Gorenstein's scripts for Amber, etc.

[nmrlearner]

The following Perl scripts for Amber-driven NMR structure determination are available from the website of Dr. Gorenstein:

• carnal.aveminclusters.in Calculates the average structure from sander restrt files and
  calculates the RMSD for each vs. the average structure.
  
• addcio.pl Add Na+ counterions to DNA
  
• amber_2_charm.pl
  
• amber_dna_pdb_to_star.pl
  
• amber_pdb_to_star.pl
  
• amber_protein_pdb_to_star.pl
  
• average_starpdb.pl Calculates an average PDB from an RCSB ensemble.
  
• talos_to_amber_restr.pl Creates AMBER dihedral restraints from a TALOS program prediction table. Only the restraints designated as "Good" are converted.
• distance_matrix.pl Create a text file showing all proton-proton distances less than 5 Angstroms from a model PDB structure.
  
• HA_HA_distance.pl Finds all HA-HA distances less than 3.5 Angstrom (cutoff can be changed).
  
• comp_listout.pl Compare Sander listout files for recurring bad noes.
  
• g98allpdbs.pl Converts a Gaussian98.out file (with XYZ coord) into multiple PDB files.
  This is usefule for making a movie of a calculation.
  
• g98xyztoPDB.pl Creates a PDB file from the LAST coordinates of a Gaussian 98 output file.
  
• gvxyzcom_2_pdb.pl Converts a GaussView.com file (with XYZ coords) to a PDB file.
  
• listout_noesy_sorter.pl Counts and sorts sander listout file into intra, seq., medium and long range NOES.
  
• make_protein_dihedrals.pl Makes AMBER format angle restraints for Helices and Beta Sheets.
  
• make_ribose_dihedrals.pl Makes B-DNA AMBER dihedral restraints.
  
• vnmr2morassfinal.pl Convert assigned VNMR 2D peak file into a MORASS program input file.