CHARMM c28a3 support.doc

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                    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

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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

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

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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.

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NIH/DCRT/Laboratory for Structural Biology
FDA/CBER/OVRR Biophysics Laboratory
Modified, updated and generalized by C.L. Brooks, III
The Scripps Research Institute