From chemistry-request@server.ccl.net Fri Oct 25 04:43:06 2002
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From: Patrik Johansson <patrikj@fy.chalmers.se>
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Hi CCLers

I have seen this Q in the archives (many times) - but no answer:

What are the units used by G98 for polarisabilities and
hyperpolarisabilities? I.e. are they a.u.**3 or Angstrom**3 ?

I've sent the same Q to Gaussian - and if I get response I will post it
to the list.

regards

/Patrik
--

From chemistry-request@server.ccl.net Fri Oct 25 04:56:22 2002
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To: "'Nikolaus Stiefl '" <nikolaus.stiefl@mail.uni-wuerzburg.de>,
   "'chemistry@ccl.net '" <chemistry@ccl.net>
Subject: RE: Problem with iodine in GRID
Date: Fri, 25 Oct 2002 10:59:06 +0200
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Dear Nikolaus,

This is what I found in GRID manual about your error:

(N970-W)  SUSPECTED ERROR IN NUMBER OF COVALENTLY BOUND NEIGHBOURS, OR THE
NUMBER OF NEIGHBOURS ONE PLACE REMOVED FROM HETATM .......
When Programme GRIN computes the positions of the hydrogen atoms on a HETATM
in the Target molecule, it starts by identifying all the other HETATMS which
are bonded to that HETATM.  It will need to know the positions of some of
these nearby HETATMS in order to calculate the hydrogen- positions, but it
sometimes does not find the expected number of neighbours.  This error
message will then be printed.

Message N970 often indicates that the structure of the Target molecule is
unusual, or that it is strained, or that it is a transition state.  GRID is
not calibrated for highly strained molecules or transition states, but we
would be grateful at Molecular Discovery if can let us know when this
message is given for a regular atom in a regular molecule

Another possibility is that the structure is wrong, or that an error has
been introduced into Datafile GRUB, or that the name of a HETATM is
incorrect, or that the molecule name, number or chain identifiers have been
misassigned.  These possibilities should be checked.


Or, in other words, that if you checked your structure and think it is ok,
you better send an e-mail to  support@moldiscovery.com

Regards,
Hugo

-----Original Message-----
From: Nikolaus Stiefl
To: chemistry@ccl.net
Sent: 10/24/2002 7:26 PM
Subject: CCL:Problem with iodine in GRID

Sorry, forget the subject. Hope this is now better.

Hi, 

I am currently investigating a set of molecules of which two contain an
iodine 
atom covalently bound to an aromatic ring. When running this dataset
through 
GRID everything works fine except for the iodine containing structures.
For 
both of them i get the following error message: 

(N970-W)  SUSPECTED ERROR IN NUMBER OF COVALENTLY BOUND 
               NEIGHBOURS, OR THE NUMBER OF NEIGHBOURS ONE PLACE 
               REMOVED FROM HETATM:      8*    8  I   <1>     1 

Now, I checked the GRID-readable pdb file and it looks o.k to me.
Therefore I 
just build iodbenzole in SYBYL (saved as mol2) and tried this with GREAT
as 
well as GREATER which results again in the mentioned error message. To
me the 
converted pdb file looks o.k. again :-(( 

I am sure someone already used GRID on iodine containing molecules so I
hope 
this someone might be able to help me ... 

Cheers 
Nik
 
----------------------
Nikolaus Stiefl
Chemometriks and Drug Design
University Wuerzburg
Dept. of Pharmacy
Am Hubland
D-97074 Wuerzburg
Germany
Phone: +49 - 931 8885473


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From chemistry-request@server.ccl.net Fri Oct 25 06:11:53 2002
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Subject: GAMESS: SCF convergence
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Dear All,

I want to optimize a model to the B3LYP/6-31++G** theory level (TL) using
GAMESS. If I optimize it directly to this TL the first SCF computation does not
converge (with GUESS=HUCKEL). So, to be able to get a B3LYP/6-31++G** optimized
structure, I proceed in two times. I first optimize my model to the 6-31++G** TL
(with GUESS=HUCKEL) and then from the new 6-31++G** optimized Cartesian
coordinates I reoptimized it to the B3LYP/6-31++G** TL (with GUESS=MOREAD) 
providing the 6-31++G** $VEC group. I have the same probleme with a single point
energy determination using the same B3LYP/6-31++G** basis set if I do not
provide a previous $VEC group. 

- However, I am interested in getting B3LYP/6-31++G** energy value using a
SINGLE input and not TWO as I am doing. Is there a way to do this ?

- I do not have this SCF convergence problem if I use MP2 computations for
instance. Is it a known probleme for B3LYP/DFT calculations ?

Thanks, regards, Francois




From chemistry-request@server.ccl.net Fri Oct 25 03:09:59 2002
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	boundary="=====================_58141600==_"


--=====================_58141600==_
Content-Type: text/plain; charset="us-ascii"; format=flowed


>>>>Dear colleagues:
>>>>I have attempted to convert the geometry contained in the attached file 
>>>>to cartesian (or internal) coordinates using Babel, but I have not 
>>>>achieved to make it.
>>>>Would someone help me, please.
>>>>I will be very gratefully.
>>>>Thank you in advance
>>>>
>>>>Victor Ferro.

--=====================_58141600==_
Content-Type: text/plain; charset="us-ascii"
Content-Disposition: attachment; filename="subPc-rX.cif"


#######################################################################
#
#                 Cambridge Crystallographic Data Centre
#                                CCDC 
# 
#######################################################################
# 
#   This CIF contains data from an entry in the Cambridge Structural
#   Database and may include bibliographic, chemical, crystal, 
#   experimental, refinement, atomic coordinates and geometry data,
#   where available.
#     
#   Copyright  2002  The Cambridge Crystallographic Data Centre
# 
#   For further information visit CCDC www.ccdc.cam.ac.uk
#   To view the CIF, please download Mercury from this site. 
#
# 
#######################################################################

data_CSD_CIF_PHTLBC
_audit_creation_date 1975-02-01
_audit_creation_method CSD-ConQuest-V1
_database_code_CSD PHTLBC
_chemical_formula_sum 'C24 H12 B1 Cl1 N6'
_chemical_formula_moiety
;
C24 H12 B1 Cl1 N6
;
_journal_coden_Cambridge 214
_journal_volume 105
_journal_year 1974
_journal_page_first 405
_journal_name_full 'Monatsh.Chem.'
loop_
_publ_author_name
"H.Kietaibl"
_chemical_name_systematic
;
15c-Chloro-tri-isoindolo(1,2,3-cd.1',2',3'-gh.1'',2'',3''-kl)(2,3a,5,6a,8,9a,9
b)hexa-azaboraphenalene
;
_chemical_name_common
;
B-Chloro-subphthalocyanine
;
_cell_volume   1865.044
_exptl_crystal_density_diffrn 1.534
_diffrn_ambient_temperature ?
_diffrn_special_details
;
The study was carried out at room temperature,in the range 283-303K

;
#These two values have been output from a single CSD field.
_refine_ls_R_factor_gt 6.4
_refine_ls_wR_factor_gt 6.4
_symmetry_cell_setting orthorhombic
_symmetry_space_group_name_H-M 'P n m a'
_symmetry_Int_Tables_number 62
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 x,y,z
2 1/2-x,1/2+y,1/2+z
3 x,1/2-y,z
4 1/2-x,-y,1/2+z
5 -x,-y,-z
6 -1/2+x,-1/2-y,-1/2-z
7 -x,-1/2+y,-z
8 -1/2+x,y,-1/2-z
_cell_length_a 12.123(5)
_cell_length_b 14.824(7)
_cell_length_c 10.378(4)
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_cell_formula_units_Z 4
loop_
_atom_type_symbol
_atom_type_radius_bond
C 0.68
H 0.20
B 0.83
Cl 0.99
N 0.68
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
B1 B 0.29050 0.25000 0.05890
Cl1 Cl 0.31380 0.25000 0.23640
C1 C 0.43720 0.17260 -0.06820
C2 C 0.00320 0.20150 -0.03350
C3 C -0.09270 0.15410 -0.06720
C4 C -0.18450 0.20250 -0.09420
C5 C 0.45370 0.08250 -0.12030
C6 C 0.53870 0.04340 -0.18970
C7 C 0.52680 -0.04490 -0.22840
C8 C 0.43030 -0.09260 -0.20600
C9 C 0.34200 -0.05310 -0.14400
C10 C 0.35380 0.03450 -0.09950
C11 C 0.27720 0.09550 -0.03400
C12 C 0.11630 0.17290 -0.00580
H1 H 0.61200 0.08400 -0.20300
H2 H 0.58700 -0.07300 -0.28600
H3 H 0.42500 -0.16200 -0.22600
H4 H 0.27600 -0.08900 -0.11900
H5 H -0.09600 0.08800 -0.06900
H6 H -0.26400 0.18000 -0.15100
N1 N 0.49210 0.25000 -0.09200
N2 N 0.33750 0.17150 -0.00710
N3 N 0.16700 0.09360 -0.02760
N4 N 0.17300 0.25000 0.02470
N2B N 0.33750 0.32850 -0.00710
C1B C 0.43720 0.32740 -0.06820
C2B C 0.00320 0.29850 -0.03350
C4B C -0.18450 0.29750 -0.09420
C12B C 0.11630 0.32710 -0.00580
C11B C 0.27720 0.40450 -0.03400
C5B C 0.45370 0.41750 -0.12030
C3B C -0.09270 0.34590 -0.06720
H6B H -0.26400 0.32000 -0.15100
N3B N 0.16700 0.40640 -0.02760
C10B C 0.35380 0.46550 -0.09950
C6B C 0.53870 0.45660 -0.18970
H5B H -0.09600 0.41200 -0.06900
C9B C 0.34200 0.55310 -0.14400
C7B C 0.52680 0.54490 -0.22840
H1B H 0.61200 0.41600 -0.20300
C8B C 0.43030 0.59260 -0.20600
H4B H 0.27600 0.58900 -0.11900
H2B H 0.58700 0.57300 -0.28600
H3B H 0.42500 0.66200 -0.22600
#END

--=====================_58141600==_--



From chemistry-request@server.ccl.net Fri Oct 25 04:19:02 2002
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A very nice program for your task could be gOpenMol, downloadable at url
http://www.csc.fi/gopenmol/
Salute
Alessandro Contini

Dott. Alessandro Contini
Istituto di Chimica Organica "Alessandro Marchesini"
Facoltà di Farmacia Università degli Studi di Milano
Via Venezian, 21 20133 Milano
Tel. +390250314480  Fax +390250314476
http://users.unimi.it/istchimorg/pagconthtm.htm

On Wed, 23 Oct 2002, Andrzej Lewandowicz wrote:

>
> Dear,
> I have problem with Molecular electrostatic potential visualization by
> Molekel with cube generated by G98. For one molecule the shadows of
> the blue color represent positive values and red negative values,
> for another there is exactly reverse, so there is no way to compare MEPs
> by consistent color map.
>
> Is another program to visualize MEP from Gaussian (beside GaussView ?)
> or is any way to manage with this problem during visualization by Molekel.
> The change of Vmin/Vmax didn't help.
>
> Andrzej
>
>
>
>
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>
>
>
>
>



From chemistry-request@server.ccl.net Fri Oct 25 04:22:24 2002
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From: "lala podibaer" <angelschnur@hotmail.com>
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Subject: Summary: rotate molecules along princliple moments of inertia
Date: Fri, 25 Oct 2002 08:22:15 +0000
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Hi to all,

first of all I wanted to thank all the people that answered to my question 
(Alexandre Suman de Araujo, Ryszard Czerminsk, Gareth Jones, James J.P. 
Stewart, Richard Gillilan, Huub van Dam, Jordi Villà i Freixa, and Xiang-Jun 
Lu). It seems like the problem raised is quite widespread and very useful 
ways of handling this problem are around. I programmed the stuff last night 
and it works now.

Here is the summary of the most comprehensive emails I received. Please note 
that if close answers were given I mention only one !

Thanks again,
Mike

---------------
It seems that the method described in the Kabsch paper is what you are
looking for:

Wolfgang Kabsch "A solution for the best rotation
to relate two sets of vectors" Acta Cryst. (1976) A32, 922

Ryszard Czerminski
--------------
Least-square fitting can produce inversion, which is a problem if your
structure has chiral centers.  Fortunately there is an easy fix:

Given the two molecules Y and X centered on the origin, the SVD is defined
as Y'X = USV' and the best fit rotation is defined as VU'. U is the
eigenvector matrix. If the determinant of VU' is -1 then the fitting
includes inversion.  If this is the case find the eigenvector in U that
corresponds to the smallest eigenvalue and change it's sign (multiply by
-1).  With U modified, VU' will now be a rotation matrix.

Unfortunately, I don't have a reference for this handy.

Cheers, Gareth
Gareth Jones PhD
----------------------
The problem you describe arises from the fact that the eigenvectors of the 
rotation matrix are ill-defined by a phase.  In MOPAC, the diagonal terms 
are set positive and the phase is  locked such that the determinant has the 
value +1.  Please consider using the following code, iin which the 3x3 
rotation matrix is "evec":

!
!     MAKE DIAGONAL TERMS OBLIGATE POSITIVE
!
  do i = 1, 3
    if (evec(i, i) < 0.d0) then
      do j = 1, 3
        evec(j, i) = -evec(j, i)
      end do
    end if
  end do
!
!   NOW TO ORIENT THE MOLECULE SO THE CHIRALITY IS PRESERVED
!
  sum = evec(1, 1) * (evec(2, 2)*evec(3, 3)-evec(3, 2)*evec(2, 3)) + evec &
  & (1, 2) * (evec(2, 3)*evec(3, 1)-evec(2, 1)*evec(3, 3)) + evec(1, 3) * &
  & (evec(2, 1)*evec(3, 2)-evec(2, 2)*evec(3, 1))
  if (sum < 0) then
    sum = 1.d0
    do j = 1, 3
      if (evec(j, j) < sum) then
        sum = evec(j, j)
        i = j
      end if
    end do
    do j = 1, 3
      evec(j, i) = -evec(j, i)
    end do
  end if

James J.P. Stewart
---------------------------------------------
This same problem pops up when I have an ensemble of
identical, but randomly-oriented bodies (proteins)
in solution and I wish to transform them all back to
- the same - body coordinate system. You get to the body
system by diagonalizing the inertial matix, but I suspect
the problem is that eigenvalues can be returned by the
numerical routine in any order and with any sign. The
resulting body coordinate sytems then differ by
permutations and sign changes of axes subject to the
condition that the handedness must be preserved. I seem
to remember this has something to do with permutation groups
so that the required sign changes are related to the
parity of the permutation (swap axes and you must change a sign
to preserve handedness). At any rate, is there a way of putting
eigenvectors in some kind of canonical order with appropriate
sign so that the diagonalization routines always land you in the
same body system?

Richard Gillilan
MacCHESS
--------------------------------
The problem is not in the eigenvalues but with the phase factor of the
eigenvectors. If x is an eigenvector of a matrix -x is also an eigenvector 
with
the same eigenvalue. So what you need to do is tweak the sign of your
eigenvectors to remove the mirroring.

If your angles of rotation are small then simply calculate the inproduct of 
the
resulting coordinates with the starting coordinates. These overlaps should 
be
close to +1 if they are close to -1 you have to change a sign somewhere.
Alternatively you apply the transformation to the three unit vectors 
(1,0,0),
(0,1,0) and (0,0,1). Calculate the inproducts of the resulting vectors with 
the
unit vectors. I think you should find the same value for all of the 
inproducts.
Differences in signs mean you have to change a sign.
Of course you can always outer products to check whether your coordinate 
system
after transformation is still a right-hand coordinate system.

I hope this is of some help, although I realize this is not a complete
solution.

Huub van Dam
------------------------------
In a utility called "rotate" included in the program POLYRATE from Don 
Truhlar's group (http://t1.chem.umn.edu/polyrate/), we included a dirty 
trick to fix this problem. The
molecules had the same number of atoms, so you must figure out how to do 
this in a more general case. If the number of atoms is the same, we 
calculated the distance s between
the two sets of coordinates. Once the alignment was ok, we mirrored the 
coordinates according to several planes of simmetry and then recalculated 
the s, getting the alignment according to the minimum s.
It is dirty but it worked.

Jordi Villà i Freixa
-------------------------------
I believe your problem arises because of the ambiguity in selecting the
"direction" of the eigenvectors. Let the first and second eigenvectors be
whatever you have, you need to make sure the third one is the cross product
of the first two, thus ensuring a right-handed coordinate system.

"rotate_mol", a utility in 3DNA 
(http://rutchem.rutgers.edu/~xiangjun/3DNA/),
can do this and a bit more, and it is used to get the most extended views
for every structure in the updated Nucleic Acid Database (NDB)
(http://beta-ndb.rutgers.edu/).

Xiang-Jun
-------------------------------------
You raised a good point and there are indeed some technical details to go
into to get things "right". While I am not so sure about the mathematics and
physics involved, the procedures I used seem to work fine for my purpose:

[1] Pre-process xyz (n-by-3 matrix) to reset its orientation according to
     the reference frame of the first nucleic acid base; or as defined by 
the
     first 3 non-linear atoms. This will eliminate the ambiguity (e.g.,
     upside-down) associated with arbitrary initial orientation.
[2] get the co-variance matrix (real symmetric, 3-by-3).
[3] solve the eigensystem (using e.g. jacobi transformation as in Numerical
     Recipes), sort the eigenvalues, and normalize eigenvectors.
[4] check to make sure the third eigenvector is the cross product of the
     first two, otherwise reverse its sign. There are two more permutations
     which can be used to get three orthogonal views.

Does anyone out there have a more rigorous way?

Xiang-Jun Lu
-------------------------------





_________________________________________________________________
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From chemistry-request@server.ccl.net Fri Oct 25 09:51:26 2002
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Subject: Estimating dielectric constants...
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Thread-Topic: Estimating dielectric constants...
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From: "Axel Mathieu" <Axel.Mathieu@neokimia.com>
To: <chemistry@ccl.net>

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Hello everyone,
I was wondering if there exists a way to estimate the dielectric =
constant for a given molecule (either through functional groups or =
chemical formula). Basically, this would be useful for GBSA implicit =
solvation models where an approximate dielectic constant for the =
interior of the solute needs to be specified. For proteins, it is a =
rather simple solution from what I gathered - a dielectric constant of 4 =
or 5 is used to represent the hydrophobic nature of protein "cores" when =
the entire molecule is in polar solvent. On the other hand, it becomes =
difficult to estimate the dielectric constant of small molecules that =
should contain some "interior" character (like macrocyclic =
pharmacological compounds), especially if they contain several polar =
functional groups that interact trans-annularly. Therefore, I was =
wondering if anyone has found an efficient easy method to calculate a =
close approximation of the true dielectric constant of small molecules.
=20
Thanks,
=20
Axel Mathieu, Ph.D.
=20

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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
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<DIV><FONT face=3DArial size=3D2><SPAN class=3D171543813-25102002>Hello=20
everyone,</SPAN></FONT></DIV>
<DIV><FONT face=3DArial size=3D2><SPAN class=3D171543813-25102002>I was =
wondering if=20
there exists a way to estimate the dielectric constant for a given =
molecule=20
(either through functional groups or chemical formula). Basically, this =
would be=20
useful for GBSA implicit solvation models where an approximate dielectic =

constant for the interior of the solute needs to be specified. For =
proteins, it=20
is a rather simple solution from what I gathered - a dielectric constant =
of 4 or=20
5 is used to represent the hydrophobic nature of protein "cores" when =
the entire=20
molecule is&nbsp;in polar solvent. On the other hand, it becomes =
difficult to=20
estimate the dielectric constant of small molecules that&nbsp;should =
contain=20
some "interior" character (like macrocyclic pharmacological compounds),=20
especially if they contain several polar functional groups that interact =

trans-annularly. Therefore, I was wondering if anyone has found an =
efficient=20
easy method to calculate a close approximation of the true dielectric =
constant=20
of small molecules.</SPAN></FONT></DIV>
<DIV><FONT face=3DArial size=3D2><SPAN=20
class=3D171543813-25102002></SPAN></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2><SPAN=20
class=3D171543813-25102002>Thanks,</SPAN></FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV align=3Dleft><FONT face=3DArial size=3D2>Axel Mathieu, =
Ph.D.</FONT></DIV>
<DIV>&nbsp;</DIV></BODY></HTML>

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From chemistry-request@server.ccl.net Fri Oct 25 03:23:53 2002
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Date: Fri, 25 Oct 2002 09:25:47 +0200
From: Patrik Johansson <patrikj@fy.chalmers.se>
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To: Pradipta Bandyopadhyay <pradipta@cgl.ucsf.edu>, chemistry@ccl.net
Subject: Re: CCL:MC/sim-ann & Gamess
References: <Pine.OSF.4.44.0210241038520.885414-100000@adenine.cgl.ucsf.edu>
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Hi

Happy for your answer, but I must ask again: how does one make the two
"fragments" anion and Na+ practically in the input - if one wants both
of them to be treated ab initio? One of them (the anion) I can of course
set in $DATA, but where do I put Na+ ?

If I do a MC with all atoms in $DATA I partly loose the scope that the
position of Na+ should be varied the most and the anion only internally
relaxed somewhat or am I missing something in how the MC steps are
performed?
 
The computational time is not a big issue as the anion is rather small
(8-12 atoms) - and I've got plenty of CPU-hours :-)

best regards

/Patrik

Pradipta Bandyopadhyay wrote:
> 
>  Hi,
> 
>    You can treat your system with full ab initio description without using
>  EFP. The problem is that it is extremely expensive computationally.
> Moreover - only cartesian coordiantes are changed for ab initio part -
>  which is very inefficient. If you can give the Monte Carlo moves using
> some internal coordiantes by changing the code it would be little better.
> Another possibility is that you can make a fragment from your large
> anionic molecule and then can treat the Na+ as ab initio and the large
> molecule as efrag.
> 
> Hope this helps.
> 
>         Pradipta
> 
> On Thu, 24 Oct 2002, Patrik Johansson wrote:
> 
> > Dear CClers
> >
> > Has anyone tried to perform a MC/sim-ann calc within gamess using the
> > globop routine _and_ using two different ab initio parts (i.e. not using
> > efrag)?
> >
> > An example: to render starting positions for a Na+ ion around a large
> > anionic molecule which itself is allowed to relax and the Na-anion
> > interaction treated ab initio.
> >
> > Hints/examples anyone?
> >
> > I'll summarize the answers (if any) of course.
> >
> > best regards
> > /Patrik
> > --


From chemistry-request@server.ccl.net Fri Oct 25 11:58:16 2002
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> CHEMISTRY@ccl.net -- To Everybody

Can you please register me in the ccl net's chemistry forum?

Thank you very much,
Dimitrios Vlachakis
PhD, Med Chem Group
University of Cardiff


From chemistry-request@server.ccl.net Fri Oct 25 15:11:50 2002
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Hi all,


I'm currently trying to install autodocktools under Linux Mandrake 8.0 but 
when executing pmv, I always receive the same message :

"TclError: Togl: X server has no OpenGL GLX extension
hit enter to continue"

On the autodocktools web site it is recommended to install libglx library, 
but it is already installed because I can find the following files:



libglx.so.1.0...... in usr/X11R6/lib/modules/extensions/
nvidia.... in usr/X11R6/lib/modules/drivers/


So, I added the following lines in the XF86Config-4 file:

         in the Section"Modules"
                 Load "/usr/X11R6/lib/modules/extensions/libglx.so" with a 
link to libglx.so.1.0......

         in the Section "Device"
                 Driver "nvidia"


But when I launch PMV, only a small window opens and I receive the same 
message.

Perhaps, my XF86Config-4 file is not appropriate.
What did I wrong?

Thank you in advance for your helpful advices



**************************************************
Olivier WALKER-Research Assistant
Department of Chemistry & Biochemistry
University of Maryland
College Park, MD 20742
USA
**************************************************
Fax : 301-314-0386
Phone : 301-405-8710
E-mail : oliwalk@wam.umd.edu
**************************************************


From chemistry-request@server.ccl.net Fri Oct 25 14:40:42 2002
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Message-ID: <001101c27c56$0203f280$dbd16ba4@kiniu>
From: "Kiniu WONG \(Kin-Yiu\)" <kiniu@mps.ohio-state.edu>
To: <chemistry@ccl.net>
Subject: references/books about semi-classical methods
Date: Fri, 25 Oct 2002 14:40:35 -0400
Organization: Physics, OSU
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Dear CCLers,

    I am looking for references/books about semi-classical methods (WKB or
even higher order corrections in h) applying to molecular systems.  Thanks
in advance for any references/books about that!

Wishes,
Kiniu

----
Kiniu WONG (Kin-Yiu)
Graduate Student
Department of Physics
The Ohio State University
USA
Primary Email:   kiniu@mps.ohio-state.edu
Permanent Email:   kiniu@alumni.cuhk.net



From chemistry-request@server.ccl.net Fri Oct 25 12:44:26 2002
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From: "Iain Wallace" <wallacei@tcd.ie>
To: "CCL" <chemistry@ccl.net>
Subject: CCL: Surfnet and Ligplot and Ligbuilder
Date: Fri, 25 Oct 2002 17:53:28 +0100
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Hi all,

Sorry to bother you but does any one know how to get the programs =
ligplot and surfnet?
I have tried to ftp them from ftp.biochem.ucl.ac.uk but it asks for a =
user name and password and I don't know
how to get it. What should I do?=20

I am also having trouble installing LigBuilder. I have downloaded the =
file but I cann't manage to decrypt it as I my e-mails keep getting
bounced back when I e-mail Prof. Lai at lai@ipc.pku.edu.cn Does anyone =
know who I should e-mail ?=20

I am a postgraduate student in TCD=20

Thanks for your help again

Iain


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<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>Hi all,</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Sorry to bother you but does any one =
know how to=20
get the programs ligplot and surfnet?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>I have tried to ftp them from&nbsp;<A=20
href=3D"ftp://ftp.biochem.ucl.ac.uk"><EM>ftp.biochem.ucl.ac.uk</EM></A><E=
M>=20
</EM>but it asks for a user name and password and I don't =
know</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>how to get it. What should I do? =
</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>I am also having trouble installing =
LigBuilder. I=20
have downloaded the file but I cann't manage to decrypt it as I my =
e-mails keep=20
getting</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>bounced back when I e-mail Prof. Lai at =
<A=20
href=3D"mailto:lai@ipc.pku.edu.cn">lai@ipc.pku.edu.cn</A> Does anyone =
know who I=20
should e-mail ? </FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>I am a postgraduate student in TCD =
</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Thanks for your help again</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Iain</FONT></DIV>
<DIV>&nbsp;</DIV></BODY></HTML>

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From chemistry-request@server.ccl.net Fri Oct 25 14:21:59 2002
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Date: Fri, 25 Oct 2002 11:21:57 -0700
From: Wibke Sudholt <wibke@sdsc.edu>
To: FyD <fyd@u-picardie.fr>
cc: <chemistry@ccl.net>
Subject: Re: CCL:GAMESS: SCF convergence
In-Reply-To: <1035540712.3db918e841e0c@webmail.u-picardie.fr>
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Hi,

I observed SCF convergence problems with DFT and diffuse functions in
GAMESS myself. I solved them by

* INTTYP=HONDO and higher than default values for ITOL and ICUT in $CONTRL
  (that means higher integral accuracy)

* FDIFF=.FALSE. in $SCF (that means compute full Fock matrix in each
  iteration)

I hope this helps!

Best regards,

Wibke Sudholt
University of California, San Diego



On Fri, 25 Oct 2002, FyD wrote:

> Dear All,
>
> I want to optimize a model to the B3LYP/6-31++G** theory level (TL) using
> GAMESS. If I optimize it directly to this TL the first SCF computation does not
> converge (with GUESS=HUCKEL). So, to be able to get a B3LYP/6-31++G** optimized
> structure, I proceed in two times. I first optimize my model to the 6-31++G** TL
> (with GUESS=HUCKEL) and then from the new 6-31++G** optimized Cartesian
> coordinates I reoptimized it to the B3LYP/6-31++G** TL (with GUESS=MOREAD)
> providing the 6-31++G** $VEC group. I have the same probleme with a single point
> energy determination using the same B3LYP/6-31++G** basis set if I do not
> provide a previous $VEC group.
>
> - However, I am interested in getting B3LYP/6-31++G** energy value using a
> SINGLE input and not TWO as I am doing. Is there a way to do this ?
>
> - I do not have this SCF convergence problem if I use MP2 computations for
> instance. Is it a known probleme for B3LYP/DFT calculations ?
>
> Thanks, regards, Francois
>
>
>
>
> -= This is automatically added to each message by mailing script =-
> CHEMISTRY@ccl.net -- To Everybody  | CHEMISTRY-REQUEST@ccl.net -- To Admins
> Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | Jan: jkl@ccl.net



From chemistry-request@server.ccl.net Fri Oct 25 12:46:02 2002
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Reply-To: "K.Y.B. Williams" <lokido@tulane.edu>
From: "K.Y.B. Williams" <lokido@tulane.edu>
To: <chemistry@ccl.net>
References: <Pine.OSF.4.44.0210241038520.885414-100000@adenine.cgl.ucsf.edu> <3DB8F1FB.652C1ECF@fy.chalmers.se>
Subject: MM/PBSA Ras-Raf
Date: Fri, 25 Oct 2002 11:48:25 -0500
Organization: Theoretical Molecular Biology Group
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Dear CClers

Has anyone performed a Delta G calculation via the MM/PBSA 
method?  I used the tutorial in AMBER7 and now I am wondering
if there is a ras:raf reference (publication) that may have come out of 
the tutorial/calculation or one that shows how the data was presented
in publication.

Can anyone point me in the right direction?


Kirk
------------------------------------------------------
K. Y. B. Williams
Theoretical/Computational Biochemist
Tulane University PhD Program - MCB
Center for Bioenvironmental Research
Dept. of Molecular and Cellular Biology
1430 Tulane Ave. 
New Orleans, LA 70112
lokido@tulane.edu
504-585-6145 (Work) 
504-736-0235 (Home)
504-736-0890 (Fax)
Pager: voice/numerical 800-297-6819
or 8002976819@timex.skytel.com
------------------------------------------------------



From chemistry-request@server.ccl.net Fri Oct 25 11:37:36 2002
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	 <mol-diversity@listserv.arizona.edu>
Cc: David Evans <D.Evans@mdl.com>
Subject: Combinatorial Chemistry and Laboratory Automation Symposium - New
	 Orleans 2003 Meeting
Date: Fri, 25 Oct 2002 08:37:00 -0700
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Hello everyone:
 
      Sorry for the cross postings. I am organizing a symposium for the ACS
meeting in New Orleans, March 23-27 entitled:
 
Combinatorial chemistry and laboratory automation (Oral symposium #3275.)
 
CINF will be co-sponsoring the above symposium with the ACS Laboratory
Automation (LABA) Division.
 
      This symposium will focus on the integration of laboratory systems /
automation with chemistry and specifically combinatorial chemistry.
Combinatorial chemistry is one of the most highly automated areas in modern
chemistry. In many cases both the synthesis and analysis can be almost
completely automated. But the problems facing the chemist are how to set up
and run the machinery and how to collect, collate and analyze the resultant
data. These are becoming critical business problems as the machinery and
techniques used in combinatorial chemistry become more widely available.
 
      Papers are invited that cover all aspects of designing, planning,
performing, analyzing, reporting and archiving all of this data. Topics
include (but not limited to):
 
            *     How can informatics streamline the design and execution of
automated combinatorial chemistry experiments
            *     Planning for fully automated chemistry experiments
            *     Overlap between cheminformatics and LIMS systems
 
      The format will be 30 minute oral presentations (this includes
question time).
 
      To submit an abstract, please go to
http://oasys.acs.org/acs/225nm/cinf/papers/index.cgi
<http://oasys.acs.org/acs/225nm/cinf/papers/index.cgi>  and select the
Combinatorial Chemistry and Lab Automation symposium. Anyone without web
access who wishes to submit an abstract can contact me.
 
      I look forward to reviewing submissions to this symposium. The
abstract submission deadline is Nov. 28. Please contact me if you have any
questions on this symposium.
 
      Thanks and I look forward to an exciting and rewarding symposium,
 
      David
 
______________________________
David A. Evans Ph.D.
Product Marketing
MDL Information Systems Inc.
Tel: +1 510-357-2222 ext 1145
Email: D.Evans@mdl.com
www.mdl.com
 
Powering the Process of Invention(tm)
       
 
 

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<div class=3DSection1>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'>Hello
everyone:<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier =
New"'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'><span
style=3D'mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Sorry =
for the
cross postings. I am organizing a symposium for the ACS meeting in =
</span></font><st1:City><st1:place><font
  size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'>New
  Orleans</span></font></st1:place></st1:City><font size=3D2 =
face=3D"Courier New"><span
style=3D'font-size:10.0pt;font-family:"Courier New"'>, March 23-27 =
entitled:<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier =
New"'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'>Combinatorial
chemistry and laboratory automation (Oral symposium =
#3275.)<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier =
New"'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'>CINF
will be co-sponsoring the above symposium with the ACS Laboratory =
Automation
(LABA) Division.<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier =
New"'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'><span
style=3D'mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>This =
symposium
will focus on the integration of laboratory systems / automation with =
chemistry
and specifically combinatorial chemistry. Combinatorial chemistry is =
one of the
most highly automated areas in modern chemistry. In many cases both the
synthesis and analysis can be almost completely automated. But the =
problems
facing the chemist are how to set up and run the machinery and how to =
collect,
collate and analyze the resultant data. These are becoming critical =
business
problems as the machinery and techniques used in combinatorial =
chemistry become
more widely available.<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier =
New"'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'><span
style=3D'mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Papers =
are
invited that cover all aspects of designing, planning, performing, =
analyzing,
reporting and archiving all of this data. Topics include (but not =
limited to):<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier =
New"'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'><span
style=3D'mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp; </span>*<span
style=3D'mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp; </span>How can =
informatics
streamline the design and execution of automated combinatorial =
chemistry
experiments<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'><span
style=3D'mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp; </span>*<span
style=3D'mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp; </span>Planning for =
fully
automated chemistry experiments<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'><span
style=3D'mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp; </span>*<span
style=3D'mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp; </span>Overlap =
between
cheminformatics and LIMS systems<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier =
New"'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'><span
style=3D'mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>The =
format will
be 30 minute oral presentations (this includes question =
time).<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier =
New"'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'><span
style=3D'mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>To =
submit an
abstract, please go to <a
href=3D"http://oasys.acs.org/acs/225nm/cinf/papers/index.cgi">http://oas=
ys.acs.org/acs/225nm/cinf/papers/index.cgi</a>
and select the Combinatorial Chemistry and Lab Automation symposium. =
Anyone
without web access who wishes to submit an abstract can contact =
me.<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier =
New"'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'><span
style=3D'mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>I look =
forward to
reviewing submissions to this symposium. The abstract submission =
deadline is
Nov. 28. Please contact me if you have any questions on this =
symposium.<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier =
New"'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'><span
style=3D'mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Thanks =
and I look
forward to an exciting and rewarding =
symposium,<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier =
New"'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'><span
style=3D'mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
</span>David<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier =
New"'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier =
New"'>______________________________<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><st1:PersonName=
><font
 size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'>David
 A. Evans</span></font></st1:PersonName><font size=3D2 face=3D"Courier =
New"><span
style=3D'font-size:10.0pt;font-family:"Courier New"'> =
Ph.D.<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'>Product
</span></font><st1:PersonName><font size=3D2 face=3D"Courier New"><span
 style=3D'font-size:10.0pt;font-family:"Courier =
New"'>Marketing</span></font></st1:PersonName><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier =
New"'><o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'>MDL
Information Systems Inc.<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'>Tel:
+1 510-357-2222 ext 1145<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'>Email:
D.Evans@mdl.com<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'><a
href=3D"www.mdl.com">www.mdl.com</a><o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier =
New"'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'>Powering
the Process of Invention(tm)<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 face=3D"Courier New"><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'><span
style=3D'mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span
style=3D'mso-spacerun:yes'>&nbsp;</span><o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><o:p>&nbsp;</o:p></span></font></p>

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