From owner-chemistry@ccl.net Thu Jun  1 01:08:00 2006
From: "Jozsef Csontos jozsefcsontos]~[creighton.edu" <owner-chemistry+/-server.ccl.net>
To: CCL
Subject: CCL: negative bsse content
Message-Id: <-31877-060601010514-28039-lSavQdbgNqz9rAZl5pJVWQ+/-server.ccl.net>
X-Original-From: Jozsef Csontos <jozsefcsontos : creighton.edu>
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Date: Thu, 01 Jun 2006 00:05:02 -0500
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Sent to CCL by: Jozsef Csontos [jozsefcsontos:_:creighton.edu]
Hi Serguei,

maybe, I'm wrong, but I don't see any connection between the sign of the
bsse and the variational principle. That's "just about a limit" and
didn't say anything about the convergence (or more exactly monotonic)
behavior. Considering this I could say your argument also breaks down if
one use variational method. 
I think the guarantee for the monotonic behavior (decrease in energy) is
the increased flexibility/degrees of freedom (or as you called
variational space) - when one use larger and larger basis set. However,
this doesn't depend on whether your method is variational or not, unless
you change the order of perturbation. Of course, you are in trouble, if
your method is not size extensive.
As I said, I can be wrong, but everything is clear to me now, or at
least it seems to me ;)

Cheers,

Jozsef

On Wed, 2006-05-31 at 17:27 -0400, Serguei Patchkovskii
ps.:.ned.sims.nrc.ca wrote:
> Sent to CCL by: Serguei Patchkovskii [ps,ned.sims.nrc.ca]
> On Wed, 31 May 2006, Jozsef Csontos jozsefcsontos|a|creighton.edu wrote:
> 
> > BSSE = E_{A}^{AB}(AB) + E_{B}^{AB}(AB) - E_{A}^{A}(AB) - E_{B}^{B}(AB)
> 
> [...]
> 
> > So, apart from the signs, I should always get results on the same side
> > of zero, but I didn't.
> 
> Given the above definition, you can expect BSSE to be non-positive as long 
> as the method used to calculate the energies is variational. The argument
> goes as follows: A bigger variational space (A in the combined A+B basis set) 
> can only lead to lower energies compared a smaller variational space (A in
> the A basis set alone). Therefore, the difference E_{A}^{AB}(AB)-E_{A}^{A}(AB)
> must be negative (or zero). Same holds for the energy of B - so the sum of
> the two quantities must be non-positive as well.
> 
> This argument breaks down if:
> 
> a) the method you are using is not variational
> 
> or
> 
> b) the basis set alone does not represent the entire variational space of
>    the method
> 
> or
> 
> c) there is numerical noise in the calculations, which exceeds the magnitude
>    of the BSSE
> 
> Because MP2 energy is not variational, there is no reason to expect a
> definite sign of BSSE for MP2 (either canonical or localized).
> 
> In the case of DFT, there is both a "hidden" variational space (numerical
> integration grid) and a possibility of having significant numerical noise.
> Both effects should decrease with the use of better grids.
> 
> Serguei> 
> 
> 
-- 
Jozsef Csontos, Ph.D.

Department of Biomedical Sciences
Creighton University,
Omaha, NE


From owner-chemistry@ccl.net Thu Jun  1 04:46:00 2006
From: "Marius Retegan marius.retegan^yahoo.com" <owner-chemistry]|[server.ccl.net>
To: CCL
Subject: CCL: ONIOM-EE
Message-Id: <-31878-060601044203-3962-EPXKvjkYqodAZjOcnUdncQ]|[server.ccl.net>
X-Original-From: "Marius  Retegan" <marius.retegan ~~ yahoo.com>
Date: Thu, 1 Jun 2006 04:42:01 -0400


Sent to CCL by: "Marius  Retegan" [marius.retegan**yahoo.com]
Hello
I have a problem with a oniom-ee optimization.
This is my input file

p opt oniom(b3lyp/lanl2dz:uff=qeq)=embed nosymm pop=(mk,readradii)


From owner-chemistry@ccl.net Thu Jun  1 07:21:00 2006
From: "Barry Hardy barry.hardy-x-tiscalinet.ch" <owner-chemistry[A]server.ccl.net>
To: CCL
Subject: CCL: News on eCheminfo Drug Discovery Training Program
Message-Id: <-31879-060601071751-14306-03zkX02sCN/U2QN1GCvfuw[A]server.ccl.net>
X-Original-From: Barry Hardy <barry.hardy/./tiscalinet.ch>
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Date: Thu, 01 Jun 2006 13:05:41 +0200
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Sent to CCL by: Barry Hardy [barry.hardy-.-tiscalinet.ch]
--=====================_93165881==_.ALT
Content-Type: text/plain; charset="us-ascii"; format=flowed


The eCheminfo Latest Advances in Drug Discovery Design & Planning Methods 
Training week running at Oxford University July 3-7 has attracted an 
interesting mix of class participants working in drug discovery in big and 
medium-sized pharma, biotech and academia and from a variety of countries 
including the UK, Germany, US, Sth Africa, Italy, Pakistan, Ukraine, and 
Holland.  It should make for a stimulating class!

The Bursary Award for the week, sponsored by Lhasa Ltd, UK and Douglas 
Connect, Switzerland has been awarded to Michael Mazanetz, PhD student in 
the School of Pharmacy at the University of Nottingham (UK) in support of 
his research on developing small molecule inhibitors of kinases for the 
treatment of neurological disorders.  Subsequent to 5 years working as a 
medicinal chemist at Eli Lilly, he joined the medicinal chemistry group of 
Peter Fischer at Nottingham in Autumn 2005 to commence this research.

ChemAxon and Inhibox will be presenting their new results and software on 
virtual synthesis during the week.  More information on the Cheminfostream 
Blog at http://barryhardy.blogs.com/cheminfostream/

We still have a few places open in the class.  Academic discounts are 
available.

You can download a copy of the program brochure from:
http://barryhardy.blogs.com/cheminfostream/files/eChemProgramOxford06-v7web.pdf

Further workshop descriptions and information is available at:
http://echeminfo.colayer.net/COMTY_training


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

--=====================_93165881==_.ALT
Content-Type: text/html; charset="us-ascii"

<html>
<br>
The eCheminfo Latest Advances in Drug Discovery Design &amp; Planning
Methods Training week running at Oxford University July 3-7 has attracted
an interesting mix of class participants working in drug discovery in big
and medium-sized pharma, biotech and academia and from a variety of
countries including the UK, Germany, US, Sth Africa, Italy, Pakistan,
Ukraine, and Holland.&nbsp; It should make for a stimulating class!&nbsp;
<br>
<br>
The Bursary Award for the week, sponsored by Lhasa Ltd, UK and Douglas
Connect, Switzerland has been awarded to Michael Mazanetz,<b><i>
</i></b>PhD student in the School of Pharmacy at the University of
Nottingham (UK) in support of his research on developing small molecule
inhibitors of kinases for the treatment of neurological disorders.&nbsp;
Subsequent to 5 years working as a medicinal chemist at Eli Lilly, he
joined the medicinal chemistry group of Peter Fischer at Nottingham in
Autumn 2005 to commence this research.<br>
<br>
ChemAxon and Inhibox will be presenting their new results and software on
virtual synthesis during the week.&nbsp; More information on the
Cheminfostream Blog at
<a href="http://barryhardy.blogs.com/cheminfostream/" eudora="autourl"><font color="#0000FF"><u>http://barryhardy.blogs.com/cheminfostream/</a><br>
<br>
</u></font>We still have a few places open in the class.&nbsp; Academic
discounts are available. <br>
<br>
You can download a copy of the program brochure from:<br>
<font color="#0000FF"><u><a href="http://barryhardy.blogs.com/cheminfostream/files/eChemProgramOxford06-v7web.pdf" eudora="autourl">http://barryhardy.blogs.com/cheminfostream/files/eChemProgramOxford06-v7web.</a><a href="http://barryhardy.blogs.com/cheminfostream/files/eChemProgramOxford06-v7web.pdf" eudora="autourl">pdf<br>
<br>
</a></u></font>Further workshop descriptions and information is available
at:<br>
<font color="#0000FF"><u><a href="http://echeminfo.colayer.net/COMTY_training" eudora="autourl">http://echeminfo.colayer.net/COMTY_training</a><br>
<br>
<br>
</u></font>best regards<br>
Barry Hardy<br>
eCheminfo Community of Practice Manager<br>
Douglas Connect, Switzerland<br>
+41 61 851 0170<br>
</html>

--=====================_93165881==_.ALT--


From owner-chemistry@ccl.net Thu Jun  1 07:56:01 2006
From: "Marius Retegan marius.retegan^_^yahoo.com" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL:G: ONIOM-EE
Message-Id: <-31880-060601073128-27241-QB42uEgMSeBpRNGmPa3poQ**server.ccl.net>
X-Original-From: Marius Retegan <marius.retegan,yahoo.com>
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Date: Thu, 1 Jun 2006 04:31:22 -0700 (PDT)
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Sent to CCL by: Marius Retegan [marius.retegan]=[yahoo.com]
--0-1142704748-1149161482=:84528
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Hello
Sorry for the previous message. 
I'm trying to do a oniom calculation with electronic embedding. This is my input file:

#p opt oniom(b3lyp/lanl2dz:uff=qeq)=embed nosymm pop=(mk,readradii)
.
.
.
Fe 2.05
Zn 2.1

First I want to know if this is the correct way to do this type of calculations. If the input is correct then I have a problem, because after 2 optimization cycles I get the following error:

  60    26     .00
 GetVDW:  no radius for atom  60 atomic number  26. 

Gaussian has no problem reading the radii the first time, but the second time it crashes. 
Any ideas why?
Thank you very much.
 

--0-1142704748-1149161482=:84528
Content-Type: text/html; charset=iso-8859-1
Content-Transfer-Encoding: 8bit

<br>Hello<br>Sorry for the previous message. <br>I'm trying to do a oniom calculation with electronic embedding. This is my input file:<br><br>#p opt oniom(b3lyp/lanl2dz:uff=qeq)=embed nosymm pop=(mk,readradii)<br>.<br>.<br>.<br>Fe 2.05<br>Zn 2.1<br><br>First I want to know if this is the correct way to do this type of calculations. If the input is correct then I have a problem, because after 2 optimization cycles I get the following error:<br><br>&nbsp; 60&nbsp;&nbsp;&nbsp; 26&nbsp;&nbsp;&nbsp;&nbsp; .00<br>&nbsp;GetVDW:&nbsp; no radius for atom&nbsp; 60 atomic number&nbsp; 26. <br><br>Gaussian has no problem reading the radii the first time, but the second time it crashes. <br>Any ideas why?<br>Thank you very much.<br>&nbsp;<br>
--0-1142704748-1149161482=:84528--


From owner-chemistry@ccl.net Thu Jun  1 08:31:01 2006
From: "Mahmud Jelill mjelill!^!hiroshima-u.ac.jp" <owner-chemistry(!)server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian error : any help?
Message-Id: <-31881-060601060916-5728-B9R6nsCuVzj2liH1g5PmyQ(!)server.ccl.net>
X-Original-From: "Mahmud Jelill" <mjelill,+,hiroshima-u.ac.jp>
Content-Type: multipart/alternative;
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Date: Thu, 1 Jun 2006 18:30:10 +0900
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Sent to CCL by: "Mahmud Jelill" [mjelill###hiroshima-u.ac.jp]
This is a multi-part message in MIME format.

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	charset="gb2312"
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Dear CCLers,
 I have this error reoccuring with a number of different calculations
 sometimes at the beginning sometimes after a day or so calculation
 time.  Any help?


  Error termination request processed by link 9999.
 Error termination via Lnk1e in /usr/local/intel/g03/l9999.exe at Thu =
Jun  1 16:23:59 2006.
 Job cpu time:  0 days  5 hours 22 minutes 24.2 seconds.
 File lengths (MBytes):  RWF=3D     11 Int=3D      0 D2E=3D      0 =
Chk=3D      4 Scr=3D      1
  Job cpu time:  0 days  5 hours 16 minutes 17.5 seconds.

Best regards

M Jelill

******************************************
******************************************
Mahmud Jelill
Center for Quanrum Life Science and,
Graduate School of Science,
Hiroshima University,
Kagamiyama 1-3-1 ,Higashi Hiroshima, =20
Hiroshima=20
Japan, 739-8526
******************************************
******************************************

------=_NextPart_000_000D_01C685A9.6A824F90
Content-Type: text/html;
	charset="gb2312"
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=3DContent-Type content=3D"text/html; charset=3Dgb2312">
<META content=3D"MSHTML 6.00.2900.2873" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>Dear CCLers,<BR>&nbsp;I have this error =
reoccuring=20
with a number of different calculations<BR>&nbsp;sometimes at the =
beginning=20
sometimes after a day or so calculation<BR>&nbsp;time.&nbsp; Any=20
help?</FONT></DIV>
<DIV>&nbsp;</DIV><FONT face=3DArial size=3D2>
<DIV><BR>&nbsp; Error termination request processed by link =
9999.<BR>&nbsp;Error=20
termination via Lnk1e in /usr/local/intel/g03/l9999.exe at Thu Jun&nbsp; =
1=20
16:23:59 2006.<BR>&nbsp;Job cpu time:&nbsp; 0 days&nbsp; 5 hours 22 =
minutes 24.2=20
seconds.<BR>&nbsp;File lengths (MBytes):&nbsp; =
RWF=3D&nbsp;&nbsp;&nbsp;&nbsp; 11=20
Int=3D&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0 =
D2E=3D&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0=20
Chk=3D&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 4 =
Scr=3D&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
1<BR>&nbsp; Job cpu time:&nbsp; 0 days&nbsp; 5 hours 16 minutes 17.5=20
seconds.<BR></DIV>
<DIV>Best regards</DIV>
<DIV>&nbsp;</DIV>
<DIV>M Jelill</DIV>
<DIV>&nbsp;</DIV>
<DIV>******************************************<BR>**********************=
********************<BR>Mahmud=20
Jelill</DIV>
<DIV>Center for Quanrum Life Science and,<BR>Graduate School of=20
Science,<BR>Hiroshima University,<BR>Kagamiyama 1-3-1 ,Higashi =
Hiroshima,&nbsp;=20
<BR>Hiroshima <BR>Japan,=20
739-8526<BR>******************************************<BR>***************=
***************************<BR></DIV></FONT></BODY></HTML>

------=_NextPart_000_000D_01C685A9.6A824F90--


From owner-chemistry@ccl.net Thu Jun  1 09:06:00 2006
From: "Tanja van Mourik tanja.vanmourik:_:st-andrews.ac.uk" <owner-chemistry\a/server.ccl.net>
To: CCL
Subject: CCL: negative bsse content
Message-Id: <-31882-060601083416-25882-uNy46x+EILo1kNckC1/Z/g\a/server.ccl.net>
X-Original-From: Tanja van Mourik <tanja.vanmourik(0)st-andrews.ac.uk>
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Date: Thu, 01 Jun 2006 13:33:37 +0100
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Sent to CCL by: Tanja van Mourik [tanja.vanmourik|-|st-andrews.ac.uk]
Hi Joszef,

>> BSSE is a negative quantity: it is calculated as the difference between 
>> the sum of the monomer energies calculated in the dimer basis set and 
>> the sum of the monomer energies calculated in the monomer basis set, all 
>> of these at the geometries they adopt in the complex. 
>> Perhaps some formulas can help
>> (with latex-style sub- and superscripts):
>>
>> BSSE = E_{A}^{AB}(AB) + E_{B}^{AB}(AB) - E_{A}^{A}(AB) - E_{B}^{B}(AB)
> 
> you are right, equations can help, sorry for neglecting them.
> I calculated the interaction energy according to the original
> Boys-Bernardi procedure:
> 
> DeltaE(CP)=E_{AB}^{AB}(AB) - E_{A}^{AB}(AB) - E_{B}^{AB}(AB)

OK; this is sometimes called the "vertical" CP_corrected interaction 
energy.

> in this case the non corrected interaction energy is 
> DeltaE(noCP) = E_{AB}^{AB}(AB) - E_{A}^{A}(A) - E_{B}^{B}(B)
> 
> The difference between the two is the bsse content, which is the same as
> you stated above.

I don't think that's correct: if you take the difference between the two 
equations listed above you get:

Delta = E_{A}^{AB}(AB) + E_{B}^{AB}(AB) - E_{A}^{A}(A) -  E_{B}^{B}(B)

whereas:
  BSSE = E_{A}^{AB}(AB) + E_{B}^{AB}(AB) - E_{A}^{A}(AB) - E_{B}^{B}(AB)

(Do I interpret correctly that the first formula (Delta) is how you 
compute the BSSE?)
The difference between these two is that your last two terms are 
calculated at the equilibrium geometries of the monomers, as indicated 
by (A) and (B),  instead of at the geometries that A and B adopt in the 
complex, (AB):

Delta-BSSE = E_{A}^{A}(AB) + E_{B}^{B}(AB) - E_{A}^{A}(A) -  E_{B}^{B}(B)

which is just the sum of the monomer deformation energies:

Delta-BSSE = EdefA = EdefB


> 
> Some words about the sign, I think the sign of the bsse is the matter of
> definition:
> (+) JCC, 25, 1771, 2004
> (-) JCC, 22, 196,  2001
> 
> I used the DeltaE(CP)-DeltaE(noCP) equation which implies that the bsse
> is positive. This gave me results with opposite sign comparing to yours:
> 
>> DeltaE(CP) = DeltaE(noCP) - BSSE
> As you might noticed, I didn't correct for deformation (fragment
> relaxation), but it vanishes anyway when you subtract the interaction
> energies.

I am afraid I do not understand what you mean by "vanishing away when 
you subtract the interaction energies".

> So, apart from the signs, I should always get results on the same side
> of zero, but I didn't.

I think that is because of the deformation energies, see above. Does 
this make sense?

Best wishes,

Tanja
-- 
   =================================================================
    Tanja van Mourik
    Royal Society University Research Fellow
    School of Chemistry, University of St. Andrews
    North Haugh, St. Andrews
    Fife KY16 9ST, Scotland (UK)

    email: tanja.vanmourik!A!st-andrews.ac.uk
    web:   http://chemistry.st-and.ac.uk/staffmember.php?id=tvm
   =================================================================


From owner-chemistry@ccl.net Thu Jun  1 11:03:00 2006
From: "Jozsef Csontos jozsefcsontos(a)creighton.edu" <owner-chemistry^_^server.ccl.net>
To: CCL
Subject: CCL: negative bsse content
Message-Id: <-31883-060601104814-20861-d6BEdi8Y3+QPntd9Cq4tfw^_^server.ccl.net>
X-Original-From: Jozsef Csontos <jozsefcsontos*o*creighton.edu>
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Date: Thu, 01 Jun 2006 09:48:06 -0500
Mime-Version: 1.0


Sent to CCL by: Jozsef Csontos [jozsefcsontos[#]creighton.edu]
Hi Tanja,

> >> BSSE = E_{A}^{AB}(AB) + E_{B}^{AB}(AB) - E_{A}^{A}(AB) - E_{B}^{B}(AB)
> > 
> > you are right, equations can help, sorry for neglecting them.
> > I calculated the interaction energy according to the original
> > Boys-Bernardi procedure:
> > 
> > DeltaE(CP)=E_{AB}^{AB}(AB) - E_{A}^{AB}(AB) - E_{B}^{AB}(AB)
> 
> OK; this is sometimes called the "vertical" CP_corrected interaction 
> energy.
> 
> > in this case the non corrected interaction energy is 
> > DeltaE(noCP) = E_{AB}^{AB}(AB) - E_{A}^{A}(A) - E_{B}^{B}(B)
> > 
> > The difference between the two is the bsse content, which is the same as
> > you stated above.

> I don't think that's correct: if you take the difference between the two 
> equations listed above you get:
> 
> Delta = E_{A}^{AB}(AB) + E_{B}^{AB}(AB) - E_{A}^{A}(A) -  E_{B}^{B}(B)
> 
> whereas:
>   BSSE = E_{A}^{AB}(AB) + E_{B}^{AB}(AB) - E_{A}^{A}(AB) - E_{B}^{B}(AB)
> 
Yes, you are totally right, that wasn't correct.

I meant to write:

DeltaE(noCP) = E_{AB}^{AB}(AB) - E_{A}^{A}(AB) - E_{B}^{B}(AB)
instead of 
DeltaE(noCP) = E_{AB}^{AB}(AB) - E_{A}^{A}(A) - E_{B}^{B}(B)

> The difference between these two is that your last two terms are 
> calculated at the equilibrium geometries of the monomers, as indicated 
> by (A) and (B),  instead of at the geometries that A and B adopt in the 
> complex, (AB):
> 
> Delta-BSSE = E_{A}^{A}(AB) + E_{B}^{B}(AB) - E_{A}^{A}(A) -  E_{B}^{B}(B)
> 
> which is just the sum of the monomer deformation energies:
> 
> Delta-BSSE = EdefA = EdefB
> 
In this way,
DeltaE(CP)-DeltaE(noCP)
=
E_{AB}^{AB}(AB) - E_{A}^{AB}(AB) - E_{B}^{AB}(AB)
-
E_{AB}^{AB}(AB) - E_{A}^{A}(AB) - E_{B}^{B}(AB) 
=
- E_{A}^{AB}(AB) - E_{B}^{AB}(AB) + E_{A}^{A}(AB) + E_{B}^{B}(AB) 

= -(E_{A}^{AB}(AB) + E_{B}^{AB}(AB) - E_{A}^{A}(AB) - E_{B}^{B}(AB))

which is -1*(your equation).
That is why I'm expecting positive values.

> >> DeltaE(CP) = DeltaE(noCP) - BSSE
> > As you might noticed, I didn't correct for deformation (fragment
> > relaxation), but it vanishes anyway when you subtract the interaction
> > energies.
> 
> I am afraid I do not understand what you mean by "vanishing away when 
> you subtract the interaction energies".

According to your definitions:
DeltaE(CP) = DeltaE(noCP) - BSSE(<=0)

according to my equations:
DeltaE(CP) = DeltaE(noCP) + BSSE(>=0).

The meaning of these is the same Delta(noCP)<=Delta(CP).
"vanishing away" I meant that calculating the bsse using your
definitions the deformation energies can cancel out from the equation.

Cheers,

Jozsef
> 
> > So, apart from the signs, I should always get results on the same side
> > of zero, but I didn't.
> 
> I think that is because of the deformation energies, see above. Does 
> this make sense?
> 
> Best wishes,
> 
> Tanja
-- 
Jozsef Csontos, Ph.D.

Department of Biomedical Sciences
Creighton University,
Omaha, NE


From owner-chemistry@ccl.net Thu Jun  1 11:39:01 2006
From: "Jozsef Csontos jozsefcsontos(a)creighton.edu" <owner-chemistry[]server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian error : any help?
Message-Id: <-31884-060601113711-9432-GIGYuCzkC9DeCGTO9S4Nrw[]server.ccl.net>
X-Original-From: Jozsef Csontos <jozsefcsontos/./creighton.edu>
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Date: Thu, 01 Jun 2006 10:37:05 -0500
Mime-Version: 1.0


Sent to CCL by: Jozsef Csontos [jozsefcsontos+*+creighton.edu]
Hi,

it seems to me that you have reached the maximum number of steps in your
calculation.

Try to "grep" for "Number of steps exceeded"

grep "Number of steps exceeded" yourlogfile.log
or just grep "ps e" yourlogfile.log :)

If this is the case, then you can restart/continue your job.

Hope this helps,

Jozsef


On Thu, 2006-06-01 at 08:56 -0400, Mahmud Jelill mjelill!^!
hiroshima-u.ac.jp wrote:
> Sent to CCL by: "Mahmud Jelill" [mjelill###hiroshima-u.ac.jp]
> This is a multi-part message in MIME format.
> 
> ------=_NextPart_000_000D_01C685A9.6A824F90
> Content-Type: text/plain;
> 	charset="gb2312"
> Content-Transfer-Encoding: quoted-printable
> 
> Dear CCLers,
>  I have this error reoccuring with a number of different calculations
>  sometimes at the beginning sometimes after a day or so calculation
>  time.  Any help?
> 
> 
>   Error termination request processed by link 9999.
>  Error termination via Lnk1e in /usr/local/intel/g03/l9999.exe at Thu =
> Jun  1 16:23:59 2006.
>  Job cpu time:  0 days  5 hours 22 minutes 24.2 seconds.
>  File lengths (MBytes):  RWF=3D     11 Int=3D      0 D2E=3D      0 =
> Chk=3D      4 Scr=3D      1
>   Job cpu time:  0 days  5 hours 16 minutes 17.5 seconds.
> 
> Best regards
> 
> M Jelill
> 
> ******************************************
> ******************************************
> Mahmud Jelill
> Center for Quanrum Life Science and,
> Graduate School of Science,
> Hiroshima University,
> Kagamiyama 1-3-1 ,Higashi Hiroshima, =20
> Hiroshima=20
> Japan, 739-8526
> ******************************************
> ******************************************
> 
> ------=_NextPart_000_000D_01C685A9.6A824F90
> Content-Type: text/html;
> 	charset="gb2312"
> Content-Transfer-Encoding: quoted-printable
> 
> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
> <HTML><HEAD>
> <META http-equiv=3DContent-Type content=3D"text/html; charset=3Dgb2312">
> <META content=3D"MSHTML 6.00.2900.2873" name=3DGENERATOR>
> <STYLE></STYLE>
> </HEAD>
> <BODY bgColor=3D#ffffff>
> <DIV><FONT face=3DArial size=3D2>Dear CCLers,<BR>&nbsp;I have this error =
> reoccuring=20
> with a number of different calculations<BR>&nbsp;sometimes at the =
> beginning=20
> sometimes after a day or so calculation<BR>&nbsp;time.&nbsp; Any=20
> help?</FONT></DIV>
> <DIV>&nbsp;</DIV><FONT face=3DArial size=3D2>
> <DIV><BR>&nbsp; Error termination request processed by link =
> 9999.<BR>&nbsp;Error=20
> termination via Lnk1e in /usr/local/intel/g03/l9999.exe at Thu Jun&nbsp; =
> 1=20
> 16:23:59 2006.<BR>&nbsp;Job cpu time:&nbsp; 0 days&nbsp; 5 hours 22 =
> minutes 24.2=20
> seconds.<BR>&nbsp;File lengths (MBytes):&nbsp; =
> RWF=3D&nbsp;&nbsp;&nbsp;&nbsp; 11=20
> Int=3D&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0 =
> D2E=3D&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0=20
> Chk=3D&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 4 =
> Scr=3D&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
> 1<BR>&nbsp; Job cpu time:&nbsp; 0 days&nbsp; 5 hours 16 minutes 17.5=20
> seconds.<BR></DIV>
> <DIV>Best regards</DIV>
> <DIV>&nbsp;</DIV>
> <DIV>M Jelill</DIV>
> <DIV>&nbsp;</DIV>
> <DIV>******************************************<BR>**********************=
> ********************<BR>Mahmud=20
> Jelill</DIV>
> <DIV>Center for Quanrum Life Science and,<BR>Graduate School of=20
> Science,<BR>Hiroshima University,<BR>Kagamiyama 1-3-1 ,Higashi =
> Hiroshima,&nbsp;=20
> <BR>Hiroshima <BR>Japan,=20
> 739-8526<BR>******************************************<BR>***************=
> ***************************<BR></DIV></FONT></BODY></HTML>
> 
> ------=_NextPart_000_000D_01C685A9.6A824F90--> 
> 
> 
-- 
Jozsef Csontos, Ph.D.

Department of Biomedical Sciences
Creighton University,
Omaha, NE


From owner-chemistry@ccl.net Thu Jun  1 12:58:00 2006
From: "Yan Zhao yzhao(-)chem.umn.edu" <owner-chemistry-,-server.ccl.net>
To: CCL
Subject: CCL:G: a question aboutTDDFT calculations with G03
Message-Id: <-31885-060601124200-6537-85SrheIaI6XdYE4GVF//aA-,-server.ccl.net>
X-Original-From: Yan Zhao <yzhao[-]chem.umn.edu>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Thu, 01 Jun 2006 10:41:55 -0500
MIME-Version: 1.0


Sent to CCL by: Yan Zhao [yzhao-x-chem.umn.edu]
Dear CCLers,

 I have some problems with the TDDFT calculations in Gaussian03.
 I tried doing TDDFT calculations with G03 to test some functionals 
developed in our group. Since I am a beginner of using TDDFT, I did a 
calculation for the CO molecule with PBE0 functional  to reproduce the 
results in Adamo's JCP paper (JCP 111, 2889 (1999)). I can reproduce his 
results for almost all excited states except the highest Rydberg singlet 
state corresponding to the state with an experimental excitation energy 
of 12.4 ev.  In Adamo's paper, PBE0 gives 12.01 ev, but I can not 
extract this excitation energy from my G03 calculations. Moreover I 
failed to reproduce the HCTH and B3LYP results in Tozer and Handy's 
paper (JCP 109 10180 (1998)),  I also failed to reproduce the B97-2 
results in Teale and Tozer's recent paper (JCP 122, 034101 (2005)). They 
are using CADPAC, not G03.  Any suggestions are highly appreciated. The 
following are  my G03 input file and some output information.

Input
**************************************************
#pbe1pbe/6-311++g(d,p) TD=(50-50,Nstates=12) scf=(tight,xqc)

co pbe0

0  1
    C             0        0.000000    0.000000   -0.643075
    O             0        0.000000    0.000000    0.482306
**************************************************

Output
**************************************************
...............
 Orbital symmetries:
       Occupied  (SG) (SG) (SG) (SG) (PI) (PI) (SG)
       Virtual   (PI) (PI) (SG) (SG) (PI) (PI) (SG) (PI) (PI) (SG)
                 (SG) (PI) (PI) (SG) (SG) (SG) (PI) (PI) (DLTA)
                 (DLTA) (SG) (PI) (PI) (SG) (PI) (PI) (DLTA) (DLTA)
                 (SG) (PI) (PI) (SG) (PI) (PI) (SG) (SG) (SG)
    96 initial guesses have been made.
................
................

 Excited state symmetry could not be determined.
 Excited State  16:   Triplet-?Sym   11.2347 eV  110.36 nm  f=0.0000
       4 ->  9         0.10254
       7 -> 12         0.44192
       7 -> 13         0.52545
 
 Excited State  17:   Singlet-SG    11.3361 eV  109.37 nm  f=0.1947
       7 -> 11         0.69676
 
 Excited state symmetry could not be determined.
 Excited State  18:   Singlet-?Sym   11.4874 eV  107.93 nm  f=0.0508
       7 -> 12         0.24432
       7 -> 13         0.65817
 
 Excited state symmetry could not be determined.
 Excited State  19:   Singlet-?Sym   11.4874 eV  107.93 nm  f=0.0508
       7 -> 12         0.65817
       7 -> 13        -0.24432
 
 Excited state symmetry could not be determined.
 Excited State  20:   Triplet-?Sym   11.9391 eV  103.85 nm  f=0.0000
       4 ->  8         0.69457
       4 ->  9        -0.11693
       4 -> 12        -0.10390
       7 -> 12        -0.13267
 
 Excited state symmetry could not be determined.
 Excited State  21:   Triplet-?Sym   11.9391 eV  103.85 nm  f=0.0000
       4 ->  8         0.11693
       4 ->  9         0.69457
       4 -> 13        -0.10390
       7 -> 13        -0.13267
 
 Excited state symmetry could not be determined.
 Excited State  22:   Singlet-?Sym   13.1752 eV   94.10 nm  f=0.0665
       5 -> 10         0.69565
       6 -> 10        -0.10395
 
 Excited state symmetry could not be determined.
 Excited State  23:   Singlet-?Sym   13.1752 eV   94.10 nm  f=0.0665
       5 -> 10         0.10395
       6 -> 10         0.69565
 
 Excited state symmetry could not be determined.
 Excited State  24:   Singlet-?Sym   13.1819 eV   94.06 nm  f=0.2280
       4 -> 10        -0.13503
       5 ->  9         0.34048
       5 -> 13         0.22450
       6 ->  8         0.34048
       6 -> 12         0.22449
       7 -> 14        -0.23139

**************************************************



Yan Zhao
Department of Chemistry
University of Minnesota


From owner-chemistry@ccl.net Thu Jun  1 15:49:00 2006
From: "Jeff Nauss jnauss|-|accelrys.com" <owner-chemistry{}server.ccl.net>
To: CCL
Subject: CCL: Accelrys Customer Training for July
Message-Id: <-31886-060601153839-10772-1dQNvUFPoxi2TC/DAAuBqg{}server.ccl.net>
X-Original-From: Jeff Nauss <jnauss,+,accelrys.com>
Content-Type: text/plain; charset="US-ASCII"
Date: Thu, 1 Jun 2006 12:00:01 -0700
MIME-Version: 1.0


Sent to CCL by: Jeff Nauss [jnauss__accelrys.com]
Accelrys Inc. are holding the following training workshops during July. 
These events are designed to help you get more value from your Accelrys 
software, helping you to better accomplish your research goals.

Costs for the scheduled workshops are $500 per day for all customers.  For 
the on-line presentations, the price is $175 per three hour session for 
all customers.

BURLINGTON, MA

Structure Based Drug Design with Cerius2     17 - 18 Jul
Pharmacophore Generation with Catalyst       19 - 20 Jul
 
PARIS, FRANCE

Structure-Based Design in Discovery Studio     11 Jul
Protein Modeling in Discovery Studio           12 Jul
Simulations in Discovery Studio                13 Jul

ON-LINE

Introduction to Discovery Studio     5 Jul (9am BST)
Introduction to Discovery Studio     6 Jul (9am PDT)
Solvation Models in CHARMm          27 Jul (7am PDT)

Further details can be found on our website at 
http://www.accelrys.com/services/training/general/calendar.html.

Questions regarding scheduling and content should be directed to 
workshops^^accelrys.com

--
Jeffrey L. Nauss, Ph.D.
Lead Training Scientist
Accelrys
10188 Telesis Court, Suite 100
San Diego, CA 92121-4779

Phone: +1-858-799-5555
Fax: +1-858-799-5100
http://www.accelrys.com/training