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.