From owner-chemistry@ccl.net Thu Aug  2 09:21:00 2007
From: "Max Porrini mozz76(0)gmail.com" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL: adding hydrogens
Message-Id: <-34848-070802090331-6533-md/RRyrlb99fT55UeJh1kw:server.ccl.net>
X-Original-From: "Max Porrini" <mozz76:-:gmail.com>
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Sent to CCL by: "Max Porrini" [mozz76*|*gmail.com]
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Hi all
Does anybody know how I can add hydrogens to a system?
I've downloaded the pdb file of a enzyme and there aren't hydrogen atoms
(for instance the water molecule is formed only by the oxygen).
I'd like to saturate my system with the missing hydrogens.
Any tips will be very appreciated.
thanks a lot
MP

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Hi all<br>Does anybody know how I can add hydrogens to a system?<br>I&#39;ve downloaded the pdb file of a enzyme and there aren&#39;t hydrogen atoms<br>(for instance the water molecule is formed only by the oxygen).<br>I&#39;d like to saturate my system with the missing hydrogens.
<br>Any tips will be very appreciated.<br>thanks a lot<br><span class="sg">MP<br>
</span>

------=_Part_19459_27665787.1186059784845--


From owner-chemistry@ccl.net Thu Aug  2 09:56:00 2007
From: "Tapani Kinnunen takinnun*_*csc.fi" <owner-chemistry===server.ccl.net>
To: CCL
Subject: CCL: Workflow management/web services software
Message-Id: <-34849-070802034514-29502-kZSL/ekuTsPnuIaPx8pX7A===server.ccl.net>
X-Original-From: "Tapani  Kinnunen" <takinnun,,csc.fi>
Date: Thu, 2 Aug 2007 03:45:10 -0400


Sent to CCL by: "Tapani  Kinnunen" [takinnun],[csc.fi]

Dear Andrew,

Recently, we have open source released the source code of the SOMA2 environment developed at Finnish IT center for science CSC. SOMA2 is released under GPL license.

http://www.csc.fi/soma

SOMA2 is a web server based, offering a framework for integrating molecular modelling applications, including molecular data exchange. SOMA2 allows users to combine software available in the system into workflows, which are automatically executed.

SOMA2 provides a framework to make command-line application or combination of applications (workflows) easily accessible. The system enables data exchange between molecular modelling programs on different computing platforms by employing a general data exchange format, CML (Chemical Markup Language).

Applications are described as pluggable "capsules" with generic interfaces to manage the data. A capsule consists of an XML description, used e.g. to automatically generate a web form for the program, and scripts & configuration file templates to enable automatic program execution and processing of the program output. The XML descriptions are based on a schema, which we have developed. No programming skills are required to create a SOMA2 capsule.

A demo installation of SOMA2 with limited features is available

http://soma2demo.csc.fi

For reference please see: P. Lehtovuori, T. Nyrnen, J. Chem. Inf. Model.
2006, 46(2), 620.  

Regards,

Tapani Kinnunen


> Sent to CCL by: "Andrew Colasanti" [acolasanti.--.gmail.com]
> I am looking into workflow management software and wanted to know
> about experiences and suggestions.  The three that I am thinking about
> are
>
> 1) Taverna (taverna.sourceforge.net)
> 2) Knime (www.knime.org)
> 3) Kepler (kepler-project.org)
>
> I also know about Pipeline Pilot from SciTegic/Accelrys but the cost
> is prohibitive.
>
> I am also interested in the use of CDK and Openbabel within the
> software.  The projects will be chem-/bioinformatics based.
>
> Thanks in advance
>
> Andrew
>
>

Tapani Kinnunen, Ph.D., Application Specialist, Scientific Software Development, CSC P.O.Box 405, 02101 ESPOO, Finland, Tel +358-9-4572248, Mob +358-50-3819506, Fax. +358-9-4572302 CSC is the Finnish IT Center for Science, www.csc.fi


From owner-chemistry@ccl.net Thu Aug  2 10:31:00 2007
From: "Max Porrini mozz76|,|gmail.com" <owner-chemistry(_)server.ccl.net>
To: CCL
Subject: CCL: adding hydrogens
Message-Id: <-34850-070802074245-17681-kHFpkl7C2Iv+RIxPaBmfiw(_)server.ccl.net>
X-Original-From: "Max Porrini" <mozz76__gmail.com>
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Date: Thu, 2 Aug 2007 13:39:49 +0300
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Sent to CCL by: "Max Porrini" [mozz76**gmail.com]
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Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
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Hi all
Does anybody know how I can add hydrogens to a system?
I've downloaded the pdb file of a enzyme and there aren't hydrogen atoms
(for instance the water molecule is formed only by the oxygen).
I'd like to saturate my system with the missing hydrogens.
Any tips will be very appreciated.
thanks a lot
MP

------=_Part_19079_11125243.1186051189843
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
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Hi all<br>Does anybody know how I can add hydrogens to a system?<br>I&#39;ve downloaded the pdb file of a enzyme and there aren&#39;t hydrogen atoms<br>(for instance the water molecule is formed only by the oxygen).<br>I&#39;d like to saturate my system with the missing hydrogens.
<br>Any tips will be very appreciated.<br>thanks a lot<br>MP<br>

------=_Part_19079_11125243.1186051189843--


From owner-chemistry@ccl.net Thu Aug  2 11:06:01 2007
From: "Alex Allardyce aa!A!chemaxon.com" <owner-chemistry{=}server.ccl.net>
To: CCL
Subject: CCL: ChemAxon free US seminar and workshop series: Instant JChem v2.0, Aug 13-21.
Message-Id: <-34851-070802105737-11867-zgnCPK5oXeBrT8x/ROY91w{=}server.ccl.net>
X-Original-From: Alex Allardyce <aa{=}chemaxon.com>
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Date: Thu, 02 Aug 2007 09:55:39 -0400
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Sent to CCL by: Alex Allardyce [aa[#]chemaxon.com]
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Please excuse cross postings.

ChemAxon invites you to a series of free, open lunchtime seminars and 
workshop taking place at various locations across the United States 
(South San Francisco CA, San Diego CA, Chapel Hill NC, New Brunswick NJ 
and Boston MA) from Aug 13 to 21.

The seminars will introduce Instant JChem v2 - a desktop application for 
managing and working with chemical structure/other data and will cover; 
the application, how it can be used and future development discussions. 
The workshop, being held at the ACS National Meeting in Boston MA, will 
be an open, hands on session with key developers available to overview, 
support and answer questions. See below for coordinates. For full 
details, RSVP and complimentary pass for the ACS Exposition see this 
link: http://www.chemaxon.com/news/07_IJC_Seminar_US.html. RSVP for all 
events is requested.

Instant JChem Personal is free for all users and content distributors 
(license to distribute), Enterprise functionality is also free for 
ChemAxon academic package users. For more information and to download, 
see this link: http://www.chemaxon.com/product/ijc.html

*Lunchtime Seminar dates and locations*
*- South San Francisco, CA*: August 13th, 12.00pm - 1.30pm, Presidio 
Room, Embassy Suites Hotel, 250 Gateway Blvd. 94080.
*- San Diego, CA*: August 14th, 12.00pm - 1.30pm, Celgene Signal 
Research, 4550 Towne Centre Court, 92121.
*- Chapel Hill, NC*: August 15th, 12.00pm - 1.30pm, School of Pharmacy, 
University of North Carolina, Beard Hall, Room No. 116, South Columbia 
Street, 27599.
*- East Brunswick, NJ*: August 16th, 12.00pm - 1.30pm, Trenton Room, 
Hilton East Brunswick, 3 Tower Center Boulevard, 08816.
*
Instant JChem Workshop*
*- ACS National Meeting & Exposition, Boston, MA*: August 21st - pm, 
2007 Boston Convention & Exhibition Center, MA: Room: BCEC,102B (level 1)

We look forward to seeing you there
Alex Allardyce

-- 
Dir. Marketing, ChemAxon
Cell-US: 1-857-544-0541
skype: alex_allardyce


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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
</head>
<body bgcolor="#ffffff" text="#000000">
Please excuse cross postings.
<br>
<br>
ChemAxon invites you to a series of free, open lunchtime seminars and
workshop taking place at various locations across the United States
(South San Francisco CA, San Diego CA, Chapel Hill NC, New Brunswick NJ
and
Boston MA) from Aug 13 to 21. <br>
<br>
The seminars will introduce Instant JChem v2 - a desktop application
for
managing and working with chemical structure/other data and will
cover; the application, how it can be used and future development
discussions.
The workshop, being held at the ACS National Meeting in Boston MA, will
be an open, hands on session with key developers available to
overview, support and answer questions. See below for coordinates.
For full details,
RSVP and complimentary pass for the ACS Exposition see this link: <a
 class="moz-txt-link-freetext"
 href="http://www.chemaxon.com/news/07_IJC_Seminar_US.html">http://www.chemaxon.com/news/07_IJC_Seminar_US.html</a>.
RSVP for all events
is requested.<br>
<br>
Instant JChem Personal is free for all users and content distributors
(license to distribute), Enterprise functionality is also free for
ChemAxon academic package
users. For more information and to download, see this link:
<a class="moz-txt-link-freetext"
 href="http://www.chemaxon.com/product/ijc.html">http://www.chemaxon.com/product/ijc.html</a><br>
<br>
<b>Lunchtime Seminar dates and locations</b><br>
<b>- South San Francisco, CA</b>: August 13th, 12.00pm - 1.30pm,
Presidio
Room, Embassy Suites Hotel, 250 Gateway Blvd. 94080.<br>
<b>- San Diego, CA</b>: August 14th, 12.00pm - 1.30pm, Celgene Signal
Research, 4550 Towne Centre Court, 92121. <br>
<b>- Chapel Hill, NC</b>: August 15th, 12.00pm - 1.30pm, School of
Pharmacy,
University of North Carolina, Beard Hall, Room No. 116, South Columbia
Street, 27599.<br>
<b>- East Brunswick, NJ</b>: August 16th, 12.00pm - 1.30pm, Trenton
Room,
Hilton East Brunswick, 3 Tower Center Boulevard, 08816.<br>
<b><br>
Instant JChem Workshop</b><br>
<b>- ACS National Meeting &amp; Exposition, Boston, MA</b>: August 21st
- pm,
2007 Boston Convention &amp; Exhibition Center, MA: Room: BCEC,102B
(level 1)<br>
<br>
We look forward to seeing you there<br>
Alex Allardyce<br>
<pre class="moz-signature" cols="72">-- 
Dir. Marketing, ChemAxon
Cell-US: 1-857-544-0541
skype: alex_allardyce
</pre>
</body>
</html>

--------------030009080509070309010005--


From owner-chemistry@ccl.net Thu Aug  2 11:40:00 2007
From: "Aniko Simon aniko#simbiosys.ca" <owner-chemistry.@.server.ccl.net>
To: CCL
Subject: CCL: Attend a free Virtual Screening Workshop at the ACS by SimBioSys
Message-Id: <-34852-070802100429-1683-sh7Eqn9Y38EoD4VVc4g0bg.@.server.ccl.net>
X-Original-From: "Aniko  Simon" <aniko__simbiosys.ca>
Date: Thu, 2 Aug 2007 10:04:26 -0400


Sent to CCL by: "Aniko  Simon" [aniko],[simbiosys.ca]
Please consider registering for a complimentary ACS workshop on "Ligand-Based Screening with LASSO & Structure-Based Docking with eHiTS" by SimBioSys, Inc. Please forward this information to anyone interested:

*       "Ligand-Based Screening with LASSO & Ligand-Protein Docking with eHiTS: usage, results analysis and visualization"
*       Wednesday, August 22, from 12:30-2:30 PM
*       Boston Convention & Exhibition Center (BCEC),  room 101
*       Instructor: Darryl Reid
*       Creator of eHiTS program, Dr. Zsoldos will be available for questions

To register, please fill in this form:
http://acsboston.expoplanner.com/plworkshopregister.wcs?entryid=300007

If you are unable to attend, please come and visit us at the SimBioSys booth 619.

Dr. Zsoldos, the creator of the eHiTS and SPROUT tools, will also be presenting during the COMP,  "Phil Magee Memorial Symposium: QSAR Reborn" session on Sunday afternoon.

For a full list of SimBioSys ACS events, please visit:
http://www.simbiosys.ca/whatsnew/presentations/acs-2007-2/index.html

We look forward to seeing you at the ACS,
best regards
Aniko

--
Aniko Simon, Ph.D.
SimBioSys Inc.
http://www.simbiosys.ca/
Tel: 1-416-741-4263


From owner-chemistry@ccl.net Thu Aug  2 12:16:01 2007
From: "William F. Coleman wcoleman]*[wellesley.edu" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL: adding hydrogens
Message-Id: <-34853-070802114844-21177-zP4Of7hiYRzip7Yg9i7+iw-#-server.ccl.net>
X-Original-From: "William F. Coleman" <wcoleman-#-wellesley.edu>
Content-Transfer-Encoding: 8bit
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Date: Thu, 02 Aug 2007 11:48:11 -0400
MIME-Version: 1.0


Sent to CCL by: "William F. Coleman" [wcoleman-.-wellesley.edu]
DSV Visualizer
(http://www.accelrys.com/products/downloads/ds_visualizer/index.html) will
do this, as will GaussView. 

Cheers,

Flick
_______________
William F. Coleman
Professor of Chemistry
Wellesley College 
Wellesley MA 02481

on leave 2007-08 - please contact via email only 
wcoleman(!)wellesley.edu

www.wellesley.edu/Chemistry/colemanw.html

Editor, JCE WebWare and JCE Featured Molecules
http://www.jce.divched.org/JCEDLib/WebWare/
http://jchemed.chem.wisc.edu/JCEWWW/Features/MonthlyMolecules/index.html


From owner-chemistry@ccl.net Thu Aug  2 12:50:00 2007
From: "Reaz Uddin riaasuddin%%yahoo.com" <owner-chemistry[#]server.ccl.net>
To: CCL
Subject: CCL: adding hydrogens
Message-Id: <-34854-070802122342-16863-ibKYqJuzNb2h97BwLoQa4g[#]server.ccl.net>
X-Original-From: Reaz Uddin <riaasuddin_._yahoo.com>
Content-Transfer-Encoding: 8bit
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Date: Thu, 2 Aug 2007 09:23:18 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: Reaz Uddin [riaasuddin]~[yahoo.com]
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I dont know what do you have in terms of molecular modeling software. But Tripos sybyl can easily help you to add hydrogens. In addditon to this, you can use opeeyes omega program. I guess opeyes babel can also help you in this regard.
  Hope it helps You.
  Thanks
  REAZ

"Max Porrini mozz76(0)gmail.com" <owner-chemistry=ccl.net> wrote:
  Hi all
Does anybody know how I can add hydrogens to a system?
I've downloaded the pdb file of a enzyme and there aren't hydrogen atoms
(for instance the water molecule is formed only by the oxygen).
I'd like to saturate my system with the missing hydrogens. 
Any tips will be very appreciated.
thanks a lot
MP



REAZUDDIN 
Research Scholar 
Department of Medicinal Chemistry and Pharmacognosy, 
College of Pharmacy, (M/C 781) 
University of Illinois at Chicago 
833 S. Wood St. 
Chicago, IL 60612 
Email: ruddin=uic.edu, riaasuddin=yahoo.com
Web: http://medchem.pharm.uic.edu/
       
---------------------------------
Yahoo! oneSearch: Finally,  mobile search that gives answers, not web links. 
--0-146589544-1186071798=:13167
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<div><FONT color=#00007f>I dont know what do you have in terms of molecular modeling software. But Tripos sybyl can easily help you to add hydrogens. In addditon to this, you can use opeeyes omega program. I guess opeyes babel can also help you in this regard.</FONT></div>  <div><FONT color=#00007f>Hope it helps You.</FONT></div>  <div><FONT color=#00007f>Thanks</FONT></div>  <div><FONT color=#00007f>REAZ<BR></FONT><BR><B><I>"Max Porrini mozz76(0)gmail.com" &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">Hi all<BR>Does anybody know how I can add hydrogens to a system?<BR>I've downloaded the pdb file of a enzyme and there aren't hydrogen atoms<BR>(for instance the water molecule is formed only by the oxygen).<BR>I'd like to saturate my system with the missing hydrogens. <BR>Any tips will be very appreciated.<BR>thanks a lot<BR><SPAN
 class=sg>MP<BR></SPAN></BLOCKQUOTE><BR><BR><BR><span style="color: rgb(0, 0, 127);">REAZUDDIN </span><br style="color: rgb(0, 0, 127);"><span style="color: rgb(0, 0, 127);">Research Scholar </span><br style="color: rgb(0, 0, 127);"><span style="color: rgb(0, 0, 127);">Department of Medicinal Chemistry and Pharmacognosy, </span><br style="color: rgb(0, 0, 127);"><span style="color: rgb(0, 0, 127);">College of Pharmacy, (M/C 781) </span><br style="color: rgb(0, 0, 127);"><span style="color: rgb(0, 0, 127);">University of Illinois at Chicago </span><br style="color: rgb(0, 0, 127);"><span style="color: rgb(0, 0, 127);">833 S. Wood St. </span><br style="color: rgb(0, 0, 127);"><span style="color: rgb(0, 0, 127);">Chicago, IL 60612 </span><br style="color: rgb(0, 0, 127);"><span style="color: rgb(0, 0, 127);"></span><span style="color: rgb(0, 0, 127);">Email: ruddin=uic.edu, riaasuddin=yahoo.com</span><br style="color: rgb(0, 0, 127);"><span style="color: rgb(0, 0, 127);">Web:
 http://medchem.pharm.uic.edu/</span><p>&#32;
      <hr size=1>Yahoo! oneSearch: Finally, <a href="http://us.rd.yahoo.com/evt=48252/*http://mobile.yahoo.com/mobileweb/onesearch?refer=1ONXIC"> mobile search 
that gives answers</a>, not web links. 


--0-146589544-1186071798=:13167--


From owner-chemistry@ccl.net Thu Aug  2 13:26:00 2007
From: "Elaine Meng meng%%cgl.ucsf.edu" <owner-chemistry*server.ccl.net>
To: CCL
Subject: CCL: adding hydrogens
Message-Id: <-34855-070802123838-28738-Rx7y7KsDN6qI5fqickdB6A*server.ccl.net>
X-Original-From: "Elaine  Meng" <meng||cgl.ucsf.edu>
Date: Thu, 2 Aug 2007 12:38:35 -0400


Sent to CCL by: "Elaine  Meng" [meng-$-cgl.ucsf.edu]
Hi Max,
Many programs add hydrogens, including the one I work on (Chimera,
http://www.cgl.ucsf.edu/chimera/ ).

Probably the easiest, however, if you would rather not get a program
you don't already have is to use the Richardson group's MolProbity
server:

http://molprobity.biochem.duke.edu/

You can upload a file or enter its PDB ID.  Just follow the steps;
there will be choices of what to do to the structure, including
adding hydrogens.  The hydrogen addition is high-quality and takes
local H-bonding patterns into account.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng---cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                     http://www.cgl.ucsf.edu/home/meng/index.html


From owner-chemistry@ccl.net Thu Aug  2 14:01:00 2007
From: "debjani roy\(Chattopadhyay\) debjani_2k2^yahoo.com" <owner-chemistry],[server.ccl.net>
To: CCL
Subject: CCL: adding hydrogens
Message-Id: <-34856-070802121218-5421-CglknIgecFvzZMTVLsr37w],[server.ccl.net>
X-Original-From: "debjani roy\(Chattopadhyay\)" <debjani_2k2**yahoo.com>
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Date: Thu, 2 Aug 2007 08:11:55 -0700 (PDT)
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Sent to CCL by: "debjani roy\(Chattopadhyay\)" [debjani_2k2%a%yahoo.com]
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Hi,

The program "gwh" ( Amber) sets positions of water hydrogens onto water oxygen positions present in PDB files. It is done by optimizing simple electrostatic interactions (check Amber manual for details).

USAGE

gwh [-p <prmtop>] [-w <water.pdb>] [-c] [-e] < input_pdb_file
> output_pdb_file

Hope this helps,
-Debjani 
---------------------------------------------------------------------------------------------------------------------

"Max Porrini mozz76(0)gmail.com" <owner-chemistry|-|ccl.net> wrote: Hi all
Does anybody know how I can add hydrogens to a system?
I've downloaded the pdb file of a enzyme and there aren't hydrogen atoms
(for instance the water molecule is formed only by the oxygen).
I'd like to saturate my system with the missing hydrogens. 
Any tips will be very appreciated.
thanks a lot
MP
  

       
---------------------------------
Shape Yahoo! in your own image.  Join our Network Research Panel today!
--0-2122894649-1186067515=:27457
Content-Type: text/html; charset=iso-8859-1
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Hi,<br><br>The program "gwh" ( Amber) sets positions of water hydrogens onto water oxygen positions present in PDB files. It is done by optimizing simple electrostatic interactions (check Amber manual for details).<br><br>USAGE<br><br>gwh [-p &lt;prmtop&gt;] [-w &lt;water.pdb&gt;] [-c] [-e] &lt; input_pdb_file<br>&gt; output_pdb_file<br><br>Hope this helps,<br>-Debjani <br>---------------------------------------------------------------------------------------------------------------------<br><br><b><i>"Max Porrini mozz76(0)gmail.com" &lt;owner-chemistry|-|ccl.net&gt;</i></b> wrote:<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> Hi all<br>Does anybody know how I can add hydrogens to a system?<br>I've downloaded the pdb file of a enzyme and there aren't hydrogen atoms<br>(for instance the water molecule is formed only by the oxygen).<br>I'd like to saturate my system with the missing hydrogens. <br>Any tips will
 be very appreciated.<br>thanks a lot<br><span class="sg">MP<br> </span> </blockquote><br><p>&#32;
      <hr size=1>Shape Yahoo! in your own image.  
<a href="http://us.rd.yahoo.com/evt=48517/*http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7">Join our Network Research Panel today!</a>

--0-2122894649-1186067515=:27457--


From owner-chemistry@ccl.net Thu Aug  2 14:35:00 2007
From: "Sergio Emanuel Galembeck segalemb_._usp.br" <owner-chemistry|-|server.ccl.net>
To: CCL
Subject: CCL: adding hydrogens
Message-Id: <-34857-070802125401-8323-FHIwgotlDKAzjE/ATwZh2Q|-|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 Max,

    There several free softwares that add hydrogens in the structure
of a protein, as openbabel and chimera. The first is my choice.

             Best regards,

                    Sergio

Citando "Max Porrini mozz76(0)gmail.com" <owner-chemistry * ccl.net>:

> Hi all
> Does anybody know how I can add hydrogens to a system?
> I've downloaded the pdb file of a enzyme and there aren't hydrogen atoms
> (for instance the water molecule is formed only by the oxygen).
> I'd like to saturate my system with the missing hydrogens.
> Any tips will be very appreciated.
> thanks a lot
> MP
>


From owner-chemistry@ccl.net Thu Aug  2 15:19:00 2007
From: "lrf2103- -columbia.edu" <owner-chemistry%a%server.ccl.net>
To: CCL
Subject: CCL: adding hydrogens
Message-Id: <-34858-070802121035-4236-xbItW1+VDHdwJx0tg2R2Lg%a%server.ccl.net>
X-Original-From: lrf2103**columbia.edu
Content-Transfer-Encoding: 8bit
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Date: Thu, 02 Aug 2007 11:02:33 -0400
MIME-Version: 1.0


Sent to CCL by: lrf2103{=}columbia.edu
Hi Max,

There are lots of programs out there to do this, but your choice
will depend on how accurate you want the positions to be, and how
user friendly it should be. "Reduce" is a very easy-to-use program,
available from the Richardson lab at
http://kinemage.biochem.duke.edu/software/README.reduce.html.

If you want to get very accurate positions for the rotable
hydrogens, I did a survey of several of the methods that might help
you choose (Proteins. 2005 Nov 1;61:296-309). The most accurate
methods I tested were MCCE and Charmm.

Best wishes,
Lucy Forrest

> Hi all
> Does anybody know how I can add hydrogens to a system?
> I've downloaded the pdb file of a enzyme and there aren't
> hydrogen atoms
> (for instance the water molecule is formed only by the oxygen).
> I'd like to saturate my system with the missing hydrogens.
> Any tips will be very appreciated.
> thanks a lot
> MP
>


From owner-chemistry@ccl.net Thu Aug  2 15:53:00 2007
From: "Paul Hawkins phawkins===eyesopen.com" <owner-chemistry[*]server.ccl.net>
To: CCL
Subject: CCL: adding hydrogens
Message-Id: <-34859-070802150040-27120-E/b07Yl8Tn7uCicf8E4HBQ[*]server.ccl.net>
X-Original-From: Paul Hawkins <phawkins|a|eyesopen.com>
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Sent to CCL by: Paul Hawkins [phawkins**eyesopen.com]
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Just to clarify the post from Reaz, OMEGA2 will not add hydrogens to a 
protein. However babel3, our file format interconversion app, will 
perform just this function.

If you would like to apply for a free academic license to use babel3 (or 
any other parts of the OpenEye suite) please visit www.eyesopen.com. The 
academic license application can be found at

http://www.eyesopen.com/forms/academic_license_app.php



Paul.


Reaz Uddin riaasuddin%%yahoo.com wrote:
> I dont know what do you have in terms of molecular modeling software. 
> But Tripos sybyl can easily help you to add hydrogens. In addditon to 
> this, you can use opeeyes omega program. I guess opeyes babel can also 
> help you in this regard.
> Hope it helps You.
> Thanks
> REAZ
>
> */"Max Porrini mozz76(0)gmail.com" <owner-chemistry .. ccl.net>/* wrote:
>
>     Hi all
>     Does anybody know how I can add hydrogens to a system?
>     I've downloaded the pdb file of a enzyme and there aren't hydrogen
>     atoms
>     (for instance the water molecule is formed only by the oxygen).
>     I'd like to saturate my system with the missing hydrogens.
>     Any tips will be very appreciated.
>     thanks a lot
>     MP
>
>
>
>
> REAZUDDIN
> Research Scholar
> Department of Medicinal Chemistry and Pharmacognosy,
> College of Pharmacy, (M/C 781)
> University of Illinois at Chicago
> 833 S. Wood St.
> Chicago, IL 60612
> Email: ruddin .. uic.edu, riaasuddin .. yahoo.com
> ! Web: http://medchem.pharm.uic.edu/
>
> ------------------------------------------------------------------------
> Yahoo! oneSearch: Finally, mobile search that gives answers 
> <http://us.rd.yahoo.com/evt=48252/*http://mobile.yahoo.com/mobileweb/onesearch?refer=1ONXIC>, 
> not web links. 


-- 
Paul C. D. Hawkins
Senior Applications Scientist
OpenEye Scientific Software

phawkins]|[eyesopen.com
Ph. 505-473-7385 ext. 65


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From owner-chemistry@ccl.net Thu Aug  2 17:48:00 2007
From: "Marius Retegan marius.s.retegan[A]gmail.com" <owner-chemistry=-=server.ccl.net>
To: CCL
Subject: CCL:G: "gen" keyword for ONIOM
Message-Id: <-34860-070801194327-24588-Mw+KlHeJCzABDgPI7JDWaQ=-=server.ccl.net>
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Sent to CCL by: "Marius Retegan" [marius.s.retegan!^!gmail.com]

I think that warning that you are getting is self explanatory, you
have to define a basis set for your hydrogen atoms. For example if you
have cluster of Si and H, try using something like this at the end of
your input:

Si
6-31G*
****

H
3-21G*
****

I don't know believe that geom=connectivity has any connection with you error.

Marius

On 7/31/07, Gonzalo Jim nez-Os s gonzalo.jimenez]![unirioja.es
<owner-chemistry,+,ccl.net> wrote:
>
> Sent to CCL by: "Gonzalo  Jim  nez-Os  s" [gonzalo.jimenez-x-unirioja.es]
> Dear Nihan,
>
> I frequently get similar messages using ONIOM in G03, but I think that it is not striclty related to the use of the "gen" keyword. Note that employing the AM1 method generates a lot of warnings, what is a bit disturbing...Nevertheless, the failure in the SCF step (over 129 cycles) is more related with some inconsistency within the QM part. Try to add the keyword "geom=connectivity" to the input and/or to prepare a better starting structure in order to facilitate the generation of a more realiable initial guess. I hope it helps,
>
> Regards,
>
> ========================================================
> Gonzalo Jimnez-Oss
> Complejo Cientfico Tecnolgico
> Departamento de Qumica. Universidad de La Rioja
> Grupo de Sntesis Qumica de la Rioja, U.A.-C.S.I.C.
> C/ Madre de Dios, 51. E-26006 Logroo (La Rioja). Spain
> Tfn. +34-941-299630      Fax  +34-941-299621
> gonzalo.jimenez\a/unirioja.es
> http://www.unirioja.es/cu/gojimeo
> ========================================================
>
> ------------------------
> Sent to CCL by: "Nihan  Aldis" [naldis ~~ gmail.com]
> Dear CCLers,
> When I use gen keyword in Oniom calculation on a Silicon cluster, I have some problems.  This is part of my input:
> RunGauss
> %chk=Si353Gen2
> %nproc=1
> %mem=1000MB
> p opt oniom(b3lyp/Gen:am1/sparse) gfinput iop(6/7=3)
>
> gen
>
> 0 1 0 1 0 1
>  Si               0    1.724600   -4.250418    1.968610 H
>  Si               0    3.751190   -3.034175    1.924736 L H      1
>  Si               0    5.662891   -4.357333    1.929145 L
>  Si               0    6.231758   -5.525771    3.838685 L
>  Si               0    8.593935   -5.661679    3.806473 L
>  Si               0    9.324290   -4.582704    5.732750 L
>  Si               0   11.401024   -3.435620    5.647742 L
>  Si               0   11.390783   -1.944169    3.792553 L
>  Si               0    9.600614   -0.392726    3.864778 L
>  Si               0    9.613309    0.972654    1.922365 L
>  Si               0    9.567945   -0.388159    0.000714 L
>  Si               0    9.613275    0.961448   -1.928825 L
>  Si               0    9.600508   -0.415218   -3.863267 L
>  Si               0   11.390636   -1.966275   -3.782136 L
> ......................
> ........................
>  H                0    0.000606   14.105707    3.098136 L
>  H                0    1.190799   15.481702   -0.037854 L
>  H                0   -1.202043   15.474212   -0.037516 L
>
> 40 50 107 140 152 160 0
> 6-31G*
> ****
> 1 41 51 76 93 94 108 131 0
> 3-21G*
> ****
> 132 141 153 161 169 175 185 0
> 3-21G*
> ****
>
> When it ran, I got the following error in the output:
>
>  Warning!  H  atom  172 has  1 valence electrons but only   0 basis functions.
>  This is less than a minimal basis set!
>  Warning!  H  atom  176 has  1 valence electrons but only   0 basis functions.
>  This is less than a minimal basis set!
>  Warning!  H  atom  182 has  1 valence electrons but only   0 basis functions.
>  This is less than a minimal basis set!
>  Warning!  H  atom  186 has  1 valence electrons but only   0 basis functions.
>  This is less than a minimal basis set!
>  Warning!  H  atom  195 has  1 valence electrons but only   0 basis functions.
>  This is less than a minimal basis set!
>
>  IExCor= 402 DFT=T Ex=B+HF Corr=LYP ExCW=0 ScaHFX=  0.200000
>  ScaDFX=  0.800000  0.720000  1.000000  0.810000
>  IRadAn=      0 IRanWt=     -1 IRanGd=            0 ICorTp=0
>  NAtoms=  334 NActive=   41 NUniq=   41 SFac= 1.00D+00 NAtFMM=   60 Big=F
>  Leave Link  301 at Fri Jul 27 15:31:01 2007, MaxMem=  131072000 cpu:       0.0
>  (Enter /home/g03/l302.exe)
> ........................
> ...........................
>
>  >>>>>>>>>> Convergence criterion not met.
>  SCF Done:  E(RB+HF-LYP) =  -6064.80456753     A.U. after  129 cycles
>              Convg  =    0.8803D-04             -V/T =  2.0032
>              S**2   =   0.0000
>  KE= 6.045687912820D+03 PE=-2.555956789915D+04 EE= 7.901465986937D+03
>  Convergence failure -- run terminated.
>  Error termination via Lnk1e in /home/g03/l502.exe at Sat Jul 28 13:38:31 2007.
>  Job cpu time:  0 days 22 hours  6 minutes 44.1 seconds.
>  File lengths (MBytes):  RWF=    669 Int=      0 D2E=      0 Chk=    391 Scr=      1
>
> What can I do to use both the ONIOM and the gen keyword? Is there anything to add my input?
> Thank you
> Nihan Aldishttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--
> No virus found in this incoming message.
> Checked by AVG Free Edition.
> Version: 7.5.476 / Virus Database: 269.10.25/926 - Release Date: 29/07/2007 23:14>
>
>
>


From owner-chemistry@ccl.net Thu Aug  2 18:32:00 2007
From: "Steve Bowlus chezbowlus+/-comcast.net" <owner-chemistry{:}server.ccl.net>
To: CCL
Subject: CCL: adding hydrogens
Message-Id: <-34861-070802122200-15057-uW8tJsodiG5mKwm9lWnHFA{:}server.ccl.net>
X-Original-From: Steve Bowlus <chezbowlus===comcast.net>
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Sent to CCL by: Steve Bowlus [chezbowlus:_:comcast.net]
Most if not all modeling packages have this functionality.  If you need a program to do this, ArgusLab should work.

Steve

Max Porrini mozz76(0)gmail.com wrote:
> Hi all
> Does anybody know how I can add hydrogens to a system?
> I've downloaded the pdb file of a enzyme and there aren't hydrogen atoms
> (for instance the water molecule is formed only by the oxygen).
> I'd like to saturate my system with the missing hydrogens.
> Any tips will be very appreciated.
> thanks a lot
> MP