From owner-chemistry@ccl.net Fri Feb  9 00:03:01 2007
From: "Wayne Steinmetz WES04747===pomona.edu" <owner-chemistry|*|server.ccl.net>
To: CCL
Subject: CCL:G: ERROR in running gaussian
Message-Id: <-33568-070208235958-8547-EUHSIZJ0NH8yFYOKuZpMkA|*|server.ccl.net>
X-Original-From: "Wayne Steinmetz" <WES04747 a pomona.edu>
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Sent to CCL by: "Wayne Steinmetz" [WES04747+*+pomona.edu]
Although bonds are a human creation and are not required in a strictly
ab initio quantum calculation, it helps to be heading in the right
direction.  Many programs including Gaussian require the Hessian which
is often generated from molecular mechanics.

I examined your pdb structure.  It is very strange.  The connectivity in
the 5 aromatic rings is wrong.  Two of the rings are not connected to
the central antimony.  It appears that you have a pentacoordinatd
antimony(V) species.  What is the source of the structure?  Is it an
X-ray structure?
If so, the CHCl3 is a solvent of crystallization.  Do you need it in the
calculation?  I am puzzled by the two OH's.  Are they actually waters
and two of the H's don't show up in the crystal structure because of
crystal disorder.  Many of the pdb files in the crystallographic
databases are flawed. Once one knows the stoichiometry of the substance,
once can patch up the structure and then move ahead.  I would first
start with a calculation at a lower level of theory, e.g. a
semi-empirical calculation with a PM3 Hamiltonian. 

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: Thursday, February 08, 2007 3:34 PM
To: Wayne Steinmetz
Subject: CCL:G: ERROR in running gaussian


Sent to CCL by: "neeraj misra" [misraneeraj(0)gmail.com]

 I AM REPEATEDLY GETTING AN ERROR FOR THE FOLLOWING STRUCTURE WHOSE
INPUT
FILE I AM SENDING AS AN ATTACHMENT.THE GAUSSIAN PROCESSING SIMPLY CANNOT
PROCEDD AFTER A FEW SECONDS.PLEASE HELP ME IN LOCATING THE ERROR.

The Gaussian input file can be looked at:
   http://www.ccl.net/temp/TAN2OPTAMP1-inp.txt
while the PDB file at:
   http://www.ccl.net/temp/TAN2-PDB.txt


-- 
neeraj misra
ab initio research lab
department of physics
lucknow university 226006
indiahttp://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.


From owner-chemistry@ccl.net Fri Feb  9 06:24:00 2007
From: "Roger Kevin Robinson r.robinson[A]imperial.ac.uk" <owner-chemistry[-]server.ccl.net>
To: CCL
Subject: CCL: Percentage of Excited states species per Mol,
Message-Id: <-33569-070209060519-29642-+U5AKrJKf0UwziNjq9tGUA[-]server.ccl.net>
X-Original-From: Roger Kevin Robinson <r.robinson++imperial.ac.uk>
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Sent to CCL by: Roger Kevin Robinson [r.robinson---imperial.ac.uk]
Dear CCL,

Say you have a known volume of a species say 1 mole of OH radicals.

You then apply a constant known amount of energy at the right frequency 
to excite a certain percentage of of the mole of OH radicals to the 
lowest excited state. You also know the amount of energy needed to 
promote one OH radical to that excited state.

Would it be possible to calculate an approximate percentage of excited 
radicals at any given time ?

Any help appreciated.

Roger


From owner-chemistry@ccl.net Fri Feb  9 08:01:00 2007
From: "=?ISO-8859-1?Q?St=E9phane_Vellay?= stephane.vellay]^[free.fr" <owner-chemistry|*|server.ccl.net>
To: CCL
Subject: CCL: adding a gaussview movie into a power point slide
Message-Id: <-33570-070209043106-20109-lojTyWBmB8MISMWxaLh6Ug|*|server.ccl.net>
X-Original-From: =?ISO-8859-1?Q?St=E9phane_Vellay?= <stephane.vellay[a]free.fr>
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Sent to CCL by: =?ISO-8859-1?Q?St=E9phane_Vellay?= [stephane.vellay*_*free.fr]
Hello

To capture a video of all or part of your screen, use :
- Xvidcap for Linux (http://sourceforge.net/projects/xvidcap/)
- Camstudio for Windows (http://sourceforge.net/projects/camstudio/)
I hope it will be useful.

Have a nice day,
Stéphane Vellay

Le 8 févr. 07 à 21:50, Hunter, Ken ken.hunter . uleth.ca a écrit :

> I am looking to try to add a movie of a molecule vibrating for  
> educational purposes to demonstrate the various modes.  I am  
> familiar with how to visualize a frequency file in GaussView and  
> how to display the various modes but I was wondering if there is a  
> way to actually include such visualization in power point  
> presentation.  Furthermore is there a way to add a movie for the  
> optimization of a molecule into a presentation?
>
>
>
> Ken Hunter
>


From owner-chemistry@ccl.net Fri Feb  9 08:36:00 2007
From: "Sudipta Kumar Sinha sudipta*chem.iitkgp.ernet.in" <owner-chemistry:+:server.ccl.net>
To: CCL
Subject: CCL: parallelisation of namd software
Message-Id: <-33571-070208125052-21196-BZWyLOHRPeRRpDR5s1aEIQ:+:server.ccl.net>
X-Original-From: Sudipta Kumar Sinha <sudipta.:.chem.iitkgp.ernet.in>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Date: Thu, 8 Feb 2007 22:08:01 +0530 (IST)
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Sent to CCL by: Sudipta Kumar Sinha [sudipta : chem.iitkgp.ernet.in]

hi all,
    actually i am trying to simulate water by namd software and calculate 
some properties of water .but when i have tried to run namd i
have faced lots of difficulties.i am telling you that which steps i have 
done.

1)first install namd (NAMD_2.5_Linux-i686) in  /usr/local  in a server
2)generate .psf using.coor and charmm22 force field 3)then generate a
.conf file using .coor ,.psf,charmm22 force field input file
according to the format that are given at user guide. using the command
/usr/local/NAMD/NAMD_2.5_Linux-i686/namd2 water.conf
the namd program is working fine for single processor and single .conf
file and generate a single .DCD file.


now i want to run this program in a multi processor
parallel beowulf cluster.i am telling you which steps i have done.
1)i have made a nodelist file ,/home/sudip_ta/NAMD/namd.nodelist
2)using the command which is given at userguide of namd
/usr/local/NAMD/NAMD_2.5_Linux-i686/charmrun ++verbose
++nodelist /home/sudip_ta/NAMD/namd.nodelist namd2 +p3 
water.conf>water.log
,i have tried to run namd but it gives error which i am telling below
Charmrun> charmrun started...
Charmrun> using /home/sudip_ta/NAMD/namd.nodelist as nodesfile
Charmrun> rsh (client1:0d) started
Charmrun> rsh (client2:1d) started
Charmrun> rsh (client6:2d) started
Charmrun> node programs all started
Charmrun> error 0 attaching to node:
Timeout waiting for node-program to connect

if anyone aware about this problem kindly tell me what is my wrong and 
also kindly tell me exact procedure step by step.
i have spent lot of time to solve the prblems.but ultimately
failure.please give me suggestions and help.
      thanks in advance.
                                             sudipta.


From owner-chemistry@ccl.net Fri Feb  9 09:11:01 2007
From: "Dan Maftei dan.maftei]![chem.uaic.ro" <owner-chemistry,,server.ccl.net>
To: CCL
Subject: CCL:G: adding a gaussview movie into a power point slide
Message-Id: <-33572-070209012159-4833-o5dLekg51a8hy2VhuJ3v4A,,server.ccl.net>
X-Original-From: Dan Maftei <dan.maftei/a\chem.uaic.ro>
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Date: Fri, 09 Feb 2007 08:21:41 +0200
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Sent to CCL by: Dan Maftei [dan.maftei-*-chem.uaic.ro]
This is a multi-part message in MIME format.
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Both geometry optimization and vibration modes movies can be easily made
using Molden (http://www.cmbi.ru.nl/molden/molden.html). You'll need an
X server to run Molden, so a Unix-like operating system (as Linux) may
be helpful. Once you have Molden running select "Read" from the control
dialog and select the Gaussian output. There is a small button on that
dialog (the second one) which creates one GIF file for each optimization
step. The GIFs will be created in the working directory as molxxx.gif
(so a maximum number of 999 optimisation steps are allowed, a huge
number, isn't it?). To assemble those GIFs you may try to "convert" them
by using some graphics software (i.e. ImageMagick's convert):

convert -adjoin mol*.gif animated_output.gif

Dan Maftei.

Hunter, Ken ken.hunter . uleth.ca wrote:
> I am looking to try to add a movie of a molecule vibrating for
> educational purposes to demonstrate the various modes.  I am familiar
> with how to visualize a frequency file in GaussView and how to display
> the various modes but I was wondering if there is a way to actually
> include such visualization in power point presentation.  Furthermore is
> there a way to add a movie for the optimization of a molecule into a
> presentation?
> 
>  
> 
> Ken Hunter
> 


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fn:Dan Maftei
n:Maftei;Dan
org:"Alexandru Ioan Cuza" University;Physical, Theoretical and Materials Chemistry
adr:Nr. 11;;Bd. Carol 1, ;Iasi;;700506;Romania
email;internet:dan.maftei::chem.uaic.ro
title:Faculty of Chemistry
tel;work:+40232-201307
tel;cell:+40740-262227
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url:http://www.chem.uaic.ro/~danmaftei
version:2.1
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--------------030502090201060804060703--


From owner-chemistry@ccl.net Fri Feb  9 09:46:00 2007
From: "Adlane sayede adlane.sayede###gmail.com" <owner-chemistry#,#server.ccl.net>
To: CCL
Subject: CCL: adding a gaussview movie into a power point slide
Message-Id: <-33573-070209040902-18123-nANl1vHuUK5L3Wevg0uu4Q#,#server.ccl.net>
X-Original-From: "Adlane sayede" <adlane.sayede##gmail.com>
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	boundary="----=_Part_21994_10686697.1171008291762"
Date: Fri, 9 Feb 2007 09:04:51 +0100
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Sent to CCL by: "Adlane sayede" [adlane.sayede%a%gmail.com]

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Hi,

Wink is a Tutorial and Presentation creation software.... make screen copies
(movie) from your animation and save them in avi or flash formats.

A. Sayede

On 2/8/07, Hunter, Ken ken.hunter . uleth.ca <owner-chemistry-x-ccl.net>
wrote:
>
>  I am looking to try to add a movie of a molecule vibrating for
> educational purposes to demonstrate the various modes.  I am familiar with
> how to visualize a frequency file in GaussView and how to display the
> various modes but I was wondering if there is a way to actually include such
> visualization in power point presentation.  Furthermore is there a way to
> add a movie for the optimization of a molecule into a presentation?
>
>
>
> Ken Hunter
>

------=_Part_21994_10686697.1171008291762
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Hi,<br><br>Wink is a Tutorial and Presentation creation software.... make screen copies (movie) from your animation and save them in avi or flash formats.&nbsp; <br><br>A. Sayede<br> <br><div><span class="gmail_quote">On 2/8/07, 
<b class="gmail_sendername">Hunter, Ken ken.hunter . <a href="http://uleth.ca">uleth.ca</a></b> &lt;<a href="mailto:owner-chemistry-x-ccl.net">owner-chemistry-x-ccl.net</a>&gt; wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">









<div link="blue" vlink="purple" lang="EN-US">

<div>

<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">I am looking to try to add a movie of a molecule vibrating
for educational purposes to demonstrate the various modes. &nbsp;I am familiar
with how to visualize a frequency file in GaussView and how to display the
various modes but I was wondering if there is a way to actually include such
visualization in power point presentation. &nbsp;Furthermore is there a way to add
a movie for the optimization of a molecule into a presentation?</span></font></p>

<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">&nbsp;</span></font></p>

<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">Ken Hunter</span></font></p>

</div>

</div>


</blockquote></div><br>

------=_Part_21994_10686697.1171008291762--


From owner-chemistry@ccl.net Fri Feb  9 10:20:00 2007
From: "Simmie, John john.simmie.:.nuigalway.ie" <owner-chemistry,server.ccl.net>
To: CCL
Subject: CCL: adding a gaussview movie into a power point slide
Message-Id: <-33574-070209100529-22508-Yxe8yhqMaVjTJStLIrmSSw,server.ccl.net>
X-Original-From: "Simmie, John" <john.simmie/./nuigalway.ie>
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Sent to CCL by: "Simmie, John" [john.simmie::nuigalway.ie]
SnagIt is a very good Windows capture utility from TechSmith
which will do what you want ...
John Simmie//NUI Galway, Ireland

Le 8 févr. 07 à 21:50, Hunter, Ken ken.hunter . uleth.ca a écrit :

> I am looking to try to add a movie of a molecule vibrating for  
> educational purposes to demonstrate the various modes.  I am  
> familiar with how to visualize a frequency file in GaussView and  
> how to display the various modes but I was wondering if there is a  
> way to actually include such visualization in power point  
> presentation.  Furthermore is there a way to add a movie for the  
> optimization of a molecule into a presentation?
>
>
>
> Ken Hunter


From owner-chemistry@ccl.net Fri Feb  9 10:56:00 2007
From: "Breton, Gary gbreton^_^berry.edu" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL: Drawing TS for QST2 calculations
Message-Id: <-33575-070209101412-26718-HEWPvwipItrhIggIOZBNww:server.ccl.net>
X-Original-From: "Breton, Gary" <gbreton a berry.edu>
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Sent to CCL by: "Breton, Gary" [gbreton::berry.edu]
I will often start from the adduct and work my way back.  Build the adduct
and then sever bonds to form the two reactants.  GausView allows you to move
the entire "group" upon lengthening the bonds between the two reactants.

Atom labeling may be a little more difficult if you want the software to
automatically number.  The times that I've set up QST2 calculations I've
manually written the input files and then manually pasted in the atom
coordinates (to correspond to the product) after running a simple AM1
calculation on the "transition state" to obtain the atom coordinates.

Good luck!


Gary W. Breton
Associate Professor
Department of Chemistry
Berry College
PO Box 495016
Mount Berry, GA 30149




> Sent to CCL by: "Adil  Zhugralin" [zhugrali],[bc.edu]
> Dear all:
> 
> I'm trying to get 2 molecules to react to give me an adduct. Unfortunately,
> the molecules are big (overall ~100 atoms). In GaussView, I find, it is
> practically impossible to draw them such that the proper trajectory is
> maintained and at the same time get the labeling to be consistent. Any
> suggestions about how to do it? Any software that could assist in creating
> creating starting material MolGroups? Thanks in advance.
> 
> Sincerely,
> 
> Adil> 
> 
>


From owner-chemistry@ccl.net Fri Feb  9 14:04:00 2007
From: "Shobe, David David.Shobe=sud-chemie.com" <owner-chemistry{}server.ccl.net>
To: CCL
Subject: CCL: Percentage of Excited states species per Mol,
Message-Id: <-33576-070209140000-3761-pCD1hRDbnZqri7g0G+RNMw{}server.ccl.net>
X-Original-From: "Shobe, David" <David.Shobe.:.sud-chemie.com>
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Sent to CCL by: "Shobe, David" [David.Shobe(~)sud-chemie.com]
You'd have to also know the kinetics of reversion to the ground state.  Once you have that, it's basically a calculus / diff eq problem.

Regards,
--David Shobe
  Süd-Chemie, Inc.
 
Attention to detial is essentail.
 

-----Original Message-----
> From: owner-chemistry{}ccl.net [mailto:owner-chemistry{}ccl.net] 
Sent: Friday, February 09, 2007 5:12 AM
To: Shobe, David
Subject: CCL: Percentage of Excited states species per Mol,


Sent to CCL by: Roger Kevin Robinson [r.robinson---imperial.ac.uk] Dear CCL,

Say you have a known volume of a species say 1 mole of OH radicals.

You then apply a constant known amount of energy at the right frequency to excite a certain percentage of of the mole of OH radicals to the lowest excited state. You also know the amount of energy needed to promote one OH radical to that excited state.

Would it be possible to calculate an approximate percentage of excited radicals at any given time ?

Any help appreciated.

Rogerhttp://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 Fri Feb  9 14:38:00 2007
From: "Shobe, David David.Shobe]^[sud-chemie.com" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL:G: ERROR in running gaussian
Message-Id: <-33577-070209140306-4134-gJKokDZHWSap5rm98+rrIw:server.ccl.net>
X-Original-From: "Shobe, David" <David.Shobe()sud-chemie.com>
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Sent to CCL by: "Shobe, David" [David.Shobe_+_sud-chemie.com]
It would help if we had the output also--or at least the error message.

Regards,
--David Shobe
  Süd-Chemie, Inc.
 
Attention to detial is essentail.
 

-----Original Message-----
> From: owner-chemistry!=!ccl.net [mailto:owner-chemistry!=!ccl.net] 
Sent: Thursday, February 08, 2007 6:34 PM
To: Shobe, David
Subject: CCL:G: ERROR in running gaussian


Sent to CCL by: "neeraj misra" [misraneeraj(0)gmail.com]

 I AM REPEATEDLY GETTING AN ERROR FOR THE FOLLOWING STRUCTURE WHOSE INPUT FILE I AM SENDING AS AN ATTACHMENT.THE GAUSSIAN PROCESSING SIMPLY CANNOT PROCEDD AFTER A FEW SECONDS.PLEASE HELP ME IN LOCATING THE ERROR.

The Gaussian input file can be looked at:
   http://www.ccl.net/temp/TAN2OPTAMP1-inp.txt
while the PDB file at:
   http://www.ccl.net/temp/TAN2-PDB.txt


--
neeraj misra
ab initio research lab
department of physics
lucknow university 226006
indiahttp://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 Fri Feb  9 15:49:00 2007
From: "Alfredo Mayall Simas simas .. ufpe.br" <owner-chemistry(-)server.ccl.net>
To: CCL
Subject: CCL: Lanthanum Basis sets + 28 Core ECP
Message-Id: <-33578-070209154607-26053-WCu6x8M5IuXGs45+uZ/D9A(-)server.ccl.net>
X-Original-From: "Alfredo Mayall Simas" <simas{}ufpe.br>
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Sent to CCL by: "Alfredo Mayall Simas" [simas###ufpe.br]
This is a multi-part message in MIME format.

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Dear Dr. Sanjay,

Perhaps you may also eventually need, in your research, to fully =
optimize geometries of lanthanum complexes.

In such case, I would like to suggest that you try geometries obtained =
with the Lanthanide Complexes Sparkle/AM1 model.=20

Sparkle/AM1 is presently implemented in the new MOPAC2007. For more =
information, please visit http://www.sparkle.pro.br.

Regards,
Alfredo Simas=20

  ----- Original Message -----=20
  From: CCL CCL computationalchemist##gmail.com=20
  To: Simas, Alfredo Mayall =20
  Sent: Thursday, February 08, 2007 12:16 PM
  Subject: CCL: Lanthanum Basis sets + 28 Core ECP

  Dear Folks,
  I'm Looking for a basis set and ecp, that supports 28 core and 21 =
active electrons for lanthanum to be used in turbomole calculations. Is =
there any that you come across. If so, please keep me informed.=20
  thanks in advance.
  --=20
  Regards,
  Dr. Sanjay 
------=_NextPart_000_003D_01C74C72.2462B5A0
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=3DContent-Type content=3D"text/html; =
charset=3Diso-8859-1">
<META content=3D"MSHTML 6.00.5730.11" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>Dear Dr. Sanjay,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Perhaps you may also eventually need, =
in your=20
research, to fully optimize geometries of lanthanum =
complexes.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>In&nbsp;such case,&nbsp;I would like to =
suggest=20
that you try&nbsp;geometries&nbsp;obtained&nbsp;with&nbsp;the <A=20
href=3D"http://www.sparkle.pro.br/">Lanthanide Complexes Sparkle/AM1</A> =
model.=20
</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Sparkle/AM1 is&nbsp;presently =
implemented in the=20
new MOPAC2007. <FONT face=3DArial size=3D2>For more information, please =
visit <A=20
href=3D"http://www.sparkle.pro.br/">http://www.sparkle.pro.br</A>.</FONT>=
</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Regards,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Alfredo Simas</FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<BLOCKQUOTE dir=3Dltr=20
style=3D"PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; =
BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
  <DIV style=3D"FONT: 10pt arial">----- Original Message ----- </DIV>
  <DIV=20
  style=3D"BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: =
black"><B>From:</B>=20
  <A title=3Downer-chemistry(!)ccl.net =
href=3D"mailto:owner-chemistry(!)ccl.net">CCL CCL=20
  computationalchemist##gmail.com</A> </DIV>
  <DIV style=3D"FONT: 10pt arial"><B>To:</B> <A title=3Dsimas(!)ufpe.br=20
  href=3D"mailto:simas(!)ufpe.br">Simas, Alfredo Mayall </A> =
</DIV>
  <DIV style=3D"FONT: 10pt arial"><B>Sent:</B> Thursday, February 08, =
2007 12:16=20
  PM</DIV>
  <DIV style=3D"FONT: 10pt arial"><B>Subject:</B> CCL: Lanthanum Basis =
sets + 28=20
  Core ECP</DIV>
  <DIV><FONT face=3DArial size=3D2></FONT><BR clear=3Dall>Dear =
Folks,</DIV>
  <DIV>I'm Looking for a basis set and ecp, that supports 28 core and 21 =
active=20
  electrons for lanthanum to be used in turbomole calculations. Is there =
any=20
  that you come across. If so, please keep me informed. </DIV>
  <DIV>thanks in advance.</DIV>
  <DIV>-- <BR>Regards,<BR>Dr. Sanjay </DIV></BLOCKQUOTE></BODY></HTML>

------=_NextPart_000_003D_01C74C72.2462B5A0--


From owner-chemistry@ccl.net Fri Feb  9 17:23:00 2007
From: "Mark Thompson mark^arguslab.com" <owner-chemistry..server.ccl.net>
To: CCL
Subject: CCL: Molegro
Message-Id: <-33579-070209171906-24501-jDQMNZPhiE960rJj+/LH7w..server.ccl.net>
X-Original-From: Mark Thompson <mark ~~ arguslab.com>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Fri, 09 Feb 2007 14:18:44 -0800
MIME-Version: 1.0


Sent to CCL by: Mark Thompson [mark . arguslab.com]
Hi Richard,

I would like to try a representative docking of this system in ArgusLab 
5.0.

Would you be willing to share structures with me?  I will of course keep 
the structures private and let you know my results.

Cheers,
Mark Thompson

************************************
Mark Thompson
http://www.arguslab.com
mark^^^arguslab.com
************************************



> On 2/7/07, Richard Leo Wood rwoodphd(a)msn.com <owner-chemistry _ 
> ccl.net> wrote:
>>
>> Sent to CCL by: "Richard Leo Wood" [rwoodphd!A!msn.com]
>> Hi all,
>>
>> My ligands are hexapeptides, so they are not really proteins, but I 
>> suppose could be classified as "small molecules".  They are known to 
>> inhibit the receptor I am trying to "dock" them to (actually I'm 
>> trying to estimate the binding energies to the receptor).
>>
>> I have a concern about the results that I am getting.  They don't 
>> seem to be reproducible.  That is, if I run the same docking 
>> calculation over and over again, I get different results.  I wonder 
>> why that is. I've noticed that the cavity sizes (for the largest 
>> cavity) vary from run to run, as well.
>>
>> I would think that if I used the same settings each time, I should 
>> get the same binding affinities, but I'm not.
>>
>> TIA,
>> Richardhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: 
> http://server.ccl.net/chemistry/announcements/conferences/>
>
>
>
>
>

-- 



************************************
Mark Thompson
Planaria Software LLC
http://www.arguslab.com
mark^^^arguslab.com
************************************


From owner-chemistry@ccl.net Fri Feb  9 19:59:01 2007
From: "Marc Noguera Julian marc!^!klingon.uab.es" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL:G: ERROR in running gaussian
Message-Id: <-33580-070209164816-20785-wYvFjSzW+By7szwHaIgRWg(0)server.ccl.net>
X-Original-From: Marc Noguera Julian <marc!=!klingon.uab.es>
Content-transfer-encoding: 8BIT
Content-type: text/plain; charset=iso-8859-1
Date: Fri, 09 Feb 2007 22:04:38 +0100
MIME-version: 1.0


Sent to CCL by: Marc Noguera Julian [marc ~ klingon.uab.es]
Dear Neeraj,
I'd say you are having a format problem. Are you using gaussian for linux with
a windows generated input file?
using wget to get your input on a linux machine results in obtaining a DOS
file which is not correctly processed by linux gaussian.
Try "dos2unix" for linux to convert format.
hope it helps,
Marc
On Fri, 09 Feb 2007 20:02:41 +0100, Shobe, David David.Shobe]^[sud-chemie.com
wrote
> Sent to CCL by: "Shobe, David" [David.Shobe_+_sud-chemie.com]
> It would help if we had the output also--or at least the error message.
> 
> Regards,
> --David Shobe
>   Süd-Chemie, Inc.
> 
> Attention to detial is essentail.
> 
> -----Original Message-----
> > From: owner-chemistry:-:ccl.net [mailto:owner-chemistry:-:ccl.net] 
> Sent: Thursday, February 08, 2007 6:34 PM
> To: Shobe, David
> Subject: CCL:G: ERROR in running gaussian
> 
> Sent to CCL by: "neeraj misra" [misraneeraj(0)gmail.com]
> 
>  I AM REPEATEDLY GETTING AN ERROR FOR THE FOLLOWING STRUCTURE WHOSE 
> INPUT FILE I AM SENDING AS AN ATTACHMENT.THE GAUSSIAN PROCESSING 
> SIMPLY CANNOT PROCEDD AFTER A FEW SECONDS.PLEASE HELP ME IN LOCATING 
> THE ERROR.
> 
> The Gaussian input file can be looked at:
>    http://www.ccl.net/temp/TAN2OPTAMP1-inp.txt
> while the PDB file at:
>    http://www.ccl.net/temp/TAN2-PDB.txt
> 
> --
> neeraj misra
> ab initio research lab
> department of physics
> lucknow university 226006
> indiahttp://www.ccl.net/cgi-
>
bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis
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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 
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------------------------------------------------------
Marc Noguera i Julian, PhD
Tècnic de suport a la recerca
Despatx C7-149. Edifici Cn.
Campus UAB. Bellaterra
08193. Barcelona
email: marc_at_klingon.uab.es
web: http://klingon.uab.es/marc
Tlf/Phone: 00 34 935812173
-------------------------------------------------------


From owner-chemistry@ccl.net Fri Feb  9 20:33:00 2007
From: "JanK Labanowski janl^_^speakeasy.net" <owner-chemistry~!~server.ccl.net>
To: CCL
Subject: CCL: Free MOE Workshop and Pharmacophore Modeling, UCSD, March 14, 2007
Message-Id: <-33581-070209202350-9523-wjT7iKk1U7JHwX+cYyM5AA~!~server.ccl.net>
X-Original-From: "JanK  Labanowski" <janl:speakeasy.net>
Date: Fri, 9 Feb 2007 20:23:47 -0500


Sent to CCL by: "JanK  Labanowski" [janl]-[speakeasy.net]

Chemical Computing Group (CCG) is conducing a MOE Workshop and a
Pharmacophore Modeling training session on Wednesday March 14,
2007 from 1:00 - 5:00PM at the University of California in San
Diego.

The workshop will focus on scientific discussion and a training
session on Pharmacophore Derivation, Elucidation and Searching as
well as an overview of the new features in the latest version of
MOE (2006.08). We welcome attendees to bring questions, ideas and
suggestions.

Location:
University of California, San Diego:
UCSD Extension
6925 Lusk Blvd
San Diego, CA 92121
Room 104

Details and registration available on line: 
http://www.chemcomp.com/ssupport-workshop.htm

There is no charge for attending the workshop, but space is
limited so please register in advance.

Please contact Lisa Subissati (lsubissati,+,chemcomp.com) with any
questions.


From owner-chemistry@ccl.net Fri Feb  9 21:11:01 2007
From: "Lisa Subissati subissati-.-chemcomp.com" <owner-chemistry__server.ccl.net>
To: CCL
Subject: CCL: MOE North American User Group Meeting 2007, Montreal, Canada
Message-Id: <-33582-070209204345-24135-/r9cjpIQUS9LJ2SyxJK2GQ__server.ccl.net>
X-Original-From: "Lisa  Subissati" <subissati * chemcomp.com>
Date: Fri, 9 Feb 2007 20:43:41 -0500


Sent to CCL by: "Lisa  Subissati" [subissati:-:chemcomp.com]
North American User Group Meeting 2007
June 26 - 29, 2007
Montreal, Canada
http://www.chemcomp.com/ugm-2007.htm

Meeting Format
The user group meeting will consist of scientific oral presentations by MOE users describing research projects utilizing the MOE software. CCG staff 
will present recent developments and future directions in MOE.

MOE Training
This year, training courses will be offered prior to the oral presentations. Training is included in the conference fee, and laptop computers with 
the MOE software will be available for participants.

Abstract Submission
MOE users are invited to present a talk, software demonstration, or a poster of their research. Proposals are now being accepted using the Talk & Poster Submission form. Presenters of accepted talks will be waived 
the registration fee.
Abstract deadline is March 23, 2007.

Registration
Before March 31, 2007 conference fees are 300 U.S. After April 1, 2007 fees are 400 U.S. Complete the registration form today.

More information on the meeting and accommodation details can be found from the side menu. To speak with someone directly please contact Lisa Subissati at: 514 393 1055 ext. 43.