=-=ccl.net&gt;</I></B> wrote:</DIV>
<BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid"><BR>Sent to CCL by: Vlad Cojocaru [Vlad.Cojocaru*eml-r.villa-bosch.de]<BR>Dear ccl-ers,<BR>Can somebody indicate me a good free program for LINUX that allows me to<BR>sketch, edit molecules and then save them as mol2 or Z-matrix files (or<BR>at least pdb file with CONNECT records). Sybyl can do this very well but<BR>I am wondering if there is any free software that can also do this.<BR>Thank you<BR>vlad<BR><BR><BR>-- <BR>Dr. Vlad Cojocaru<BR>EML Research gGmbH<BR>Molecular and Cellular Modeling Group<BR>Villa Bosch<BR>Schloss-Wolfsbrunnenweg 33<BR>69118 Heidelberg<BR>Germany<BR>Phone: +49-6221-533266<BR>Fax: +49-6221-533298<BR>e-mail: Vlad.Cojocaru=-=eml-r.villa-bosch.de<BR><BR><BR><BR<BR<BR<BR<BR><BR<BR>http://www.ccl.net/cgi-bin/ccl/send_ccl_message<BR><BR<BR>http://www.ccl.net/cgi-bin/ccl/send_ccl_message<BR><BR<BR>http://www.ccl.net/chemistry/sub_unsub.shtml<BR><BR<BR><BR<BR><BR<BR>http://www.ccl.net/spammers.txt<BR><BR<BR><BR><BR><BR></BLOCKQUOTE><BR><BR><DIV>--</DIV>
<DIV>Gustavo A. Mercier, Jr. MD,PhD<BR>Baylor University Medical Center</DIV>
<DIV>Radiology</DIV>
<DIV>American Radiology Associates</DIV>
<DIV>712 N. Washington, Suite 101</DIV>
<DIV>Dallas, TX 75246</DIV>
<DIV>214-826-8822</DIV>
<DIV>214-826-9792 fax<BR><A href="mailto:gamercier=-=yahoo.com"><FONT style="BACKGROUND-COLOR: white">gamercier=-=yahoo.com</FONT></A>&nbsp;<IMG src="http://us.i1.yimg.com/us.yimg.com/i/mesg/tsmileys/c.gif"></DIV>
--0-1943468745-1130095389=:97897--


From owner-chemistry@ccl.net Sun Oct 23 17:02:01 2005
From: "Peter Gannett pgannett*o*hsc.wvu.edu" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL: free software for LINUX to edit and sketch molecules
Message-Id: <-29698-051023152207-19821-ZxaCagK16A5ocYvyanSibA+*+server.ccl.net>
X-Original-From: "Peter Gannett" <pgannett:-:hsc.wvu.edu>
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Date: Sun, 23 Oct 2005 14:46:16 -0400
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Sent to CCL by: "Peter Gannett" [pgannett#,#hsc.wvu.edu]
This is a MIME message. If you are reading this text, you may want to 
consider changing to a mail reader or gateway that understands how to 
properly handle MIME multipart messages.

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Vlad:
 
Try XdrawChem from http://xdrawchem.sourceforge.net/
 
I think it meets all you want to do.
 
Pete

>>> owner-chemistry[a]ccl.net 10/23/2005 12:02:29 PM >>>


Sent to CCL by: Vlad Cojocaru [Vlad.Cojocaru*eml-r.villa-bosch.de]
Dear ccl-ers,
   Can somebody indicate me a good free program for LINUX that allows
me to
sketch, edit molecules and then save them as mol2 or Z-matrix files
(or
at least pdb file with CONNECT records). Sybyl can do this very well
but
I am wondering if there is any free software that can also do this.
Thank you
vlad


-- 
Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Villa Bosch
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
e-mail: Vlad.Cojocaru=-=eml-r.villa-bosch.dehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--=__PartC2E0D768.0__=
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<HTML><HEAD>
<META http-equiv=3DContent-Type content=3D"text/html; charset=3Diso-8859-1"=
>
<META content=3D"MSHTML 6.00.2900.2769" name=3DGENERATOR></HEAD>
<BODY style=3D"MARGIN: 4px 4px 1px; FONT: 10pt Tahoma">
<DIV>Vlad:</DIV>
<DIV>&nbsp;</DIV>
<DIV>Try XdrawChem from <A href=3D"http://xdrawchem.sourceforge.net/">http:=
//xdrawchem.sourceforge.net/</A></DIV>
<DIV>&nbsp;</DIV>
<DIV>I think it meets all you want to do.</DIV>
<DIV>&nbsp;</DIV>
<DIV>Pete<BR><BR>&gt;&gt;&gt; owner-chemistry[a]ccl.net 10/23/2005 12:02:29 =
PM &gt;&gt;&gt;<BR></DIV>
<DIV style=3D"COLOR: #000000"><BR>Sent to CCL by: Vlad Cojocaru [Vlad.Cojoc=
aru*eml-r.villa-bosch.de]<BR>Dear ccl-ers,<BR>&nbsp;&nbsp; Can somebody =
indicate me a good free program for LINUX that allows me to<BR>sketch, =
edit molecules and then save them as mol2 or Z-matrix files (or<BR>at =
least pdb file with CONNECT records). Sybyl can do this very well but<BR>I =
am wondering if there is any free software that can also do this.<BR>Thank =
you<BR>vlad<BR><BR><BR>-- <BR>Dr. Vlad Cojocaru<BR>EML Research gGmbH<BR>Mo=
lecular and Cellular Modeling Group<BR>Villa Bosch<BR>Schloss-Wolfsbrunnenw=
eg 33<BR>69118 Heidelberg<BR>Germany<BR>Phone: +49-6221-533266<BR>Fax: =
+49-6221-533298<BR>e-mail: Vlad.Cojocaru=3D-=3Deml-r.villa-bosch.de<BR><BR>=
<BR><BR>-=3D This is automatically added to each message by the mailing =
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From owner-chemistry@ccl.net Sun Oct 23 20:36:00 2005
From: "Ferenc Csizmadia fcsiz- -chemaxon.com" <owner-chemistry__server.ccl.net>
To: CCL
Subject: CCL: free software for LINUX to edit and sketch molecules
Message-Id: <-29699-051023161908-17384-FBXXr0aD7YCR+v4dD0Sesw__server.ccl.net>
X-Original-From: Ferenc Csizmadia <fcsiz() chemaxon.com>
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Sent to CCL by: Ferenc Csizmadia [fcsiz^^chemaxon.com]
Vlad,
MarvinSketch is Java-based (so it runs under Linux) and it can export 
many formats (PDB is included). It is free if you don't build it into an 
application (or if you are eligible for our free academic license: 
http://www.chemaxon.com/forum/ftopic193.html)
I suggest to download the Marvin Beans package that includes 
MarvinSketch from our web site: http://www.chemaxon.com/products.html
Best regards,
Ferenc



Vlad Cojocaru Vlad.Cojocaru()eml-r.villa-bosch.de wrote:

>Sent to CCL by: Vlad Cojocaru [Vlad.Cojocaru*eml-r.villa-bosch.de]
>Dear ccl-ers,
>   Can somebody indicate me a good free program for LINUX that allows me to
>sketch, edit molecules and then save them as mol2 or Z-matrix files (or
>at least pdb file with CONNECT records). Sybyl can do this very well but
>I am wondering if there is any free software that can also do this.
>Thank you
>vlad
>
>
>  
>


From owner-chemistry@ccl.net Sun Oct 23 21:11:00 2005
From: "Len Salgado leon_salga]^[yahoo.com" <owner-chemistry!=!server.ccl.net>
To: CCL
Subject: CCL: W:Rank structure models
Message-Id: <-29700-051023195251-20095-td4/YbMf2/5NDjTMCsIafg!=!server.ccl.net>
X-Original-From: "Len  Salgado" <leon_salga|-|yahoo.com>


Sent to CCL by: "Len  Salgado" [leon_salga%a%yahoo.com]
Dear *

I've been doing protein-protein docking calculations, and let's call to the protein complexes obtained, the basic units. My final goal is to build a supramolecular structure with these basic units. The only restraint experimentally determined, defines de distance between the centre of 2 basic units.

These supramolecular structures, could be produced by a docking procedure (and ranked accordingly), but since these structures have some thousands of residues, I've thought on obtaining them "manually", by mean of rigid rotation/translation operations on 3D space. I'm only interested on obtaining a crude view of the supramolecular protein structure, but nevertheless, want to charaterize and rank the set of supramolecular structures that I'm going to build. 

My question is.
Is there a way to rank different structure models? Is there any software/methodology which reads a set of similar structures, and ranks them by energy, for example?  
Any insights will be valuable.

Best wishes,
Len Salgado