From owner-chemistry@ccl.net Sat Jun  9 05:38:00 2007
From: "paritosh mondal paritos++tezu.ernet.in" <owner-chemistry a server.ccl.net>
To: CCL
Subject: CCL: Computational chemistry
Message-Id: <-34447-070609053327-2291-JzBuRS5Ru5KE5tbV9MHSfQ a server.ccl.net>
X-Original-From: "paritosh  mondal" <paritos+/-tezu.ernet.in>
Date: Sat, 9 Jun 2007 05:33:15 -0400


Sent to CCL by: "paritosh  mondal" [paritos : tezu.ernet.in]
Hi, 
With GAMESS program, I was tring for optimization of a 5T cluster of zeolite. I tried optimization keeping the coordinate of dangling atoms fixed. In the input files, I mention IFCART= Identity no. of all the atoms to be fixed.
 Every time message comes as   "constant list is too long"
I wanted to fixed the coordinates of 12 atoms.
What to do? Please help me.


Paritosh Mondal
paritos#%#tezu.ernet.in
Department of Chemical Sciences
Tezpur University
Tezpur
Assam
India-784028


From owner-chemistry@ccl.net Sat Jun  9 06:13:00 2007
From: "Dr. Alexander Hofmann ah**chemie.hu-berlin.de" <owner-chemistry(!)server.ccl.net>
To: CCL
Subject: CCL:G: post-Hartree claculations, advice needed
Message-Id: <-34448-070609042238-28331-Kgag8lIxvL3+EqNaX/G/SA(!)server.ccl.net>
X-Original-From: "Dr. Alexander Hofmann" <ah===chemie.hu-berlin.de>
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Date: Sat, 09 Jun 2007 08:49:16 +0200
MIME-Version: 1.0


Sent to CCL by: "Dr. Alexander Hofmann" [ah,chemie.hu-berlin.de]
Dear Matthias,

I'd like to devide your question into two parts:
- closed shell
- open shell

closed shell:
- Skip all configuration interaction (CI) methods. They are not size 
consistent and will drive you crazy in case of dimers and so on.
- The Moeller-Plesset series is a good start for having correlation 
beyond DFT, which is important for van der Waals interaction (Ar2).
Since CC scales similar like the MP series, I'd suggest to go along with 
CC. It's often the better choice for less cost, especially because you 
want (!) to consider triples excitations in your method. Just benchmark 
a little with your pet Ar2 ...
Appropriate codes are ACESII (http://www.aces2.de) or MOLPRO 
(http://www.molpro.net). The former code has best functionality, the 
latter is very fast. This choice depends on if you are going to optimze 
your structure or want to screen the potential energy surface.

- open shell
In principle the same applies, but you might run into degeneracy (multi 
configuration) challanges, where I'm no expert.

Good luck!

Alexander


Matthias Gottschalk gottschalk~~gfz-potsdam.de wrote:
> Dear colleagues
> 
> I hope that somebody could give me some advice.
> I want to calculate energies for dimers and trimers to extract accurate 
> potentials using post Hartree methods (also for "large" distances > 5 
> Angstroms). I intend to do this for closed- and open-shell systems (UHF) 
> consisting of simple atoms (in the moment).
> Because I am not a computational chemistry specialist I did some reading 
> and as a result I concluded that methods like MP4, CCSD and QCISD might 
> be appropriate using a basis set like aug-cc-pVQZ might be appropriate.
> I did success-full calculations for Ar dimers with gaussian g03 
> reproducing published results which made me confident. I failed for 
> trimers using these evolved methods so long, however (might be due to 
> that I have only a 32 bit compiled version and the required real memory 
> exceeds 2.2 GB possible with 32 bit, I do have 8 GB, however). MP2 
> trimers with more simple basis sets work, but that might be not what I want?
> 
> Now my questions are:
> 
> 1. are the methods described above adequate?
> 2. which of the many programs available could be recommended to use?
> 
> Thanks
> 
> Matthias
> 
> -- 
> 
> Prof. Dr. Matthias Gottschalk
> GeoForschungsZentrum
> Sektion 4.1
> Telegrafenberg
> 14473 Potsdam
> Germany
> 
> tel/fax  +49 (0) 331 288-1418/1402
> 
> 

-- 

Dr. Alexander Hofmann

Humboldt-Universitaet zu Berlin
Institut fuer Chemie
Arbeitsgruppe Quantenchemie

Post:     Unter den Linden 6
           10099 Berlin
Visitors: Brook-Taylor-Strasse 2
           12489 Berlin

ah chemie.hu-berlin.de
   **

Tel.: +49-30-2093-7138
Fax.: +49-30-2093-7136

http://www.chemie.hu-berlin.de/ag_sauer/index.html

PGP-Key: wwwkeys.de.pgp.net ID: D9D62D35


From owner-chemistry@ccl.net Sat Jun  9 11:12:00 2007
From: "Marius Retegan marius.s.retegan-x-gmail.com" <owner-chemistry- -server.ccl.net>
To: CCL
Subject: CCL:G: calculation
Message-Id: <-34449-070608131548-19163-sR7aJxqWE69zAeRO9RrZnw- -server.ccl.net>
X-Original-From: "Marius Retegan" <marius.s.retegan+*+gmail.com>
Content-Type: multipart/alternative; 
	boundary="----=_Part_64861_25829868.1181318988603"
Date: Fri, 8 Jun 2007 18:09:48 +0200
MIME-Version: 1.0


Sent to CCL by: "Marius Retegan" [marius.s.retegan=gmail.com]
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I might be wrong, but as far as I know there are no PM3 parameters for iron
in Gaussian 03.

On 6/8/07, Mevlut YILDIZ mewlutyildiz=gmail.com <owner-chemistry]^[ccl.net>
wrote:
>
>
> Sent to CCL by: "Mevlut  YILDIZ" [mewlutyildiz(!)gmail.com]
>
> Dear all,
>      I am using Gaussian 03W program to optimize inorganic molecule
> containing Fe with 257 atoms applying PM3 method. the job has stopped at
> 43rd iteration. I decided to change the method as oniom (B3LYP with LANL2DZ
> basis set for high layer and PM3 for low layer). altought B3LYP/LANL2DZ was
> applied to the part of the molecule which contain Fe, I have obtain same
> results:the job has stopped at 43rd iteration. I would like to thanks your
> kind attention and advices.
>                          REGARDS.>
>
>
>

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I might be wrong, but as far as I know there are no PM3 parameters for iron in Gaussian 03.<br><br><div><span class="gmail_quote">On 6/8/07, <b class="gmail_sendername">Mevlut YILDIZ mewlutyildiz=<a href="http://gmail.com">
gmail.com</a></b> &lt;<a href="mailto:owner-chemistry]^[ccl.net">owner-chemistry]^[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;">
<br>Sent to CCL by: &quot;Mevlut&nbsp;&nbsp;YILDIZ&quot; [mewlutyildiz(!)gmail.com]<br><br>Dear all,<br>&nbsp;&nbsp;&nbsp;&nbsp; I am using Gaussian 03W program to optimize inorganic molecule containing Fe with 257 atoms applying PM3 method. the job has stopped at 43rd iteration. I decided to change the method as oniom (B3LYP with LANL2DZ basis set for high layer and PM3 for low layer). altought B3LYP/LANL2DZ was applied to the part of the molecule which contain Fe, I have obtain same results:the job has stopped at 43rd iteration. I would like to thanks your kind attention and advices.
<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; REGARDS.<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;&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> or use<br>&nbsp;&nbsp;&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
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From owner-chemistry@ccl.net Sat Jun  9 11:46:01 2007
From: "Warren DeLano warren-.-delsci.com" <owner-chemistry^_^server.ccl.net>
To: CCL
Subject: CCL: Download free trial of a new generation computer aided drug design software (Quantum 3.3.)
Message-Id: <-34450-070609035043-24588-BtDTh5VEM6DS1zO811ALQw^_^server.ccl.net>
X-Original-From: "Warren DeLano" <warren{:}delsci.com>
Content-class: urn:content-classes:message
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Date: Sat, 9 Jun 2007 01:00:40 -0700
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Sent to CCL by: "Warren DeLano" [warren],[delsci.com]

This is a multi-part message in MIME format.

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Dear Maxim,
=20
Congratulations on your product release!  It is quite gratifying to see =
another company taking PyMOL seriously as a development platform, =
despite its shortcomings.  Quantum is an impressive early example of one =
of the many types of things the unrestricted open-source PyMOL source =
code is intended to enable.  In fact, I am astounded by all that your =
company has accomplished independently using PyMOL, with nary a word =
> from Moscow! =20
=20
However, one condition from the PyMOL open-source (top-level) LICENSE =
file seems to have been inadvertently overlooked (note text between =
asterisks):   "Permission to use, copy, modify, distribute, and =
distribute modified versions of this software and its documentation for =
any purpose and without fee is hereby granted, **** provided that the =
above copyright notice appears in all copies and that both the copyright =
notice and this permission notice appear in supporting documentation, =
****"
=20
Please remedy this (presumed unintentional) breach of the Copyright =
terms as soon as practical by (1) enclosing a copy of PyMOL's original =
LICENSE file in all product distributions (buried in a Quantum =
subdirectory is fine), and by (2) including the text of the PyMOL =
copyright and permission notices somewhere in the supporting =
documentation (fine as an appendix at the end of the manual).  Prompt =
action will surely alleviate concerns that have been raised regarding =
the legal status of the Quantum product vis-=E0-vis PyMOL. =20
=20
Just to reiterate, so that everyone is clear: =20
=20
In addition to development of new free and open-source tools, it is also =
my desire to see new independent commercial products built on the PyMOL =
foundation.  PyMOL is BSD-ish rather than GPL-ish for precisely that =
reason, and I do hope that Quantum and other like efforts will prove =
successful and have numerous positive impacts on the field.  However, it =
is of critical import that such efforts rest on a solid foundation of =
compliance with the very minimal legal requirements associated with =
derivative use of the PyMOL open-source code. =20
=20
If ever there is any doubt regarding terms, the best way to achieve =
certainty is to check in with me in advance of product release (before =
it becomes a public matter).  Another reason to talk to me early on is =
that, in some cases, I may even be available to help with the =
development work.
=20
Thank you and everyone else for compliance with the PyMOL open-source =
terms!
=20
Cheers,=20
=20
Warren L. DeLano, Ph.D.
warren(!)delsci.com
Author of PyMOL
Founder of DeLano Scientific LLC


________________________________

	From: owner-chemistry(!)ccl.net [mailto:owner-chemistry(!)ccl.net]=20
	Sent: Friday, June 08, 2007 8:33 AM
	To: Warren DeLano
	Subject: CCL: Download free trial of a new generation computer aided =
drug design software (Quantum 3.3.)
=09
=09
	Dear Colleagues,=20
	=20
	Let me introduce you a  free trial of new CADD software, which is  all =
CCL community is=20
	invited to download, compare and discuss at CCL.
=09
	Quantum  contains modules for  industrial strength docking / virtual=20
	screening of compound libraries  on  flexible proteins, accurate IC50 =
calculations and chemical properties=20
	prediction tools (Water and DMSO solubility and LogP) and protein =
analysis=20
	tools.
=09
	 QUANTUM software employs advanced molecular simulations techniques =
rather
	 than statistically trained scores to obtain binding free energies of =
the
	 docked compounds. As a result QUANTUM can be used as a robust and =
accurate
	 in silico tool for hit identification and lead optimization.
=09
	This physically-solid approach provides a number of definite advantages =
and=20
	opens new opportunities in drug discovery. The main of them are as =
follows:
=09
	1. ACCURACY
=09
	2. PREDICTION OF NEW CLASSES OF INHIBITORS
=09
	3. POSSIBILITY TO IDENTIFY INHIBITORS FOR TARGETS WITH NO KNOWN =
LIGANDS.
=09
	4. DRAMATICAL REDUCTION IN FALSE POSITIVES
=09
	5. FULL PROTEIN FLEXIBILITY IS TAKEN INTO CONSIDERATION
=09
	6. NO TRAINING SETS
=09
	7. UNDERSTANDING OF NATURE OF PROTEIN-LIGAND INTERACTIONS
=09
=09
	 You can evaluate QUANTUM software immediately by downloading free =
trial at
	 www.q-pharm.com <http://www.q-pharm.com> .
=09
	A detailed description of technology, and  variety of Computer Aided =
Drug Design products and services can also be found at www.q-pharm.com =
and www.q-lead.com
	=20
	=20
	=20
	Feel free to post or contact me directly at =
maxim.kholin-at--q-pharm.com
	=20
	Kindest regards,
	Maxim
	=20

	=20
	=20
	=20


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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 6.00.2900.3086" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV dir=3Dltr align=3Dleft><FONT face=3DArial color=3D#0000ff =
size=3D2>Dear=20
Maxim,</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV dir=3Dltr align=3Dleft><FONT face=3DArial color=3D#0000ff =
size=3D2>Congratulations on=20
your product release!&nbsp; It is quite gratifying to see another =
company taking=20
PyMOL seriously as a development platform<SPAN =
class=3D248524607-09062007>,</SPAN>=20
despite its shortcomings.&nbsp; Quantum is an impressive early example =
of one of=20
the many types of things the unrestricted open-source PyMOL source code =
is=20
intended to enable.&nbsp; In fact, I am astounded by all that your =
company has=20
accomplished independently using PyMOL, with nary a word from =
Moscow!&nbsp;=20
</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV dir=3Dltr align=3Dleft><FONT face=3DArial color=3D#0000ff =
size=3D2>However, one=20
condition from the PyMOL open-source (top-level) LICENSE file seems to =
have been=20
inadvertently overlooked (note text between asterisks):&nbsp;&nbsp; =
=93Permission=20
to use, copy, modify, distribute, and distribute modified versions of =
this=20
software and its documentation for any purpose and without fee is hereby =

granted, **** provided that the above copyright notice appears in all =
copies and=20
that both the copyright notice and this permission notice appear in =
supporting=20
documentation, ****=94</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV dir=3Dltr align=3Dleft><FONT face=3DArial color=3D#0000ff =
size=3D2>Please remedy this=20
(presumed unintentional) breach of the Copyright terms as soon as =
practical by=20
(1) enclosing a copy of PyMOL=92s original LICENSE file in all product=20
distributions (buried in a Quantum subdirectory is fine), and by (2) =
including=20
the text of the PyMOL copyright and permission notices somewhere in the=20
supporting documentation (fine as an appendix at the end of the =
manual).&nbsp;=20
Prompt action will surely alleviate concerns that have been raised =
regarding the=20
legal status of the Quantum product vis-=E0-vis PyMOL.&nbsp; =
</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV dir=3Dltr align=3Dleft><FONT face=3DArial color=3D#0000ff =
size=3D2>Just to reiterate,=20
so that everyone is clear:&nbsp; </FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV dir=3Dltr align=3Dleft><FONT face=3DArial color=3D#0000ff =
size=3D2>In addition to=20
development of new free and open-source tools, it is also my desire to=20
see&nbsp;<SPAN class=3D248524607-09062007>new </SPAN>independent =
commercial=20
products built on the PyMOL foundation.&nbsp; PyMOL is BSD-ish rather =
than=20
GPL-ish for precisely that reason, and I do hope that Quantum and other =
like=20
efforts will prove successful and have numerous positive impacts on the=20
field.&nbsp; However, it is of critical import that such efforts rest on =
a solid=20
foundation of compliance with the very minimal legal requirements =
associated=20
with derivative use of the PyMOL open-source code.&nbsp; </FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV dir=3Dltr align=3Dleft><FONT face=3DArial color=3D#0000ff =
size=3D2>If ever there is=20
any doubt regarding terms, the best way to achieve certainty is to check =
in with=20
me in advance of product release (before it becomes a public =
matter).&nbsp;=20
Another reason to talk to me early on is that<SPAN=20
class=3D248524607-09062007>,</SPAN> in some cases<SPAN=20
class=3D248524607-09062007>,</SPAN> I may even be available to help with =
the=20
development work.</FONT></DIV>
<DIV><FONT face=3DArial color=3D#0000ff size=3D2></FONT>&nbsp;</DIV>
<DIV dir=3Dltr align=3Dleft><FONT face=3DArial color=3D#0000ff =
size=3D2>Thank you and=20
everyone else for compliance with the PyMOL open-source&nbsp;<SPAN=20
class=3D248524607-09062007>terms</SPAN>!</FONT></DIV>
<DIV><FONT face=3DArial color=3D#0000ff size=3D2></FONT>&nbsp;</DIV>
<DIV dir=3Dltr align=3Dleft><FONT face=3DArial color=3D#0000ff =
size=3D2>Cheers,=20
</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV dir=3Dltr align=3Dleft><FONT face=3DArial color=3D#0000ff =
size=3D2>Warren L. DeLano,=20
Ph.D.<BR><A =
href=3D"mailto:warren(!)delsci.com">warren(!)delsci.com</A><BR>Author of=20
PyMOL<BR>Founder of DeLano Scientific LLC</FONT></DIV><BR>
<BLOCKQUOTE dir=3Dltr=20
style=3D"PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #0000ff 2px =
solid; MARGIN-RIGHT: 0px">
  <DIV class=3DOutlookMessageHeader lang=3Den-us dir=3Dltr align=3Dleft>
  <HR tabIndex=3D-1>
  <FONT face=3DTahoma size=3D2><B>From:</B> owner-chemistry(!)ccl.net=20
  [mailto:owner-chemistry(!)ccl.net] <BR><B>Sent:</B> Friday, June 08, =
2007 8:33=20
  AM<BR><B>To:</B> Warren DeLano<BR><B>Subject:</B> CCL: Download free =
trial of=20
  a new generation computer aided drug design software (Quantum=20
  3.3.)<BR></FONT><BR></DIV>
  <DIV></DIV>
  <DIV><FONT face=3DArial size=3D2><FONT face=3D"Times New Roman"=20
  size=3D3>Dear&nbsp;Colleagues, </FONT></FONT></DIV>
  <DIV><FONT face=3DArial size=3D2><FONT face=3D"Times New Roman"=20
  size=3D3></FONT></FONT>&nbsp;</DIV>
  <DIV><FONT face=3DArial size=3D2><FONT face=3D"Times New Roman" =
size=3D3>Let me=20
  introduce&nbsp;you a &nbsp;free trial of new&nbsp;CADD software, which =
is=20
  &nbsp;all CCL community is <BR>invited to download, compare and =
discuss at=20
  CCL.<BR><BR>Quantum&nbsp; contains modules for&nbsp; industrial =
strength=20
  docking / virtual <BR>screening of compound libraries&nbsp;=20
  on&nbsp;&nbsp;flexible proteins, accurate IC50 calculations and =
chemical=20
  properties <BR>prediction tools (Water and DMSO solubility and LogP) =
and=20
  protein analysis <BR>tools.<BR><BR>&nbsp;QUANTUM software employs =
advanced=20
  molecular simulations techniques rather<BR>&nbsp;than statistically =
trained=20
  scores to obtain binding free energies of the<BR>&nbsp;docked =
compounds. As a=20
  result QUANTUM can be used as a robust and accurate<BR>&nbsp;in silico =
tool=20
  for hit identification and lead optimization.<BR><BR>This =
physically-solid=20
  approach provides a number of definite advantages and <BR>opens new=20
  opportunities in drug discovery. The main of them are as =
follows:<BR><BR>1.=20
  ACCURACY<BR><BR>2. PREDICTION OF NEW CLASSES OF INHIBITORS<BR><BR>3.=20
  POSSIBILITY TO IDENTIFY INHIBITORS FOR TARGETS WITH NO KNOWN=20
  LIGANDS.<BR><BR>4. DRAMATICAL REDUCTION IN FALSE POSITIVES<BR><BR>5. =
FULL=20
  PROTEIN FLEXIBILITY IS TAKEN INTO CONSIDERATION<BR><BR>6. =
NO&nbsp;TRAINING=20
  SETS<BR><BR>7. UNDERSTANDING OF NATURE OF PROTEIN-LIGAND=20
  INTERACTIONS<BR><BR><BR>&nbsp;You can evaluate QUANTUM software =
immediately by=20
  downloading free trial at<BR>&nbsp;</FONT><A=20
  href=3D"http://www.q-pharm.com"><FONT face=3D"Times New Roman"=20
  size=3D3>www.q-pharm.com</FONT></A><FONT face=3D"Times New Roman"=20
  size=3D3>.</FONT><BR><BR>A detailed description of technology, =
and&nbsp; variety=20
  of Computer Aided Drug Design products and services&nbsp;can&nbsp;also =
be=20
  found at <A href=3D"http://www.q-pharm.com">www.q-pharm.com</A> and <A =

  href=3D"http://www.q-lead.com">www.q-lead.com</A></FONT></DIV>
  <DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
  <DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
  <DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
  <DIV><FONT face=3DArial size=3D2>Feel free to post or contact me =
directly at=20
  maxim.kholin-at--q-pharm.com</FONT></DIV>
  <DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
  <DIV><FONT face=3DArial size=3D2>Kindest regards,</FONT></DIV>
  <DIV><FONT face=3DArial size=3D2>Maxim</FONT></DIV>
  <DIV><FONT face=3DArial size=3D2>&nbsp;</DIV>
  =
<DIV><BR>&nbsp;<BR>&nbsp;<BR>&nbsp;</FONT></DIV></BLOCKQUOTE></BODY></HTM=
L>

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