Support Programs and Data Files This section describes supplimentary programs and data files included in the CHARMM 22.0.b package. * Menu: * Boundary:: Deformable boundary potential files * IMTRAN:: Image transformation files
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.
NIH/DCRT/Laboratory for Structural Biology
FDA/CBER/OVRR Biophysics Laboratory
Modified, updated and generalized by C.L. Brooks, III
The Scripps Research Institute