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
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.
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.
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
CHARMM Documentation / Rick_Venable@nih.gov