MORASS

The MORASS program uses a full hybrid matrix eigenvalue/eigenvector solution to the Bloch equations to derive cross-relaxation rates and interproton distances. MORASS analyzed 2D NMR NOESY data from oligonucleotides and proteins to evaluate cross-relaxation rates from which interproton distances are obtained. These are output in a format suitable for use as distance constraints in molecular dynamics calculations. MORASS2.5 is the most current version available.

Read the general MORASS README file.

Download the MORASS2.5 Manual in pdf format.

Download the entire MORASS2.51 software package in .gz format.

The MORASS program was written by R. P. Meadows, C.B. Post, Bruce Luxon and David G. Gorenstein.

MPACK

The MPACK program is a homology modeling package that integrates several packages from the Braun group: PCPmer to identify conserved regions, EXDIS to extract angle and distance constraints, DIAMOD to generate protein models from geometric constraints, and FANTOM to optimize the protein geometry with the ECEPP force field.

The MPACK program was written by Venkatrajan Mathura and Werner Braun, with contributions by Surendra S Negi.

David Volk's NMR Scripts


carnal.aveminclusters.in Calculates the average structure from sander restraint 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 useful 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.

redundant_picker.pl Pulls out the redundant internal coordinates from a Gaussian98 output file.

vnmr2morassfinal.pl Convert assigned VNMR 2D peak file into a MORASS program input file.