Welcome: an Introduction to this Site
NMRPipe: a Comprehensive Software System for Biomolecular NMR
Special Applications: NMR Drug Screening, Automation, and so on
Dipolar Couplings, Chemical Shifts, and Protein Structure
Miscellaneous

Frank's CV, Recent Slides, and Thesis

 

  

 

  Frank Delaglio, Ph.D.

   Software Science Consultant
  13840 Grey Colt Drive
  North Potomac MD 20878 USA

  Tel: 301 806-0867
  Fax: 301 309-8717
  E-mail: delaglio@nmrscience.com



NMRWish Built-In TCL Functions
dynEnergy: Evaluate the energy at a given step of a simulated annealing molecular structure calculation.

dynEnergy: Calculate Energy & Forces.
Restraint sources:
Flag Argument Default Description
 -src pdbSrc Source of Structure.
 -bond bSrc Covalent Bonds.
 -dist dSrc Generic Distances.
 -angle aSrc Covalent Geometry Angles.
 -uangle uaSrc User-Supplied Angle Limits.
 -improper iSrc Planarity/Chirality Torsions.
 -torsion tSrc User-Supplied Torsion Limits.
 -j jSrc J-Couplings.
 -noe nSrc NOE Distances.
 -ds dsSrc Pairwise Symmetry Distances.
 -ac acSrc Atom Coord Constraints.
 -radGyr rgSrc Radius of gyration.
 -vdwex vdwSrc van der Waals exclusions.
 -dt dtSrc DELPHIC torsions.
 -dcList dcSrcList Dipolar Couplings for All Tensors.
 -pcs pcsSrc Pseudo-Contact Shifts.
 -hbond hbSrc Hydrogen Bonds.
 -dc dcSrc Dipolar Couplings.
 -dcA dcASrc Dipolar Couplings for Tensor A.
 -dcB dcBSrc Dipolar Couplings for Tensor B.
 -dcC dcCSrc Dipolar Couplings for Tensor C.
Force constant scaling factors:
 -bondFC bFC 1.0 Bond Force.
 -distFC dFC 1.0 Distance Force.
 -angleFC aFC 1.0 Angle Force.
 -uangleFC aFC 1.0 User Angle Force.
 -improperFC iFC 1.0 Improper Force.
 -torsionFC tFC 1.0 User Torsion Force.
 -jFC jFC 1.0 J-Coupling Force.
 -noeFC nFC 1.0 NOE Force.
 -dsFC dFC 1.0 DS Force.
 -acFC aFC 1.0 AC Force.
 -radGyrFC rFC 1.0 Radius of Gyr Force.
 -radGyrSize rSize 1.0 Radius of Gyr Size Scale.
 -hbondFC hFC 1.0 H-Bond Force.
 -dtFC tFC 1.0 Delphic Torsion Force.
 -dpFC pFC 1.0 Delphic Position Force.
 -dcFC dFC 1.0 Tensor A Dipolar Force.
 -dcAFC dFC 1.0 Tensor A Dipolar Force.
 -dcBFC dFC 1.0 Tensor B Dipolar Force.
 -dcCFC dFC 1.0 Tensor C Dipolar Force.
 -csFC cFC 1.0 Chemical Shift Force.
 -pcsFC pFC 1.0 Pseudo-Contact Shift Force.
 -vdwFC vFC 1.0 Van der Waals Force.
Van der Waals Settings:
 -vdwSize vSize 0.0 VDW Radius Scale.
 -vdwMin vMin 0.0 VDW Min Distance.
 -vdwMaxMove vMove 0.5 Max Move in Angstroms for Recalculation of Neighborhood.
 -vdwNeighborDist vDist 6.0 Size of Neighborhood, in Angtroms.
Notes:
  The forms -dcA -dcB etc are depricated in favor of -dcList

Under Construction

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last updated: Jan 22, 2009 / big frank

Contact site designer mimi at mdelaglio@hotmail.com