support (c39b2)
Support Programs and Data Files
This section describes supplementary programs and data files
included in the CHARMM package.
* Boundary | Deformable boundary potential files
* IMTRAN | Image transformation files
* NUCS | Solvation electr. screening by Non-Uniform Charge Scaling
This section describes supplementary programs and data files
included in the CHARMM package.
* Boundary | Deformable boundary potential files
* IMTRAN | Image transformation files
* NUCS | Solvation electr. screening by Non-Uniform Charge Scaling
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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
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.
» sbound for details on the SBOUND
command.
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
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.
» sbound for details on the SBOUND
command.
Top
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.
» images and *note
Crystl: » chmdoc/crystl , for details.
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.
» images and *note
Crystl: » chmdoc/crystl , for details.
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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
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