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From: "Michael G. Razumov" <michraz@analyt.chem.msu.ru>
To: <CHEMISTRY@ccl.net>
Subject: SUMMARY: MM calculation of the stacking structures
Date: Fri, 2 Jun 2000 13:41:23 +0300
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Hi!

Some time ago I've asked a question about molecular mechanics calculations
of stacking structures:

//////// ORIGINAL MESSAGE /////////////
Could anybody help me with a problem, concerning MM calculation of the
stacking structures?

I have (theoretically) two plane aromatic structures (Ni(II)
phtalocyaninates), one above another, bound with each other between benzene
rings by some flexible carbon chains.

The question is: will the planes come off each other if the length of these
chains is long enough? Or will they fix at some distance from each other?

For example, calculating these systems with standard molecular mechanics
with electrostatic interactions turned off, one will result in two planes at
distance about sum of van-der-Waals radii (C-C) as there is a minimum of
this function here.

_Is there any physical sense of such structure?_ Maybe, pi-pi interaction
should be also taken into account?

Probably, I need to turn on electrostatic interactions? If so, were from to
take partial atomic charges?
////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////


Thanks to Luigi Cavallo and Michael Charlton for the help.


/////////////// Luigi Cavallo's <cavallo@chemna.dichi.unina.it> answer
////////////////////
To properly simulate benzene dimer, for example, you MUST use atomic
charges. Usually, the C charge is something between -0.10 and -0.15, but
you have to check for the particular force field you're using.

Without charges, the benzene dimer minimizes to a geometry with the 2
rings one on top of the other, at the minimum C-C vdw distance, as you
find. However, this geometry is overstabilized with respect to the "real"
minimum, which has the 2 rings perpendicular each other. At least as it
come from ab initio calculation, as it is in the X-ray structure of solid
benzene, as it comes when you add charges with a MM force field.
////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////

////////////// Charlton, Michael's <mcharlto@oai.co.uk> answer
/////////////////////
Although I am no longer involved in modelling PCs, in my old job, my
colleagues examined stacking interactions, and got reasonable lattice /
sumblimation enthalpies using force fields with atom-centred point charges.
We often used AM1 for these charges, but this is not applicable in your Ni
case.  We also used either Gasteiger-Marsili or QEq (from Cerius) charges -
these are more applicable to metals.  I seem to remember relatively little
sensitivity of the lattice energy on the choice of charges.
HOWEVER, Chris Hunter (Sheffield University (UK), and a much greater
authority on these systems than I am) showed that to reproduce pi-pi
stacking geometries effectively, you have to use non atom centred charges.
In particular, he placed partially-charged dummy sites above and below the
system to mimic pi effects and reproduced aromatic stacking very well.  (I
believe he Christened them "Zeds". ) Unfortunately, I don't have a reference
to this work to hand, but you may be able to find Chris on the university
web site.

As a final note, pi-pi stacking makes up a large proportion of the
phthalocyanine packing energy, which is itselfe very strong.  If you are
trying to model pulling the system apart, you will need to include it in
your calculations.
////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////


----------------------------------------------------------------------------
---------
Michael G. Razumov,  Postgraduate Student of
Kurnakov Institute of General and Inorganic Chemistry
and Lomonosov Moscow State University
E-Mail: michraz@analyt.chem.msu.ru  michael@analyt.chem.msu.su
ICQ UIN: 25169010



From chemistry-request@server.ccl.net  Fri Jun  2 09:49:39 2000
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Date: Fri, 2 Jun 2000 14:49:21 +0100 (BST)
From: Simon Cross <pcxsc@nottingham.ac.uk>
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To: chemistry@ccl.net
Subject: AUTODOCK 3.0
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Has anyone used soft potentials with Autodock 3.0, or used other methods
to overcome problems with 'gating' in a fixed receptor? I am specifically
working on antibodies and find that Autodock can only reproduce the ligand
location in the crystal structure if it is initiated within the binding
pocket - if the ligand is placed outside the binding pocket it docks in
the correct location but only 'half in' the pocket, presumably due to the
lack of flexibility of the antibody in this system. I am trying to get
around this by using soft potentials but am not entirely sure how to do
this. Any comments much appreciated.   

-----------------------------------------

Simon Cross
School of Chemistry
University of Nottingham
tel. 0115 9514193
Email: pcxsc@nottingham.ac.uk




From chemistry-request@server.ccl.net  Fri Jun  2 10:57:09 2000
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Date: Fri, 2 Jun 2000 10:56:42 -0400 (EDT)
From: "C.F. Matta" <mattacf@mcmail.cis.McMaster.CA>
To: CHEMISTRY@www.ccl.net
Subject: Optimum memory allocation in GAUSSIAN94
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Hello everybdy,

In GAUSSIAN94, I noticed that the job CPU time as recorded in the log file
increases when I allocate too much memory (instead of decreasing). 

For example, a geometry optimization of benzene at the restricted
Hartree-Fock level using a 3-21G basis set on a LINUX 5.2 platform
with a PENTIUM III 600MHz processor (768MBs RAM), took the following
times:

	200 MB ----> 1 minutes 18.5 seconds
        600 MB ----> 2 minutes 11.6 seconds

I noticed the same with other systems as well, larger memory=slower
job.  There must be a way to estimate the optimum memory allocation for a
specific job.

I would much appreciate your help.  Thank you very much.

(I will summarize)

Cherif 
___________________________________________________________________________

  Cherif F. Matta		    	  tel. (905) 525-9140 ext. 22502
  Chemistry Department                    fax  (905) 522-2509
  McMaster University                               _______________________ 
  Hamilton, Ontario, CANADA L8S 4M1.                | * "You'll always miss
....................................................| 100% of the shots you
 Member of the Board of Governors of the University | don't take".Anonymous 
___________________________________________________________________________


From chemistry-request@server.ccl.net  Fri Jun  2 11:07:36 2000
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From: "Adrian Radomir Jaszewski" <ADRIAN@WCHUWR.CHEM.UNI.WROC.PL>
Organization:  University of Wroclaw (Chemistry)
To: chemistry@server.ccl.net
Date:          Fri, 2 Jun 2000 17:09:44 MET
Subject:       van Duijneveldt/IGLO-III basis sets
Priority: normal
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Message-ID: <C2A3D64ED@wchuwr.chem.uni.wroc.pl>

Dear CCLers,

I am looking for the basis set of van Duijneveldt as well as IGLO-III
set of Kutzelnigg et al. The original reference are:
F.B.van Duijneveldt, IBM Res.J. 1971, p.945 for the (13s8p,8s)
[7s4p,5s] basis set and
W.Kutzelnigg, U.Fleischer, M.Schindler, NMR-Basic Principles and 
Progress, Springer-Verlag, Heidelberg, 1990, vol.23 for 
the (11s7p2d,6s2p) set contracted to [7s6p2d/4s2p].
 
Unfortunately, I haven't access to this paper/book. 

I would like to know all exponents and contraction coefficients 
for hydrogen, carbon, nitrogen and oxygen atoms.

I will be very grateful for any information on this theme.

Thank you in advance
Best regards, 
Adrian

===============================================
Adrian R. Jaszewski
Faculty of Chemistry
UNIVERSITY OF WROCLAW
14 Joliot-Curie St.
50-383 Wroclaw
Poland
e-mail: adrian@wchuwr.chem.uni.wroc.pl
================================================ 

From chemistry-request@server.ccl.net  Fri Jun  2 13:39:25 2000
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Date: Fri, 02 Jun 2000 18:38:37 +0100
To: chemistry@ccl.net
From: "Miss L.M.P. Galvao" <l.galvao@ic.ac.uk>
Subject: Re: CCL:AUTODOCK 3.0
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 ngham.ac.uk>
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Hi!

I am trying to dock a few furazan derivatives into the active site of
P450-BM3.

As a control I am using the natural enzyme subtrate palmitoleic acid and I
am  trying to reproduce its original location in the crystal structure
using autodock 3.0.3. 

I have tried only a genetic algorithm (LGA) and although I generated
solutions that 
closely resemble the position of the crystal structure, I have failed to
obtain a location idental to that of the crsytal structure.

Do you know how I could overcome this with a genetic algorithm?

Looking forward to hear from you.  

Leonor Galvao




From chemistry-request@server.ccl.net  Fri Jun  2 17:12:40 2000
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 2 Jun 2000 17:12:33 EDT
Date: Fri, 02 Jun 2000 17:16:45 -0400
From: elewars <elewars@trentu.ca>
Subject: ZINDO/S, HISTORY
To: chemistry@ccl.net
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Friday, 2000 June 2

Hello,

Just a couple questions about the history and status of ZINDO/S:

Is it correct to say that ZINDO/S is a better version of INDO/S,
developed by the group of the late M. C. Zerner?  And that ZINDO/S is
one program in a package of (mostly semiempirical) programs called ZINDO
(available from a couple chemistry software firms)?

Thanks

E. Lewars
=========


From chemistry-request@server.ccl.net  Fri Jun  2 12:23:34 2000
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Date: Fri, 02 Jun 2000 18:20:55 +0200
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From: Theoretical Chemistry Group <teorica@ch.unito.it>
Subject: AB INITIO MODELLING IN SOLID STATE CHEMISTRY
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                    European Summerschool
         AB INITIO MODELLING IN SOLID STATE CHEMISTRY
                     September 16-20, 2000
                        Torino, Italy 
                       mssc@ch.unito.it                      
        http://www.ch.unito.it/ifm/teorica/mssc.html

                     LAST ANNOUNCEMENT

The Theoretical Chemistry Group of the Torino University is 
organizing a Summer School on the ab initio simulation 
of crystalline and defective solids. The school is addressed 
to PhD students with interests in solid state chemistry, 
physics, materials science, surface science, catalysis.
The school will provide an overview of the possibilities 
offered by ab initio quantum mechanical techniques when 
applied to characterize solid state materials. 
The school is open to 32 participants.

The Director of the school is Professor Roberto Dovesi.

Teachers

The local staff of the Torino Group (R. Dovesi, E. Giamello, 
C. Pisani, C. Roetti, P. Ugliengo, S. Casassa, A. Ferrari, 
Ph. Baranek, B. Civalleri, A. Damin, A. D'Ercole, G. Mallia, 
G. Pinarello from Torino University and M. Causà, R. Orlando 
>from the University of Eastern Piedmont) will be supported 
by highly qualified European scientists, including:

U. Birkenheuer MPI (Dresden)  Germany
M. Catti       Università di Milano Bicocca (Milano)  Italy
F. Corà        The Royal Institution (London) U.K.
Ph. D’Arco     Université Pierre et Marie Curie (Paris) France
N.M. Harrison  CLRC(Daresbury) and Imperial College(London)U.K.
F. Illas       Universitat de Barcelona Spain
A. Lichanot    Universite' de Pau et des Pays de l'Adour France
R. Resta       Università di Trieste Italy
V. R. Saunders CLRC(Daresbury) U.K. - to be confirmed
A. Savin       Université Pierre et Marie Curie (Paris) France
M.D. Towler    Cavendish Lab., University of Cambridge U.K.
C.M. Zicovich  Instituto de Tecnologia Química (Valencia) Spain
W. Weyrich     Universität Konstanz Germany

Program

The school will last five days (from Saturday morning to 
Wednesday evening).
The morning sessions will be devoted to presentations by 
experts in various aspects of the field, which are outlined 
below. 
The afternoons will be dedicated to practical sessions. 
The seminar part will show how to obtain information concerning
various observables using CRYSTAL98, a periodic code which can 
perform Hartree-Fock and DFT calculations for perfect and 
defective systems in a Gaussian basis. 
Two levels of tutorials are envisaged in the afternoon 
sessions, basic and advanced. The choice for the tutorial level
must be indicated in the application form.
 
Location

The school will be held at the Chemistry Departments of the 
Torino University. Accommodation will be at the University 
guest house, in double rooms.

The total price of the school will be 500,000 Italian Lire 
(258.23 Euro). This price includes a registration fee of 
200,000 Italian lire, lecture notes, lodging (6 nights, 
>from 15 to 20 September included), lunch, and coffee breaks 
for the duration of the school. 
Breakfast and dinner are not included.
Additional information can be obtained from: mssc@ch.unito.it

Application deadline is moved to 

June 10, 2000.

The application form: 
http://www.ch.unito.it/ifm/teorica/modulo.pdf
can be sent by fax or e-mail. 
We will send an acceptation letter by June 15. 
The registration will be effective after we receive the 
payment of the participation fee, following instructions 
included in the acceptance letter. 

Morning Sessions

 1 Translational symmetry, point symmetry and space groups
 2 Translational symmetry: Bloch Functions, Reciprocal Space	
 3 Hamiltonians; HF vs DFT; LDA, GGA, B3LYP			
 4 Basis set, solution techniques and hamiltonian.
 5 The structure of the CRYSTAL code
 6 Total energy, formation energy;  relative stability of phases
 7 Equation of states, effect of pressure, phase transitions, 
   elastic constants.
 8 Density matrix, charge density, X-ray structure factors.
 9 Superexchange in TM compounds; model hamiltonians; 
   cluster and periodic
10 Spin polarized solutions: the supercell approach	
11 Ferroelectric and dielectric properties. From theory to 
   experiment.
12 From bulk to surface. Relaxation and reconstruction.	
13 Surface Chemistry and catalysis:models, and strategies.
14 Local defects in crystalline materials.	
15 Defects: the structure of the EMBED code.	
16 Spin densities and related quantities in paramagnetic 
   defects.
17 Catalysis in 3D: the case of zeolites.
18 Simulation for new chemistry: the case of  W and Mo 
   perovskites.
19 EPR and ENDOR experiments in bulk and at the surface.
20 Monte Carlo calculation and the correlation problem.


Afternoon Sessions

Basic level tutorial

1. Geometry and its visualization. From literature data to the 
   CRYSTAL input; crystallographic tables; loss of symmetry. 
   Manipulation of the cell: creating a supercell (magnetic 
   systems, defects), slabs (surfaces), molecules from the 3D 
   crystal (molecular crystals). 
   Visualization tools interfaced with CRYSTAL.
2. Choice of the basis set for crystalline systems; where to 
   get it; what is important; molecular vs crystalline basis 
   sets; ECP vs all electron; HF and DFT; auxiliary basis set.
3. Total energy and related quantities. SCF convergence tools.
4. Properties and wave function analysis: band structure, 
   density of states, charge and spin density maps, 
   electrostatic potential, X-ray structure factors; 
   Mulliken population analysis (covalent, ionics, metals, 
   molecular crystals, spin polarized systems, surfaces). 

Advanced level tutorials

A. Total energy and Hamiltonian; equation of state of a simple 
   compound (CaO, NaCl); B1-B2 phase transition.
B. Geometry optimization techniques.
C. Adsorption and catalysis: how to create a surface from the 
   bulk; evaluation of the surface energy; relaxation; 
   adsorption (MgO, TiO2).
D. Adsorption and catalysis: zeolites and analogues.
E. Defects: How to calculate the most relevant quantities for a
   defect (vacancies, substitutional impurities, F centres, 
   paramagnetic defects) with CRYSTAL and EMBED.
F. Ferromagnetism; magnetic supercells; 'tricks ' and CRYSTAL 
   input tools: a simple case (NiO, KMnF3).
G. Perovskites and their peculiar properties.
H. Wave-function analysis: AIM, ELF applied to solids.

Evening open discussions

U. Birkenheuer, R. Dovesi, R. Resta, V.R. Saunders, C. Zicovich;
Delocalized (Bloch) and localized (Wannier) crystalline orbitals; 
how to generate them in CRYSTAL; are they useful? 
How well are they localized?

R. Orlando and U. Birkenheuer
Beyond HF: are MP2, IEPA and CEPA possible for solids? 
State of the art at Dresden and Torino.



From chemistry-request@server.ccl.net  Fri Jun  2 18:25:09 2000
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From: "Armando Navarro" <qoajnv@usc.es>
To: <CHEMISTRY@ccl.net>
Subject: formatted g98w checkpoint
Date: Sat, 3 Jun 2000 00:13:11 +0200
Message-ID: <01bfccdf$bd794d40$eb4a90c1@qogolem.usc.es>

Dear members:
I have observed that when I modify the molecular orbitals coefficients
by hand in a g98w formatted checkpoint file, and then II tranlate the .fch
file to the unformatted check point and then I read the modified 
orbitals with guess=3D(read,only), the printed coefficients are not the
modified values but some other values. I suppose that g98 makes some
check of the wavefunction. There is some way to prevent this?.
Thanks in Advance
Armando Navarro
Departamento de quimica organica
Facultade de quimica

e-mail qoajnv@usc.es




From chemistry-request@server.ccl.net  Fri Jun  2 22:04:06 2000
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Date: Fri, 2 Jun 2000 19:02:00 -0700
From: "Garrett M. Morris" <garrett@scripps.edu>
To: Simon Cross <pcxsc@nottingham.ac.uk>
cc: chemistry@ccl.net
Subject: Re: CCL:AUTODOCK 3.0
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Dear Simon,

On Fri, 2 Jun 2000, Simon Cross wrote:

> Has anyone used soft potentials with Autodock 3.0, or used other

AutoGrid 3.1 has not yet been released, but it has a new form of
pairwise potential smoothing, which ramps the potential to a finite
value at separation zero.  This finite value can be varied by the
user, and so could help dramatically in the early stages of the
docking.

> methods to overcome problems with 'gating' in a fixed receptor? I
> am specifically working on antibodies and find that Autodock can
> only reproduce the ligand location in the crystal structure if it
> is initiated within the binding pocket - if the ligand is placed

Are you using SA (simulated annealing) to do this?  You can only start
the ligand at a pre-defined position using SA and LS (Solis and Wets).
The GA and LGA start from a population of random initial genomes.

> outside the binding pocket it docks in the correct location but
> only 'half in' the pocket, presumably due to the lack of
> flexibility of the antibody in this system.

The LGA is the most efficient search method: SA seems to be the least
efficient.  You should get better results with the LGA than with the
SA, for the same number of energy evaluations. We found this even
though both were started from random initial states or populations of
states.

If you are using LGA, with a population size of 50, an elitism number
of 1, and a crossover rate of 0.80, you might want to try increasing
elitism to 5.  Then there is a 20% chance that one of the top five do
not experience crossover, and thus will survive into the next
generation.

Another pointer: increase the maxium number of evaluations, by a
factor of 10.  This might help to improve the search results.

> I am trying to get around this by using soft potentials but am not
> entirely sure how to do this. Any comments much appreciated.
> 
> -----------------------------------------
> 
> Simon Cross
> School of Chemistry
> University of Nottingham
> tel. 0115 9514193
> Email: pcxsc@nottingham.ac.uk
> 
> 
> 
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I hope this helps,

Garrett

___
Dr Garrett M. Morris, MA, DPhil
The Scripps Research Institute,       tel: (858) 784-2292
Dept. Molecular Biology,  MB-5,       fax: (858) 784-2860
10550  North Torrey Pines Road,       email: garrett@scripps.edu
La Jolla,  CA 92037-1000,  USA.       www.scripps.edu/pub/olson-web/gmm


