Under the Gentle Guidance and Support of Ad Bax ...

DYNAMO NMR Molecular Structure Engine Version 3.1

Frank Delaglio and John Kuszewski

Previous Documentation:

DYNAMO Original (Version 1.0) User Guide
Specifying a Sequence with the GMC Editor
Creating New Residue Types
DYNAMO Reference Guide

Last updated Feb 17, 2004 by FD

How to get DYNAMO?

DYNAMO is part of the NMRPipe System. See the NMRPipe Home Page for information on getting the software.

What is DYNAMO?

DYNAMO is a system of software tools and scripts for calculating and evaluating molecular structures. DYNAMO includes a cartesian-coordinate simulated annealing engine, and facilities for NMR homology search to assemble collections of molecular fragments which are consistent with NMR observables. The tools of DYNAMO are accessed via scripts written in the TCL/TK scripting language.

This current version of DYNAMO can use the following kinds of experimental restraints during a simulated annealing protocol:

NOE derived interproton distance restraints.
NMR-derived torsion angle restraints.
J-coupling constants.
Radius of gyration.
Pseudo-Contact Shifts.
Dipolar couplings.

Some Examples of DYNAMO Applications

List Backbone or Sidechain Angles in a Given Structure
Change Backbone or Sidechain Angles in a Given Structure

NMR Structure Prediction Using Simulated Annealing

Compute RMS Between Two Structures
Compute Average Structure

Simulate Chemical Shifts Based on Secondary Structure
Simulate J-couplings Based on Karplus Curves
Simulate Dipolar Couplings
Measure Alignment Tensor Parameters via Known Secondary Structure Elements
Homology Search Based on Chemical Shifts, J-Couplings, Torsions
Homology Search Base on Dipolar Couplings

Visualize NMR Parameters:
- Observed vs Simulated Shifts and Couplings.
- Alignment Tensor Axis with Respect to PDB.
- Ramachandran maps of sequence, with Phi/Psi trajectories of Given Structures or Fragments.
- Ramachandran maps of sequence, hilited with contours of regions most consistent with NMR observables.

Steps in a DYNAMO Structure Calculation

DYNAMO organizes a structure calculation project in a "GMC" (Generalized Molecular Coordinate) directory. This directory starts with a collection of tables which describe the covalent geometry of the molecular system. These tables are created by DYNAMO based on sequence information. After the GMC directory has been created, additional tables can be added containing the experimental restraints. The typical steps are as follows:

Specify the residue sequences of the segments in the molecule or complex. This can be done in a few ways:
- gmcEdit, a graphical interface where the sequence information is entered interactively. This option supports canonical protein, DNA, and RNA residues, as single molecules or complexes. It also has options for modification of the molecular system (delete or add atoms, bonds, etc).
- pdb2gmc.tcl, a script which extracts sequence information from and existing PDB file. Currently, this procedure is for proteins and nucleic acids only.
- seq2gmc.tcl, a script which extracts sequence information from an existing NMRPipe-format file (for example a TALOS chemical shift table) which contains DATA SEQUENCE lines. Currently, this procedure is for single-chain proteins only.
- Text Editor: the information used by DYNAMO to define the covalent geometry is stored in a text file "gmc_record.txt". This file contains the sequences of one of more segments of the molecular system. It can also contain optional statements to delete or insert atoms, bonds, etc, to build cylclic structures and other modifications:
```
   version JUNE2001

   gmc_filename chr.gmc
   
   segment A 1 protein nontermamine noctermacid no5primephos no3primephos
    met ser ile gly orn lys orn (cis) ser
   end

   delete_atom A 6 LYS HZ1
   delete_atom A 6 LYS HZ2
   delete_atom A 6 LYS HZ3

   atom A 6 LYS HZ1 1.0 0.0498 1.4254 0.43 

   bond A 6 LYS HZ1 A 6 LYS NZ 0.980 1000.0
   bond A 6 LYS NZ  A 8 SER C  1.400  100.0
   
   angle A 8 SER CA A 8 SER C  A 6 LYS NZ  116.20 500.0
   angle A 8 SER O  A 8 SER C  A 6 LYS NZ  123.00 500.0
   angle A 8 SER C  A 6 LYS NZ A 6 LYS CE  121.70 500.0
   angle A 8 SER C  A 6 LYS NZ A 6 LYS HZ1 120.00 500.0

   torsion A 8 SER O   A 8 SER C  A 6 LYS NZ A 6 LYS CE   0.0 500.0
   torsion A 6 LYS CE  A 6 LYS NZ A 8 SER C  A 8 SER CA 180.0 500.0
   torsion A 6 LYS HZ1 A 6 LYS NZ A 8 SER C  A 8 SER CA   0.0 500.0

   mass 100
```

Based on the sequence information, DYNAMO automatically creates the definitions of covalent geometry. In DYNAMO, these are stored as a series of NMRPipe-format tables with specific names in a General Molecular Coordinate (GMC) directory:

File Name	Contents
atoms.tab	Specification of All Atoms
bonds.tab	Specification of Bonds
angles.tab	Covalent Geometry Angles
impropers.tab	Covalent Geometry Torsions
vdwex.tab	Van der Waals Exclusions

During creation of the GMC, DYNAMO also creates an initial structure in the GMC directory, called "random.pdb" with random (!) atomic coordinates.

After GMC creation, one or more user-supplied experimental restraint tables, also with specific names, are added to the GMC directory. As a convenience, some example TCL scripts are provided to help prepare these tables from existing restraints in XPLOR format (Note: these scripts are only examples, they may not work with every variation in restraint format, and they may require that input atom names match the DYNAMO ones exacty).

The DYNAMO user-supplied restraint tables can include:

File Name	Contents
noes.tab	NOE Distances
torsions.tab	Torsion Restraints
radgyr.tab	Radius of Gyration Restraints
jcoup.tab	3J Couplings
ac.tab	Atom Coordinate Restraints
ds.tab	Distance Symmetries
pcsObs.tab	Pseudo-Contact Shifts
dObsA.tab	Dipolar Couplings (A, B, C etc.)

A DYNAMO simulated annealing script is used to read the GMC directory contents and execute one or more simulated annealing runs.

Subsequent DYNAMO scripts are executed to calculate and refine an average structure, and evaluate results.

The DYNAMO Annealing Stages are:

      Keyword:   Meaning:

      init       Initialization
      high       High-Temperature
      coolStart  Cooling
      coolEnd    Done
      cool       Sets parameters for both "coolStart" and "coolEnd"
      all        Sets parameters for all stages to one given value.

There are three parameter classes:

      -sa   Annealing Schedule Parameters
      -fc   Force Constant Scaling
      -size Size or Radius Scaling

Parameters are set via triplets of "parameterName stageName value", for example:

dynSimulateAnnealing -graph -print 10 -nocenter \
    -sa    stepCount   init       100 \
           stepCount   high       100 \
           stepCount   cool      3000 \
           temperature init       500 \
           temperature high       500 \
           temperature coolStart  500 \
           temperature coolEnd      0 \
    -fc    ac          init       8.0 \
           ac          high       8.0 \

Parameter Names and Default Values:

      -----------------  ---- ------- -----  ------ --------- -------  
      parameter name     type scaling init   high   coolStart coolEnd
      -----------------  ---- ------- -----  ------ --------- -------  

      stepCount          sa   none       500   2000   12000        0
      temperature        sa   other   4000.0 4000.0  4000.0        0
      temperatureStep    sa   none       0.0    0.0    25.0     25.0
      temperatureControl sa   none       1.0   10.0    10.0     10.0
      timeStep           sa   none       3.0    5.0     5.0      5.0

      bond               fc   power      1.0    1.0     1.0      1.0
      dist               fc   power      1.0    1.0     1.0      1.0
      angle              fc   power      0.5    0.5     0.5      1.0
      improper           fc   power      0.1    0.1     0.5      1.0
      torsion            fc   power     10.0   10.0    10.0    200.0
      j                  fc   power      0.0    0.0     0.1      1.0
      dt                 fc   power      0.0    0.0     0.0      0.0
      ds                 fc   power      0.0    0.0     0.0      0.0
      noe                fc   power      2.0    2.0     2.0     30.0
      ac                 fc   power      0.0    0.1     0.1      3.0
      dc                 fc   power      0.0    0.0     0.005    0.5
      dcA                fc   power      0.0    0.0     0.005    0.5
      dcB                fc   power      0.0    0.0     0.005    0.5
      dcC                fc   power      0.0    0.0     0.005    0.5
      pcs                fc   power      0.0    0.0     1.0      1.0
      cs                 fc   power      0.0    0.0     1.0      1.0
      radGyr             fc   power      0.0  100.0    10.0    100.0
      vdw                fc   power      0.0    0.0     0.004    4.0

      radGyr             size linear     1.0    1.3     1.3     0.90
      vdw                size power      0.0    0.0     0.9     0.81

DYNAMO Arguments for Reading GMC Directory:

dynReadGMC
   -gmc gmcDirName    Name of DYNAMO Input GMC Directory.
   -pdb pdbFileName   Name of Initial PDB Structure, Created by DYNAMO.

   -user              Read User-Supplied Restraint Files (Default).
   -nouser            Read Only DYNAMO Covalent Geometry Files.

   -vdw               Read and Use DYNAMO Van der Waals Table (Default).
   -novdw             No Van der Waals Terms Used.

DYNAMO Arguments for Executing a Simulated Annealing Schedule:

dynSimulateAnnealing
   -sa   [saArgTriplets]    Simulated Annealing Protocol Arguments.
   -fc   [fcArgTriplets]    Force Constant Scaling Arguments.
   -size [sizeArgTriplets]  Size Scaling Arguments.

   -center                  Remove Center of Mass Motion at each step (Default).
   -nocenter                Do not remove motion.

   -graph                   Display Energy Curve Graphs.
   -nograph                 No Display of Energy Curves.

   -print  printCount       How often to print status.
   -rasmol drawCount        How often to draw current structure via rasmol.

   -tensorProc tclProcName  TCL Procedure for DC or PCS tensor calculation;
                            default proc is in dynamo/tcl/dynEvalTensor.tcl

The Ubiquitin NOE/DC Simulated Annealing Structure Calculation Demo

The files for this demo can be found in the "demo/ubiq" directory of the dynamo installation. The directory "orig" contains the experimental restraint tables for use with DYNAMO, along with some examples of table format conversion. The experimental tables used in this demo are:

noes.tab	NOE Distances
jcoup.tab	J Coupling Values
torsions.tab	TALOS phi/psi restraints
dObsA.tab	Dipolar Couplings in Alignment Medium A
dObsB.tab	Dipolar Couplings in Alignment Medium B

The script "all.com" goes through a complete example of NOE structure calculation and subsequent refinement including dipolar couplings.

The files for this demo can be found in the "dynamo/demos/ubiq" directory
editGMC Creates DYNAMO Molecular Decscription by interactive specification of the sequence

init.com An alternative to interactively specifying the sequence; this script uses tools to extract sequence from existing file (in this case, a TALOS chemical shift file), and to create an initial extended structure. Output: ubiq.gmc GMC Directory and contents. ext.pdb Initial Extended structure.

ac.com Like "init.com", but creates a DYNAMO structure which conforms to an input PDB of the X-ray structure. Output: ubiq.gmc GMC Directory and contents. ac.pdb Conforms to X-ray structure. ext.pdb Initial Extended structure. ac.tab Restraints for conforming to PDB input. init.pdb Initial structure based on PDB input.

sa.tcl Computes 54 structures via high-temperature annealing, with DC terms off. Output: ubiq.com/dyn_*.pdb

avg.com Computes average structure of "sa.tcl" annealing results. Output: avg.pdb

pdbSelect.tcl Used by "avg.com" to select the lowest-energy structures produced by "sa.tcl".

refineAvg.tcl Refines average structure to restore proper geometry. Output: refinedAvg.pdb

refineDC.tcl Low temperature annealing to refine average structure by including dipolar couplings. Output: dc.pdb

ov.tcl Computes Backbone RMSD between calculated structure and reference structure, and also overlays both molecules in a single PDB output. Output: overlay.pdb

saDC.tcl Computes a series of structures via high-temperature annealing, with DC terms on. Output: ubiq.com/dynDC_*.pdb

simDC.tcl Simulate Dipolar Couplings for Given Structure

simCS.tcl Simulate Chemical Shifts for Given Structure

Some General Scripts for DYNAMO

noeConvert.tcl	Convert XPLOR NOE Table to DYNAMO Format
jConvert.tcl	Convert XPLOR NOE Table to DYNAMO Format
dcConvert.tcl	Convert XPLOR NOE Table to DYNAMO Format
torsionConvert.tcl	Convert XPLOR NOE Table to DYNAMO Format
talos2dyn.tcl	Convert TALOS Phi/Psi Table to DYNAMO Format
name2torsion.tcl	Convert Named Torsions to DYNAMO Format
pdb2dyn.tcl	Extract DYNAMO Residue Creation Info from PDB
pdb2ac.tcl	Extract DYNAMO Atom Coord Restraints from PDB
pdb2torsion.tcl	Extract DYNAMO Torsions Restraints from PDB
pdb2gmc.tcl	Extract DYNAMO Sequence Information from PDB
seq2gmc.tcl	Extract DYNAMO Sequence Information from Table
dynAvg.tcl	Compute and Average PDB Structure
dynCenter.tcl	Center a PDB Structure at the Origin
dynBasicExt.tcl	Create an Extended Structure
dynEval.tcl	Evaluate PDB According to Restraints
ov.tcl	Overlay PDB files, Report Coord and Torsion RMS
addPDBNoise.tcl	Add Random Structural Noise to PDB
addTabNoise.tcl	Add Random Noise to a Table
dcNoise.tcl	Dipolar Coupling Noise Analysis
pdbSelect.tcl	Select DYNAMO PDB Based on Eneregy, Etc
resetPhiPsi.tcl	Reset Protein Backbone Angles
ss.tcl	Analyze Secondary Structure and H-Bond Info
mapPDB.tcl	Map DYNAMO Table Values onto PDB
mfr.tcl	Perform Molecular Fragment Search
mfr2init.tcl	Create Initial Structure from MFR Angles
mfr2dyn.tcl	Create Torsion Restraints from MFR Angles
dynAngles.tcl	Display Backbone and Sidechain Angles
showCS.tcl	Show Chemical Shift Table
showDC.tcl	Show Dipolar Coupling Table
rotDC.tcl	Add Dipolar Coupling Tensor Info to PDB
scrollRamaCS.tcl	Display Backbone Angle Trajectories
showTab.tcl	Show X/Y Table Graphs

editGMC	Creates DYNAMO Molecular Decscription by interactive specification of the sequence
init.com	An alternative to interactively specifying the sequence; this script uses tools to extract sequence from existing file (in this case, a TALOS chemical shift file), and to create an initial extended structure. Output: ubiq.gmc GMC Directory and contents. ext.pdb Initial Extended structure.
ac.com	Like "init.com", but creates a DYNAMO structure which conforms to an input PDB of the X-ray structure. Output: ubiq.gmc GMC Directory and contents. ac.pdb Conforms to X-ray structure. ext.pdb Initial Extended structure. ac.tab Restraints for conforming to PDB input. init.pdb Initial structure based on PDB input.
sa.tcl	Computes 54 structures via high-temperature annealing, with DC terms off. Output: *ubiq.com/dyn_.pdb**
avg.com	Computes average structure of "sa.tcl" annealing results. Output: avg.pdb
pdbSelect.tcl	Used by "avg.com" to select the lowest-energy structures produced by "sa.tcl".
refineAvg.tcl	Refines average structure to restore proper geometry. Output: refinedAvg.pdb
refineDC.tcl	Low temperature annealing to refine average structure by including dipolar couplings. Output: dc.pdb
ov.tcl	Computes Backbone RMSD between calculated structure and reference structure, and also overlays both molecules in a single PDB output. Output: overlay.pdb
saDC.tcl	Computes a series of structures via high-temperature annealing, with DC terms on. Output: *ubiq.com/dynDC_.pdb**
simDC.tcl	Simulate Dipolar Couplings for Given Structure
simCS.tcl	Simulate Chemical Shifts for Given Structure

DYNAMO NMR Molecular Structure Engine Version 3.1 Frank Delaglio and John Kuszewski