CHARMM c42b2 support.doc



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                    Support Programs and Data Files


    This section describes supplementary programs and data files
included in the CHARMM package.


* Menu:

* Boundary::        Deformable boundary potential files
* IMTRAN::          Image transformation files
* NUCS::            Solvation electr. screening by Non-Uniform Charge Scaling



File: Support -=- Node: Boundary
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                  Deformable Boundary Potential Files


    A deformable boundary potential (DBP) file is required to run the
stoichastic boundary molecular dynamics (SBMD) simulatiuon.  Only
spherical DBP's are included in the current release.  In the future
release, cylindrical boundaries and plane shape boundaries will be
incorporated and the DBP generation routine will also be available
through CHARMM.

    ~/charmm/support/bpot (or [...CHARMM.SUPPORT.BPOT] on VMS
machines) contains DBP files for the TIP3P water in a spherical
simulation zone with 8 to 25 angstrom effective radius.  These DBP
files are generated by using Charlie Brooks' MFFGEN1 program and the
CHARMM SBOUND command.  The effective radius is set to the Langevin
and reservior region boundary (the reaction zone radius).  Then, the
boundary radius used in the DBP generating program (e.g., MFFGEN1.EXE
on HUCHE1.HARVARD.EDU) should be larger than the reaction zone radius
by the water oxygen van der Waals radius.  The reaction zone radius
plus 1.7682 angstrom (the TIP3P water oxygen vdW radius) is used to
generate the DBP for a given effective radius sphere.  The nonbonded
cutoff of 7.5 angstrom is used in the DBP generation procesure.  Those
DBP files can be used in simulations with different nonbonded cutoff
distances.

    See *note Sbound: (sbound.doc), for details on the SBOUND
command.


File: Support -=- Node: IMTRAN
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                        Image Transformation Files


    ~/charmm/support/imtran contains the following image
(transformation) files reproduced from the Harvard lecture notes.

  alpha.img     Image file for alpha-I helix
                Parameter 1 is set to the translation / unit cell along z.
                Parameter 2 is set to the rotation / unit cell around z.

  dnahelix.img  Image file to generate infinite DNA-helix
                Helix axis is along z, and the second strand is generated
                from the first through a 180 deg rotation around x.
                Parameter 1 is set to the translation / unit cell along z.
                Parameter 2 is the rotation / unit cell around z
                ("helical twist"), degrees. 

  p21c.img      Image transformation file for P21 crystals
                The 32 nearest neighbors are kept.
                Parameters 6,7,8 and 9 are used to set unit cell parameters.

  tips.img      Image file for cubic transformation
                Parameter 9 is set to the box size.

    See *note Images: (images.doc), and *note 
Crystl: (crystl.doc), for details.





File: Support -=- Node: NUCS
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   Non-Uniform Charge Scaling (NUCS): an implicit solvent screening method.
   ========================================================================

As described in:
  "Non-Uniform Charge Scaling (NUCS):
   a practical approximation of solvent electrostatic screening in proteins."
   S.M. Schwarzl, D. Huang, J.C. Smith and S. Fischer.
   J. Comp. Chem. 26, 1359-1371 (2005).

The NUCS procedure is a practical approach of implicit solvation 
that approximates the solvent screening effect by individually scaling 
the partial charges on the explicit atoms of the macromolecule 
so as to reproduce electrostatic interaction energies obtained 
from an initial Poisson-Boltzmann analysis. 
The solvation "Born" self-energy of the partial charges is neglected.  

The approach is particularly suitable for minimization-based simulations, 
such as normal mode analysis, certain conformational reaction path or 
ligand binding techniques for which bulk solvent cannot be included explicitly,
for combined quantum mechanical/molecular mechanical calculations, 
or when the interface to more elaborate continuum solvent models is lacking.

'Global' scaling :
------------------
The scaling of the partial atomic charges of the protein is done in such a way
that all possible pairwise interactions between groups of the protein 
computed with the standard Coulomb potential optimally reproduce the 
corresponding electrostatic pairwise interaction in solution.  
This is achieved by introducing non-uniform scaling factors, 
which are used to scale the partial atomic charges while conserving 
the local electrostatic multipoles of small groups of atoms. 
The solvated interaction energies that serve as a reference to derive 
the scaling factors are obtained from an initial solution of the 
Poisson-Boltzmann equation. 
The NUCS procedure thus allows solvent screening effects to be included 
while preserving the speed of a Coulombic energy.
The scaling factors need to be evaluated only once and can then be used
for any type of simulation requiring an implicit solvent representation.


Mixing global and targeted scaling :
------------------------------------
In QM/MM calculations of enzymatic reactions, the QM region is often 
surrounded by a flexible MM region, which in turn is surrounded by 
a region in which protein atoms are kept fixed. In such simulations 
it is necessary to adequately represent the electrostatic potential 
at the QM and flexible regions, whereas it is not necessary to correctly 
represent the electrostatic potential at the fixed region. Mixing
the global NUCS procedure with a 'targeted' charge-scaling procedure
allows to satisfy the following points:

1) The interaction energy between the QM region and any given protein group 
calculated with scaled charges remain close to the Poisson-Boltzmann 
interaction energy. This ensures that the electrostatic potential at 
the positions of the QM atoms is adequately represented and thus the 
electrostatic QM/MM interactions are appropriately captured. 

2) The interaction energies between two group within the flexible region 
calculated with scaled charges remain close to the Poisson-Boltzmann 
interaction energies. This ensures that the electrostatic forces 
between any two mobile MM atoms are adequate. 

3) The interaction energy between a group in the flexible region and all 
other groups calculated with scaled charges remain close to the 
Poisson-Boltzmann interaction energy. This ensures that the overall 
electrostatic potential at the position of a mobile MM atom is 
adequately captured.


Files:
------
 ~/charmm/support/nucs_solvation/*.pdf             = Documentation

 ~/charmm/support/nucs_solvation/scripts/global/   = global NUCS
 ~/charmm/support/nucs_solvation/scripts/targeted/ = targeted/mixed scaling


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