CHARMM c28a3 charmmrate.doc


File: Polyrate ]-[ Node: Top
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              *      CHARMM/POLYRATE INTERFACE       *

CHARMMRATE: A Module for Calculating Enzymatic Reaction Rate Constants
            with POLYRATE and CHARMM

     CHARMMRATE is an inteface of CHARMM and POLYRATE for carrying out
variational transition state theory (VTST) calculations to predict reaction
rate constants and other properties.  Although CHARMMRATE allows execution 
of POLYRATE with all existing capabilities, the present implementation is
primarily intended for predicting reaction rates in enzyme catalyzed
reactions.  The procedure involves a partition of the system into a
frozen bath region and a dynamics region that is used in the dynamics
calculation.  The method has been applied to the proton transfer step
in the conversion of 2-phosphoglycerate to 2-phosphopyruvate by
yeast enolase.  More details can be seen in J. Am. Chem. Soc. 121, 2553 
(1999) by C. Alhambra, J. Gao, J. Corchado, J. Villa, and D. G. Truhlar.

     CHARMMRATE can be combined with semiempirical combined QM/MM potentials
with numerical second derivatives that are computed by the POLYRATE
inerface programs.  The current version has not been parallelized.

     This documentation contains a short version, and a long, detailed
version following the short CHARMM-command description.  Users are
encouraged to read both parts.

* Menu:

* Description::         Description of the POLYRATE driver in CHARMM
* Using::               How to run POLYRATE in CHARMM
* Installation::        How to install POLYRATE in CHARMM
* Status::              Status of the interface code


File: Polyrate ]-[ Node: Description
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        * Syntax for the CHARMMRATE Method                 *

POLYRATE is initiated with the POLYrate command.

[Syntax POLYrate]

POLYrate [ atom-selection] [RUNIT int] [PUNIT int] [TSUNit int] [OPUNit int]
[POLYRATE commands]

      atom-spec::= {residue-number atom-name}
                   { segid  resid atom-name }
                   { BYNUm  atom-number     }

RUNIt [int]:   Unit specification for input of initial coordinates of the
               Reactant species.  The current limitation is that only
               CHARMM format is allowed for the coordinate file.

PUNIt [int]:   Unit specification for input of initial coordinates of the
               Product species.  The current limitation is that only
               CHARMM format is allowed for the coordinate file.

TSUNit [int]:  Unit specification for input of initial coordinates of the
               Transition State.  The current limitation is that only

               CHARMM format is allowed for the coordinate file.

OPUNit [int]:  Unit to write out coordinates of the optimized structures,
               of any of the Reactant, Product, and TS, depending on
               request.   The current limitation is that only

               CHARMM format is used.

[POLYRATE commands]
This section contains standard POLYRATE commands.  They must follow immediately
after the [POLYrate] command in the CHARMM input stream.  This section is
terminated by the key word [*finish], lower case with a star in the beginning.
For details of POLYRATE commands, see POLYRATE documentation.


File: Polyrate ]-[ Node: Usage
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Note: The version number of charmmrate is 1.0/P8.1.1-C28a2.  This means that 
charmmrate-version 1.0 is based on polyrate-version 8.1.1 and charmm-version 
28a2. The version number may be abbreviated to 1.0 when no confusion will result.

CHARMMRATE is a module of charmm for interfacing it with polyrate. The polyrate 
main program becomes a subprogram of CHARMM. POLYRATE can be called to carry out 
variational transition state theory calculations with multidimensional
semiclassical tunneling contributions. When polyrate needs the value or gradient 
of the potential energy surface, it calls a set of interface routines called 
hooks. The hooks in turn call charmm routines for energies and gradients
calculated by molecular mechanics or QM/MM methods.

Referencing for charmmrate

The rate constant (or reaction path or geometry optimization, etc.) calculations 
were carried out using the charmmrate program[1-3].

[1].    C. Alhambra, J. C. Corchado, M. L. Sanchez, J.  Villa, J. Gao, and D. G. 
Truhlar, charmmrate-version 1.0, University of Minnesota, Minneapolis, 1999, a
module of charmm (Ref. 2) for interfacing it with polyrate (Ref. 3).

[2].    Chemistry at HARvard Macromolecular Mechanics (charmm) computer program, 
as described in B. R.  Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States,
S. Swaminathan, and M. Karplus, J. Comput. Chem. 4, 187 (1983).

[3].    Y.-Y. Chuang, J. C. Corchado, P. L. Fast, J.  Villa, W.-P. Hu, Y.-P. Liu, 
G. C. Lynch, C. F.  Jackels, K. A. Nguyen, M. Z. Gu, I. Rossi, E. L.  Coitio, 
Clayton, V. S. Melissas, R. Steckler, B.  C. Garrett, A. D. Isaacson, and 
D. G. Truhlar, polyrate-version 8.1.1, University of Minnesota, Minneapolis, 1999.


File: Polyrate ]-[ Node: Usage
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        * Availability of CHARMMRATE                       *

     CHARMMRATE-version 1.0 is a module of charmm-version 27 for interfacing it 
with polyrate-version 8.1.1.  CHARMMRATE-version 1.0 will be distributed as part 
of the CHARMM program, beginning with version 27 of charmm. The user will also 
require the crate utility for modifying polyrate to make it compatible with charmm. 
The prospective user of charmmrate should obtain a valid license for charmm from an 
authorized charmm licenser and valid licenses for polyrate and crate from the 
University of Minnesota (


     charmmrate is an interface of charmm and polyrate for carrying out variational 
transition state theory (VTST) calculations to predict reaction rates and other 
properties of enzymatic systems. Although charmmrate allows execution of polyrate 
with all existing capabilities for reactions with only one reactant and only one 
product, the present implementation is primarily intended for prediction of the
reaction rates of enzyme-catalyzed reactions. The secondary- zone potential (SZP) 
approximation involves the partition of the system into a frozen bath (secondary 
subsystem) and a moving primary subsystem; only the atoms of the primary subsystem 
are allowed to have kinetic energy in the dynamics calculation.

     The SZP method has been applied to the proton transfer step in the conversion 
of 2-phosphoglycerate to 2- phosphopyruvate by yeast enolase. For additional
descriptions of the methods, see C. Alhambra, J. Gao, J.  Corchado, J. Villa, and 
D. G. Truhlar, J. Amer. Chem. Soc.  121, 2253-2258 (1999).

1.A. Capabilities added to charmm by charmmrate and references for methods

     polyrate includes a very large number of options and has multiple capabilities. 
The user of charmmrate is encouraged to read the polyrate manual to learn more about
these capabilities. The present section summarizes a few of the capabilities that 
are liable to be of most interest to charmmrate users.

     1.A.1. Transition state optimization

     Saddle point geometry optimizations for the primary (dynamic) zone in the 
frozen protein-plus-solvent bath may be performed in various ways. The default 
option is the Newton-Raphson method with Brent line minimization as described in 
W. H. Press, S. P. Flannery, S. A.  Teukolsky, and W. T. Vetterling, Numerical 
Recipes (Cambridge University Press, Cambridge, 1986), p. 254.  The default option 
for optimization of the stationary points for reactants and products is to use the 
BFGS method that has been implemented in POLYRATE. See the POLYRATE manual for 
further information about the optimization methods available in POLYRATE.

     1.A.2. Reaction path

     In general, reaction paths (RPs) may be defined in various ways. The simplest 
general method that is reasonably sure to give physically meaningful vibrational 
frequencies for motions transverse to the reaction path (and hence also physically 
meaningful free energy of activation profiles) is the steepest descents path in 
isoinertial coordinates. (An isoinertial coordinates system is one in which the 
kinetic energy is a sum of square terms and the coordinates are scaled or weighted 
so that each kinetic energy term has the same reduce mass. All isoinertial 
coordinate systems are related to each other by orthogonal transformations, and 
steepest descents paths are invariant under orthogonal transformations.) A steepest 
descents path is also called a minimum energy path (MEP). The signed distance from 
the saddle point along the reaction path is called the reaction coordinate, usually 
denoted s. The isoinertial MEP is sometimes just called the MEP, or it may just be 
called the RP; other workers prefer to append the word intrinsic, e.g., intrinsic 
MEP, intrinsic reaction path, intrinsic reaction coordinate, etc.

     In charmmrate, the reaction path refers to a multidimensional path for the 
primary-zone (dynamic) atoms in the presence of the secondary-zone (frozen) atoms

     charmmrate may be used to calculate the isoinertial minimum energy path (MEP) 
as described in B. C. Garrett, M. J. Redmon, R. Steckler, D. G.  Truhlar, K. K. 
Baldridge, D. Bartol, M. W. Schmidt, M.  S. Gordon, J. Phys. Chem. 92, 1476-1488 

     1.A.3. Free energy of activation profile and variational transition state theory

     Vibrational partition functions and generalized free energies of activation 
are computed along the reaction path by using the quantum mechanical harmonic
oscillator approximation in 3N1 - 1 degrees of freedom, where N1 is the number of 
atoms in the primary zone, and the reaction coordinate is projected out. This kind
of calculation is described in S. E. Wonchoba, and D.  G. Truhlar, J. Chem. Phys. 
99, 9637-9651 (1993). The generalized free energy of activation as a function of
the reaction coordinate (which is the signed distance along the MEP) is called the 
free energy of activation profile, and it may be used to calculate reaction rate
constants by variational transition state theory (VTST) as described in D. G. 
Truhlar and B. C. Garrett, Accounts Chem. Res. 13, 440-448 (1980). VTST for a
canonical ensemble (i.e., a system at a fixed temperature) is also called canonical 
variation theory (CVT).

     1.A.4. Transmission coefficient

     In charmmrate the transmission coefficient accounts for tunneling 
(transmission through the barrier at energies below the barrier top) and non-
classical reflection (reflection caused by diffraction from the barrier top even 
when the energy is above the barrier); often we just refer to the combination of
these effects as tunneling (the tunneling is more important than the reflection 
because the energies where tunneling occurs have larger Boltzmann factors than the 
energies where non-classical reflection occurs).

     charmmrate can calculate the transmission coefficient in various ways. The 
most complete method is the microcanonical optimized multidimensional tunneling 
(mOMT) approximation as described in Y.-P.  Liu, D.-h. Lu, A. Gonzalez-Lafont, 
D. G. Truhlar, and B. C. Garrett, J. Amer. Chem. Soc. 115, 7806-7817 (1993). 
In this calculation, tunneling and non- classical reflection along the reaction 
path are included by calculating both the large-curvature tunneling (LCT) 
approximation and the small-curvature tunneling (SCT) approximation and, at each 
tunneling energy, accepting whichever tunneling approximation yields the larger 
tunneling probability. This is a poor man's version of a more complete search for 
the semiclassical tunneling paths that minimize the imaginary action integrals, 
and it has been extensively validated as summarized by T. C. Allison and D. G.
Truhlar, in Modern Methods for Multidimensional Dynamics Computations in Chemistry, 
edited by D. L.  Thompson (World Scientific, Singapore, 1998), pp.  618-712.

     One may also limit the calculation to just the LCT or SCT approximation or 
to the zero-curvature tunneling approximation (ZCT) or even the Wigner approximation.
The mOMT, LCT, SCT, and ZCT approximations are multidimensional, whereas the 
Wigner approximation is one-dimensional. The ZCT approximation calculates tunneling 
along the isoinertial MEP, whereas the mOMT, LCT, and SCT approximations include 
various amounts of corner cutting, i.e., tunneling on the concave side of the 
isoinertial MEP, with the amount and nature of the corner cutting depending on 
the curvature of the reaction path. The computational cost decreases in the
following order: mOMT, LCT, SCT, ZCT, Wigner.  When tunneling is included, the 
final rate constant is written as

               k(T) = k(T) kCVT(T)

where kCVT(T) is the CVT rate constant, and k(T) is the transmission coefficient 
that accounts for tunneling and non-classical reflection.

     1.A.5. Calculation of primary and secondary kinetic isotope effects (KIEs)

     An application to the calculation of KIEs for the proton transfer catalyzed 
by enolase is described in C.  Alhambra, J. Gao, J. Corchado, J. Villa, and 
D. G.  Truhlar, J. Amer. Chem. Soc. 121, 2253-2258 (1999).  Background for the 
calculation of KIEs by VTST with multidimensional tunneling approximations is 
given in D. G. Truhlar, D.-h. Lu, S. C. Tucker, X. G. Zhao, A.  Gonzalez-Lafont, 
T. N. Truong, D. Maurice, Y-.P. Liu, and G. C. Lynch, in Isotope Effects in 
Chemical Reactions and Photodissociation Processes, edited by J.  A. Kaye 
(American Chemical Society Symposium Series 502, Washington, DC, 1992), 
pp. 16-36.

1.B. charmm options that are of particular interest for use with charmmrate

     charmmrate is of particular interest for calculations of rate constants 
for enzymatic reactions. Although the program would allow the use of pure 
molecular mechanics (the CHARMM22 force field) for such calculations, combined
quantum mechanical and molecular mechanical (QM/MM) potentials are much more 
realistic than pure molecular mechanics for chemical reactions. Using charmm, 
QM/MM calculations can now be performed at the ab initio level using gamess 
(B. Brooks and M. Hodoscek, unpublished results), at the density functional 
level using cadpac (P.  D. Lyne, M. Hodoscek, and M. Karplus, J. Phys. Chem. A 
103, 3462-3471 (1999)), and at semiempirical levels with mopac (M. J. Field, 
P. A. Bash, and M. Karplus, J. Comput. Chem.  11, 700-733 (1990)). Typically, 
the "link-atom" approach is used to saturate the valence of the QM fragment, 
which requires that certain atomic charges in the MM fragment that are close 
to the QM region be deleted to avoid convergence problems. In addition, extra 
degrees of freedom are added to the system. This sometimes leads to 
unrealistically large atomic charges on the link atoms and the carbon atoms that
they are attached to. One possibility to avoid these problems is to use the 
generalized hybrid orbital (GHO) method described in J. Gao, P. Amara, C. 
Alhambra, and M.  Field, J. Phys. Chem. A 102, 4714-4721 (1998). The GHO
method is currently available for semiempirical calculations, and it is being 
extended to ab initio and DFT methods. It will be made available in charmm-
version 28.  Another way to correct the link atom artifacts in the original 
formulation is proposed in C. Alhambra, L.Wu, Z.-Y.  Zhang, and J.Gao, J. 
Amer. Chem. Soc. 120, 3858-3866 (1998).


2.A. Molecular dynamics and free energy calculations

     Molecular dynamics simulations of an enzyme-solvent system can be carried 
out either using periodic boundary conditions or using stochastic boundary 
conditions; see C.  L. Brooks, A. Brunger, and M. Karplus, Biopolymers 24,
843-865 (1985). Free energy perturbation and umbrella sampling techniques can 
be used to determine the potential of mean force or generalized free energy 
of activation profile for the enzymatic reaction.

2.B. Semiclassical dynamics

     In the secondary-zone potential (SZP) approximation, dynamics calculations 
for an enzymatic system reaction are carried out in two stages: the first stage 
is classical mechanical (CM), and the second stage is semiclassical (SC).
In the first stage, molecular dynamics and umbrella-sampling free-energy 
simulations using the combined QM/MM potential are first carried out, using 
charmm, to determine the potential of mean force (PMF) for the chemical reaction 
in the enzyme active site. The purposes of this step are two fold. On one hand, 
comparing with the experimental free energy of activation to the computed PMF 
for the enzymatic reaction provides a critical test of the accuracy of the
potential energy function used to describe the system. On the other hand, the 
CM simulation allows one to generate a set of protein-solvent configurations 
that are to be analyzed and selected for the second stage, i.e., for SC
dynamics calculations.

     The SC step is carried out using charmmrate, the interface module for 
charmm and polyrate. The key feature of the SC calculation is that the system 
is partitioned into an N1-atom primary zone, and an N2-atom secondary zone, where
N1 + N2 = N, the total number of atoms in the system. During the SC step, the 
secondary-zone atoms are frozen at a structure selected from the CM step 
(see 2.C). The reaction path calculations are carried out for the primary-zone
atoms, in the presence of the force field of the secondary-zone atoms, from 
which a canonical variational theory (CVT) rate constant (with or without 
tunneling) is determined.

2.C. Criteria for selecting configurations in semiclassical dynamics calculations

     The selection of the configuration or configurations used in the SC step 
is very important in a charmmrate calculation of rate constants for enzymatic 
reactions. Two criteria are essential for the secondary zone to provide a
qualitatively reasonable representation of the interaction potential with the 
enzyme along the reaction path. First, the bath structure that is frozen in the 
SC step should yield a barrier height in accord with some other level of
theory that is being modeled or an activation energy in agreement with experiment. 
Second, the overall heat of reaction or free energy of reaction should also be
realistic. When both criteria are met, the enzyme-solvent configuration is a 
reasonable choice for an SC calculation.

     The selection criteria are being improved, and more systematic and 
reliable procedures are under development. In particular, the four-stage 
equilibrium secondary zone (ESZ) method to be described in an upcoming 
publication (C.  Alhambra, J. Corchado, M. L. S nchez, J. Gao, and D. G.
Truhlar, J. Am. Chem. Soc., 122, 0000 (2000)) will provide a more systematic 
procedure than was used in the prototype original application (enolase ref. 
given above).

     The user should see the test run for an example of how to use a typical 
solvent configuration.


3.A. Overall design

     The charmmrate interface for charmm and polyrate takes advantage of the 
modular nature of both programs, and, consequently, minimal modifications of 
charmm and polyrate were required. The charmm program is the main driver of the
integrated program, which makes a FORTRAN call to the interface subprogram, 
charmmrate, to initiate VTST calculations by polyrate. The energy and energy 
gradients for the primary-zone atoms required by polyrate are determined by 
charmm through the interface subprogram and are supplied to polyrate through 
a set of subroutines called the polyrate hooks. Efforts are being made to make 
all large arrays adjustable by charmm.

3.B. Modifications and additions to charmm

     Only two modifications are made in the charmm program: (1) addition of a 
one-line keyword processing command in the charmm_main.src module to initiate 
the subroutine call to charmmrate; (2) addition of the charmmrate module.

3.C. Modifications and additions to POLYRATE

     Specific modifications of the original polyrate program have been made 
primarily for efficient transfer of information between charmm and polyrate and 
to eliminate conflicts and other problems during compilation. These 
modifications are described in the crate manual.


4.A. Program distribution

  charmmrate-version 1.0 is distributed as a module in charmm. charmm is a 
copyrighted program distributed by Professor Martin Karplus's research group 
at Harvard University and by Molecular Simulations, Inc. In addition to
charmm, which includes the charmmrate module, users also need to obtain the 
polyrate program, which is a copyrighted program distributed by the University 
of Minnesota ( and the crate utility, also available 
from Minnesota. The crate utility will automatically make the changes to the 
source code of polyrate to allow the interface between the two programs.
When the charmm program (which, beginning with version 27, will automatically 
include the charmmrate module), the polyrate program and the crate utility 
have been obtained, integration of the codes into a single executable file is
straightforward as described below.

4.B. Installation

     The user should carry out the following steps:

     1.   Obtain the polyrate program (see and untar it.

     2.   Set an environmental variable, called pr, to the

       absolute path name of the directory where the polyrate

       program is stored. Example:

        C shell

        % setenv pr /my_home/polyrate

        Bourne shell

        $ pr = /my_home/polyrate

        $ export pr

     3.   Obtain the crate utility (see
       and untar it. Change the dimensions specified in the file located in the newly created directory,
       crate8.1.1, in order to make them large enough for the
       system(s) to be studied, but small enough to run in the
       memory available on the computer chosen to carry out the
       work. Or use the file distributed as part of
       crate. See the polyrate manual for further discussion if the
       dimensions in polyrate.

     4.   Set an environmental variable, crate, to the absolute

       path name of the directory where the crate module is stored.


       C shell

          % setenv crate /my_home/crate

       Bourne shell

          $ crate = /my_home/crate

          $ export crate

     5.   Obtain the charmm program, choose the charmmrate option
       for activation, and follow the installation instructions.



     charmmrate is run from the charmm main input stream.  The syntax to 
execute polyrate from charmm's input stream for a reaction with only one 
reactant (e.g., an enzyme- substrate precursor complex) and only one product 
(e.g., an enzyme-substrate successor complex) is:

POLYrate SELEction { atom-spec } end RUNIt int PUNIt int TSUNit int [OPUNit int]

We note the use of the charmm convention by which one needs to enter only the 
first four letters of POLYrate and other words with the first four letters 
capitalized. Furthermore the parts in brackets are optional. The meanings of the
various keywords are:

SELEction { atom-spec } specifies the primary-zone atoms in
               atom-spec = { residue-number atom-name }
                          { segid resid atom-name }
                          { BYNUm atom-number }
RUNit int:     Unit specification for input of initial coordinates of the 
               REACTANT species. The current limitation is that only charmm format
               is allowed for the coordinate file.
PUNit int:     Unit specification for input of initial coordinates of the PRODUCT 
               species. The current limitation is that only charmm format
               is allowed for the coordinate file.
TSUNit int:    Unit specification for input of initial coordinates of the 
               TRANSITION STATE. The current limitation is that only charmm format
               is allowed for the coordinate file.
OPUNit int:    Unit to write out coordinates of the optimized structures of any 
               of the Reactant, Product, and TS, depending upon which of these is 
               requested (elsewhere) to be written.  The current limitation is that 
               only charmm format is used. The coordinate files assigned to these 
               units must be in the CARD format (see charmm documentation for 
               details). This section is optional. After this command, the
               standard polyrate input should follow.
_polyrate_input_    This section contains a standard polyrate fu5 input file. 
               It must follow immediately after the polyrate command in the
               charmm input stream. For details of polyrate input, see the 
               polyrate documentation. The initial coordinates have already been 
               setup through the POLYrate command; therefore the GEOM record 
               in the POLYRATE fu5 input file may be omitted. If, however, the 
               GEOM record is present, the Cartesian coordinates given in this 
               record will replace the data set up through the POLYrate command. 
               This is not recommended.
*finish        The last record to be read by polyrate from the charmm main input 
               stream. This will terminate I/O operations from unit 5 by
               polyrate, and polyrate calculations will proceed.

     This section describes two test runs. Each test job includes a full input 
file, initial coordinates and parameter files, and at least part of an output file
containing some critical output that can be checked against the user's output so 
that he or she will be confident that the code has performed correctly on his or 
her machine.
6.1 Test Job 1 - Direct dynamics of chorismate to prephenate in the gas phase

     This test job reads in three initial guess coordinates for the reactant 
state, product state and transition state, optimizes their geometries, and 
performs a CVT calculation to yield the predicted rate constants at various
temperatures. This test job takes roughly 7 hours on a SGI/R10000 computer.  
Run Test Job 2 if you are not a patient user.

     6.1A.  Input files

     The cr01.inp file contains the CHARMM input stream for a direct dynamics 
calculation of the chorismate to prephenate rearrangement reaction.  Similar 
calculations can be carried out for the substrate in the enzyme active site,
provided that appropriate boundary conditions are set up in the CHARMM input.

     The and charmm22.par files are the CHARMM topology and 
parameter files.  They are required, of course, for all CHARMM calculations.
     Three coordinate files are provided for this test job, corresponding to the 
initial guess coordinates for the reactant (gs.crd), product (prod.crd) and 
transition state (ts.crd) for the dynamics calculation with POLYRATE.
     6.1B.  Description of the CHARMM input stream
     The majority of the CHARMM commands are straightforward.  The three 
initial guess coordinate files must be opened as formatted files before  
the POLYrate command is initiated.  Certain FORTRAN unit numbers are
reserved by POLYRATE.  Therefore, these numbers should not be used in the 
CHARMM input file.  Please consult the POLYRATE documentation for a full 
list and description of these files.
     Five (5) FORTRAN files will be used by POLYRATE to write out the 
computational results.  They are unit number 14, 25, 26, 27, and 61, which 
should be opened before CHARMMRATE calculations.  

     6.1C summarizes the contents of these files.
     All input instructions immediately following the POLYrate command are 
those of POLYRATE.  A full description of these commands can be found in 
the POLYRATE documentation.
     6.1D.  Description of CHARMMRATE output
     cr0114.out - computed reaction rates at various temperatures using the 
TST and CVT methods.
     cr0125.out - potential energy along the minimum energy path (MEP) s, 
and computed transmission coefficient if requested.
     cr0126.out - computed vibrational frequencies that are requested for 
printing out along s.
     cr0127.out - coordinates along s.
     cr0161.out - optimized geometries, energies, vibrational frequencies, 
and the Hessian for the reactant, product and transition state.
6.2 Test Job 2 - Geometry Optimization of Chorismate in a Water Bath
     This test job performs geometry optimization of chorismate in the 
presence of a frozen water bath, arbitrarily taken from the trajectory of 
a molecular dynamics simulation of chorismate in water.  This test job
illustrates that similar calculations can be carried out for substrate-
enzyme systems.
     The cr02.inp file is the CHARMM input stream command file.  In addition 
to the CHARMM topology and parameter files, the cr02.crd file is required, 
which contains the instantaneous (initial) coordinates of chorismate in water
from a molecular dynamics simulation.
     The file optcr02.crd contains the optimized coordinates of chorismate 
in water.

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