Subject: summary of responses about esff

From: <[email-masked]>
Date: Mon, 7 Aug 95 17:06 +0200

hi,
This  is the  summary   of  answers  i got   about the
esff  force field.

Dear Alexandra Kilshtain,

     I am sorry that version 235 is a very first beta release for ESFF that
can only handle systems where there  are no more than 25 molecules and
each molecule has no more than 200 atoms.
However, the later versions, 236, 237, 940 and 950
could handle a systems having no more than 15000 atoms.

Please try the new versions and let me know if you have any questions.

                                     Best wishes,

                                               shenghua

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

Hi,

I have been using both the cvff and cff91 forcefields in discover
and discover 94 on a solvated protein (~15,000) atoms including
a Zn cation.  I modified the cvff and cff91 forcefields to include
my parameters for Zn.  The Zn cation is treated totally as a
nonbonded entity.  If this is suitable for your problem, I can provide
you with the necessary changes to cvff or cff91.

Lee Bartolotti

--

--------------------------------------------------------------------------------
Lee Bartolotti			North Carolina Supercomputing Center
Computational Scientist		3021 Cornwallis Rd.
Research Institute		Research Triangle Park, NC 27709

[email-masked]
 (919) 248-1185	
--------------------------------------------------------------------------------

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

Dear Alexandra:

	As you experienced, only 200 atoms in each molecule and 15 molecules per
crystal cell are allowed using ESFF force field with Biosym release 2.3.5.  This
limitation will be lifted in our upcoming release 95.0 and ESFF force field will
be able to treat molecular systems up to 10,000 atoms.

Lisa Yan
Biosym Technologies, Inc.                       Tel (619)546-5547
9685 Scranton Road                              email [email-masked]
San Diego, CA  92121

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

Hi Alexandra,

I'm sorry for not beeing able to give you any help. There's just a comment, I
want to make:

I'm doing MM for transition metals with insight/discover. I tried to use the
ESFF because Biosym told me, it should be better than UFF of A. Rappe and so
forth. They told me, that I should help them in testing ESFF. But I wanted to
have a description , what ESFF actually does and how the parameters are
generated from the atomic parameters (which is all published for UFF). But they
didn't tell me. So I couldn't say, why some calculations gave reasonable result
and others not. I can't publish all that and so I stopped the project. I really
have to say, that I lost all (I don't know a better word) trust in Biosym.

My suggestion: the advantage of ESFF would be to model your zinc environement
(probably !!!!) reasonable. All the rest is calculated well by cff91, I guess.
Why don't you use cff91 together with discover 94.0 (discover_3) and use some
BTCL restraints to model just your zinc environement. Maybe you can overcome
the 200 atom limit by that.

Good luck,

Greetings from Munich,

Rochus

--

********************************************************************************
Rochus Schmid
Technische Universitaet Muenchen	Tel. 	++49 89 3209 3140
Anorganisch Chemisches Institut 1	Fax. 	++49 89 3209 3473
Prof. W. A. Herrmann			E-mail:	
Lichtenbergstrasse 4			[email-masked]
85747 Garching
********************************************************************************

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

Shalom Alexandra!

   I just want to worn you about using the esff seriously. First of
all it has no parameters for Zn ion ( Look at the parameter table
Page 3-23 Discover 2.9.5/94 Users Guide). Secondly, this ff, as I
understand the things, is just under development. I even have an
impression that the BIOSYM people themselves are not exactly aware of
what they want this ff to work for - they write in the same Users guide
that it is being designed for organic and organometallic compounds. I tested
it for our organic compounds ( crown ether like mols) and it was
completely wrong. I had a possibility to speak it over with BIOSYM people
and they said that it was not at all a surprise for them because they design
the esff for inorganics!
    So, use maybe AMBER or some other known ff (obligatory test them before
for your comds!) and keep in touch with BIOSYM . I think your experience
could help them.

  Yours,

Lara.
    ________________________________________________________________________
   /                                                                        \
   |  Dr.Larisa Golender                     tel. +972-3-6408437            |
   |  School of Chemistry                    fax: +972-3-6409293            |
   |  Tel Aviv University                    e-mail: [email-masked] |
   |  Ramat Aviv, Tel Aviv 69978                                            |
   |  ISRAEL                                                                |
   \________________________________________________________________________

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

Dear Alexandra  Kilshtain,

re: support request #45580

>1. Is their  a version  of discover that can deal with
>more than 200 atoms and have esff potentials ?

In the upcoming release, which should be out Mid-September, ESFF
will have a 10,000 atom limit.

>2. Is there any reference or manual section that  you  could send me
>that  will explain  how to use the esff force field potentials for zinc?

I don't know what you have received previously, below is a release note
for ESFF for Insight235. Also, if you want to know what the atom type names refer
to you can look in the esff.frc file in

	$BIOSYM/iris405/irix405_r3/biosym_lib

For example the Zn atom types are:
 1.0   1      Zn  65.390000    Zn          10       Zinc atom with s orbitals involved in bonding
 1.0   1     Zn+  65.390000    Zn          10       Zinc +1 free ion
 1.0   1    Zn+2  65.390000    Zn          10       Zinc +2 free ion
 1.0   1   Zn022  65.390000    Zn          10       Zinc with 2 coordinations
 1.0   1   Zn023  65.390000    Zn          10       Zinc with 3 coordinations
 1.0   1   Zn024  65.390000    Zn          10       Zinc with 4 coordinations
 1.0   1   Zn025  65.390000    Zn          10       Zinc with 5 coordinations
 1.0   1  Zn025s  65.390000    Zn          10       Zinc with 5 coordinations, D4h symmetry
 1.0   1  Zn025t  65.390000    Zn          10       Zinc with 5 coordinations, D3h symmetry
 1.0   1   Zn026  65.390000    Zn          10       Zinc with 6 coordinations
 1.0   1  Zn026o  65.390000    Zn          10       Zinc with 6 coordinations, oh symmetry

If you still have questions after reading this note, you can always send us
your .car and .mdf files and we can take a look at them.

The ESFF Forcefield-Release Note
--------------------------------

The Discover 94.1 release of ESFF a new rule-based forcefield. The initial goal
of ESFF was to provide the widest possible coverage of the periodic table
at a level of accuracy capable of producing reasonable structures.
The limit for the total number of atoms in a system is 200 (for 235 release)
and 10,000 (for 950 release).

Setting up ESFF:

-	In the 235 release, before starting up the Insight program, esff_setup
must be entered at the UNIX prompt:

>	esff_setup

This command sets the appropriate environmental variables to access the ESFF
data sets.
It is not possible to select ESFF within the Insight environment with the
Forcefield/Select command.  The reason for this is the elements.dat file,
which defines the properties of the elements, differs (in ESFF) from that of
other forcefields and the Select command does not change the variable which
reads the elements.dat. It is still possible to switch from ESFF to one of the
other forcefields using this command. However, the elements.dat file will
remain as the one associated with the ESFF forcefield. Because of this, you
must exit the Insight program, unset the INSIGHT_DATA environmental variable
by running cvff_setup and restart the Insight program.

Building Pi Bonded Systems:

-	pi bonds are created by first defining a pseudoatom as the center of a
set of ligand atoms and then bonding this pseudo atom to the metal.  What
appears are bonds between the metal and each atom that defines the pseudo atom.
For an example see the tutorial below.

Assigning Atom Types, Partial Charges and Formal Charges:

-	The procedure for assigning atom types and charges in ESFF differs from
that of other forcefields.  With ESFF the total charge of a molecule is used to
determine the oxidation state of the metal which in turn is used in determining
the atom types.

-       The oxidation number of the metal is given by the following expression:

        Nox = Qt - Sum(Fqi)/Nm - Sum(Fqj/Nb)

where Qt is the total charge on the complex, and the sums over Fqi and Fqj are
the sums of formal charges on atoms not bonded to metals and bonded to metals,
respectively. Nm is the number of metal atoms in the complex, and Nb is the
number of metal atoms bonded to the jth ligand atom.

-	Once you have built a molecule, the first step in assigning the atom
types is to set the total charge of the molecule.  Insight will sum all partial
charges on the molecule and consider this the total charge.  Therefore, the
simplest way to set the total charge is to change the partial charge of an
arbitrary atom to the value of the total charge and zero all other partial
charges. This step can be carried out using an existing BCL macro,
initialize_charge.bcl. To do so enter:

	source $BIOSYM/data/discover/esff/initialize_charge.bcl

This will insert the command Set_Molec_Chg into the Forcefield pulldown.
Choosing this command results in a prompt for the name of the molecule. The
macro then zeros all partial charges and sums the formal charges in the
molecule. The resulting sum is reported as a suggested total molecular charge.
You may either accept this or specify a different value. When the Set_Molec_Chg
command is executed, the macro places this charge on the first atom in the
molecule and zeros all other partial charges.
If the total charge on your molecule is zero and you have checked that all
partial charges are zero or if all the partial charges add up to the desired
total charge, you will not need to use this command.  However, it is important
to verify this before continuing (non-zero partial charges can result from
previous calculations with other forcefields or from fragment libraries).
The next step is to derive formal charges and assign the atom types using the
Forcefield/Potentials command.

-	In the 235 release the fix partial charges action has been disabled. The
reason for this is that ESFF calculates charges on the fly based on atom type as
well as other topological considerations (see the Discover User Guide ). The
charges used in the calculation can be displayed in the Insight program after
the calculation has completed and the structure has been updated. The charges
are also written to the .cor and .mdf files.

-	The atom types for metals are based on the symmetry of the metal complex
as well as the oxidation state and coordination number of the metal. For
example, Ag024t specifies that Ag has an oxidation level of 2+, is 4-coordinated
and has a tetrahedral symmetry. The following table describes the atom type
suffixes:

Symbol  Symmetry        Coordination    Description
================================================================================
d       Dip 	        2               Linear (ligands are pseudo atoms)
t       Dih 	        2               Linear (ligands are real atoms)
        C2v		2		Bent
--------------------------------------------------------------------------------
l	C2v		3		T-shaped
  	D3h		3		Planar
  	C3v		3		Pyramide
--------------------------------------------------------------------------------
t       Td              4               Tetrahedral
s       D4h             4               Square Planar
l       C2v             4               Trigonal Bipyramide less an equatorial
--------------------------------------------------------------------------------
t       D3h             5               Trigonal Bipyramide
s,l     D4h             5               Square Pyramide
l       C2v             5               Tetragonal Octahedral less an equatorial
--------------------------------------------------------------------------------
        D2h             6               Rhombic Octahedral
        D4h             6               Tetragonal Octahedral
o       Oh              6               Octahedral
--------------------------------------------------------------------------------
p       D5h             7               Pentagonal Bipyrimide
l       C2v             7               Hexagonal Bipyrimide less an equatorial
--------------------------------------------------------------------------------
h       D6h             8               Hexagonal Bipyrimide
--------------------------------------------------------------------------------

Note, that there are several combinations that do not have a symbol for the
symmetry in these cases only the oxidation number and coordination are specified
in the atom type name.
Some metals with differing oxidation numbers may be treated with the same
parameters. In these cases, the atom type is a generic atom type associated
with the metal.

ESFF Forcefield Editor Option (only available in the 236 release):

You may modify the explicit parameters of the ESFF forcefield for a particular
molecular system.  To do so, first run a job for that system in the default
mode.  An explicit parameter file, run_name.epa, is output when the job
(run_name) is finished.  You can then edit run_name.epa to modify the explicit
parameters; force constants, alphas and reference values.  To rerun the job with
the modified parameters, you must add the following line to the command input
file (run_name.inp) after the "begin" command:

	set esffOverrideParameters 1

When this flag is set to 1 (the default is 0), only the parameters contained in
the file run_name.epa are used.

Tutorial on Use of the ESFF Forcefield
--------------------------------------
The following tutorial is given as an example of how to use the organometallic
builder. It is strongly recommended that you run through this example before
using the Builder.
This tutorial is written in outline form and assumes that you already have some
familiarity with the Insight molecular modelling program and its Discover_3
module.

Tutorial -Creating and Minimizing Dichloro(Dicyclopentadienyl) Titanium (IV),
(C5H5)2TiCl2, with ESFF

Before starting the Insight program, enter the following at the UNIX prompt:
>	esff_setup
1.	Start the Insight program by entering insightII at the UNIX prompt.
2.	Add the Set_Molec_Chg command to the Forcefield pulldown by entering on
the Insight command line (near the bottom of the Insight screen):
source $BIOSYM/data/discover/esff/initialize_charge.bcl
3.	The Builder module is automatically accessed.
4.	Select the Fragment/Get command and set Type Of Fragment to
Metal_Templates. Click any atom in the Coord4-Td fragment (set Scroll to Next
until you see it near the top of the Insight window) and select Execute.
*Note, be sure to select the template that best represents the symmetry of the
structure you wish to build, subsequent atom type assignments will depend on it.
5.	Select the Atom/Replace command, choose Ti (scroll to find it by using
the scrollbar to the right of the Element Type list), and then click the Mx
(central atom) of the molecule in the display area.
*Note that the central atom should be replaced by a metal before adding any
ligands. This is to ensure that the metal-ligand bond lengths are correct.
6.	In the same way, replace two of the ligand atoms with Cl.
7.	Select the Fragment/Get command and set Type Of Fragment to
Metal_Ligands. Toggle the To_Modify_Bond parameter off and click the
Lg_pentadien fragment twice (followed by selecting Execute) to retrieve two
cyclopentadienyl rings.
8.	Connect to each of the rings in turn and move it so it is near the
unbound ligand positions of the metal complex.
9.	Define a pseudoatom at the center of one of the rings by using the
Pseudo_Atom/Define command and specifying the ring carbons.
10.	Bond the pseudoatom to one of the ligand atoms (use the Modify/Bond
command with Bond Operation set to Create)
11.	Repeat Steps 9 and 10 with the other cyclopentadienyl ring, bonding it
to the last ligand atom.
12.	You will see that the pseudoatom associated with the first ring bound
disappears when the second ring is bound. Create a new pseudoatom for this ring.
13.	Select the Forcefield/Set_Molec_Chg command and choose the molecule name
from the value-aid. After a short time, a recommended charge based on the
molecule's formal charges appears in the Charge parameter box. In this example
there are no formal charges, so zero will appear. Accept this charge by
selecting Execute.
In this case this step is not necessary however if you would want to place a net
charge on the molecule you woulddo so here.
14.	Select the Forcefield/Potentials command. Assure that Potential Action
is set to Fix, Partial Chg Action to Accept, and Formal Chg Action to Fix.
Select Execute.
15.	Go to the Discover_3 module (by clicking the Biosym logo).
16.	Select the Setup/System command and click the Ti complex.
17.	Select the Commands/Minimize command and select Execute (this accepts
the default parameter values).
18.	Select the D_Run/Run command and select Execute.
19.	Quit the Insight interface by entering quit on on the command line.

I hope that you find this helpful. Please let us know if you have any
further questions.

Jodi

++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Jodi Shaulsky
BIOSYM Technologies
[email-masked]
619-546-5542

end