Contents
INTRODUCTION
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.
DYNAMO can use the following kinds of experimental restraints during a simulated annealing protocol:
Some Examples of DYNAMO Applications include:
Molecular Dynamics with DYNAMO
The DYNAMO molecular dynamics engine is used to generate structures of proteins and nucleic acids which are consistent with both standard covalent geometry and also any user-supplied NMR-derived structural constraints such as interproton distances. As such, DYNAMO does not perform a realistic physical simulation of molecular dynamics; rather it is used as an optimization tool to generate structures for best agreement with measured data. Structure determination from NMR data is particularly challenging because the number of structural constraints available from NMR spectroscopy is small compared to the number of degrees of freedom in a biological macromolecule.
DYNAMO is able to use a variety of NMR-derived constraints: NOE distances, torsion angles, J couplings (in the form of Karplus expressions), and dipolar couplings. In addition, protein backbone chemical shifts can be translated into backbone torsion angle constraints through the use of the program TALOS.
In addition to experimental constraints, DYNAMO also incorporates structural restraints that are known on the basis of the covalent geometry of the molecule. These are expressed in terms of Van der Waals radius parameters for the atoms, expected bond distances and angles, and torsions which describe any planarity or stereochemistry in the molecular system.
DYNAMO uses molecular dynamics based simulated annealing to find sets of atomic coordinates that are consistent with the experimental and covalent constraints. Molecular dynamics is a computational technique that uses numerical integration to simulate Newton's equations of motion. Simulated annealing is a computational technique for function optimization. In simulated annealing, a system's temperature begins at a high value and is slowly reduced. Thus, early in a simulated annealing procedure, the system has sufficient kinetic energy to jump over large potential energy barriers. But as the system cools, its movement is gradually restricted to lower and lower energy structures. A sufficiently high starting temperature ensures that all the relevant conformational space is sampled, and a sufficiently slow cooling rate ensures that a very low energy structure is finally chosen.
The DYNAMO energy function
Molecular dynamics uses numerical integration to simulate a system's movement by Newton's equations of motion. The forces on each atom are the partial derivatives of the potential energy function. DYNAMO's potential energy function includes terms that describe the current coordinates' agreement with both experimental and a priori constraints:
Etot = Ebond + Eangle + Eimpr + Evdw + Enoe + Ejcoup + Etorsion + Edipo + Epcs Ergyr ...
where
Etot is the total energy.
Ebond describes the structure's agreement with expected covalent bond lengths:
Ebond = kbond Σ (expected_distance - actual_distance)2
Eangle describes the structure's agreement with expected covalent bond angles:
Eangle = kangle Σ (expected_angle - actual_angle)2
Eimpr describes the structure's agreement with expected "improper" torsion angles. Improper torsion angles are constraints on the geometry of groups of four atoms that are used to maintain correct chirality of chiral centers and the planarity of planar groups:
Eimpr = kimpr Σ (expected_impr - actual_impr)2
Evdw describes the structure's steric overlap, using a simple repulsive potential:
Evdw = kvdw Σ ((size_scale * expected_min_distance)2 - actual_distance2)2
Enoe describes the structure's agreement with observed NOE distances. It uses a "square well" potential that is zero if the actual distance is within a given range:
Enoe = knoe Σ delta_dist2
if actual_dist > observed_dist_upperbound:
delta_dist = actual_dist - observed_dist_upperbound
if actual_dist < observed_dist_lowerbound:
delta_dist = actual_dist - observed_dist_lowerbound
otherwise:
delta_dist = 0
Ejcoup describes the structure's agreement with observed J-couplings. Karplus parameters can be specified for each type of J-coupling.
Ejcoup = kjcoup Σ (observed_J - calculated_J)2
calculated_J = A cos2 (phi + phase) + B cos (phi + phase) + C
Etorsion describes the structure's agreement with experimental torsion angle constraints. Like the NOE term, it uses a square well potential:
Etorsion = ktorsion Σ delta_torsion2
if actual_torsion > observed_torsion_upperbound:
delta_torsion = actual_torsion - observed_torsion_upperbound
if actual_torsion < observed_torsion_lowerbound:
delta_torsion = actual_torsion - observed_torsion_lowerbound
otherwise:
delta_torsion = 0
Edipo describes the structure's agreement with experimentally observed dipolar couplings. Data from one or more different alignment tensors can be used simultaneously. The expected dipolar couplings are calculated from the structure as described the section on Options for Dipolar Coupling Data below.
Epca = kpcs Σ (observed_pcs - calculated_pcs)2
Epcs describes the structure's agreement with experimentally observed pseudo-contact shifts between a given atom and a paramagnetic center. Data from one or more paramagnetic centers can be used simultaneously.
Edipo = kdipo Σ (observed_dipo - calculated_dipo)2
Ergyr describes the structure's agreement with its expected overall size. NMR structures are typically expanded relative to crystal structures, because there are so many forces from the vdw term pushing atoms apart, with relatively few forces from the NOE term pulling them back together. The radius of gyration is a measure of a structure's overall size--specifically, it is the RMS distance of a group of atoms to their centroid. It can be predicted reasonably accurately for globular proteins just from the number of residues:
expected_Rgyr = 2.2 Nresidues0.38
Ergyr = krgyr Σ (expected_Rgyr - actual_Rgyr)2
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:
version JAN2012
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
| 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.
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 | J Couplings |
| ac.tab | Atom Coordinate Restraints |
| ds.tab | Distance Symmetries |
| pcsObs.tab | Pseudo-Contact Shifts |
| dObsA.tab | Dipolar Couplings (A, B, C etc.) |
DYNAMO Restraint Table Format
The constraint files within a GMC directory are all variations
on the nmrPipe table format. Generally, each line will specify a restrain
involving one or more atoms. A given atom is specified according
to four parameters: atom name (ATOMNAME) residue ID (RESIDRESNAME) and segment name (SEGNAME). In the case of restraints which involve two or more atoms, the
atoms within a restraint are referred to as atom I, atom J, etc.
For example, in the table of covalent bond length restraints ("bonds.tab")
each entry describes a bond distance between two atoms I and J,
with an expected bond distance (D) and a force constant
for the bond (FC):
VARS SEGNAME_I RESNAME_I RESID_I ATOMNAME_I SEGNAME_J RESNAME_J RESID_J ATOMNAME_J D FC
FORMAT %8s %3s %4d %4s %8s %3s %4d %4s %8.3f %8.3f
UBIQ MET 1 C UBIQ MET 1 O 1.231 1000.000
UBIQ MET 1 CA UBIQ MET 1 C 1.525 1000.000
UBIQ MET 1 CA UBIQ MET 1 CB 1.530 1000.000
UBIQ MET 1 CA UBIQ MET 1 HA 1.080 1000.000
UBIQ MET 1 CB UBIQ MET 1 CG 1.530 1000.000
The first two lines identify the contents of each data column. The two atoms involved are identified by their segment name, residue name, residue number, and atom name. Other information relevant to the constraint (the equilibrium bond length in Ångstroms and the force constant in kcal/mol/Å2) are defined in the last two columns.
Similar formats are used to define the other covalent geometry restraints in atoms.tab, angles.tab, and impropers.tab. Since these are generated automatically by the GMC Editor, they rarely need to be examined or edited.
The experimental restraints tables follow a similar format. For example, each line in a torsion angle restraint table contains specifications for the four atoms decsribing the torsion, I, J, K and L. And, a given torsion restraint is specified in terms of allowed lower and upper bounds in degrees (ANGLE_LO and ANGLE_HI). Each restraint also includes a unique INDEX number to identify the restraint:
VARS INDEX SEGNAME_I RESID_I RESNAME_I ATOMNAME_I \
SEGNAME_J RESID_J RESNAME_J ATOMNAME_J \
SEGNAME_K RESID_K RESNAME_K ATOMNAME_K \
SEGNAME_L RESID_L RESNAME_L ATOMNAME_L \
ANGLE_LO ANGLE_HI FC
FORMAT %4d %4d %4s %4s %4s %4d %4s %4s %4s %4d %4s %4s %4s %4d %4s %4s %4s %8.3f %8.3f %8.3f
1 UBIQ 1 MET C UBIQ 2 GLN N UBIQ 2 GLN CA UBIQ 2 GLN C -138.00 -66.00 1.0
2 UBIQ 2 GLN C UBIQ 3 ILE N UBIQ 3 ILE CA UBIQ 3 ILE C -173.00 -109.00 1.0
3 UBIQ 3 ILE C UBIQ 4 PHE N UBIQ 4 PHE CA UBIQ 4 PHE C -149.00 -93.00 1.0
4 UBIQ 4 PHE C UBIQ 5 VAL N UBIQ 5 VAL CA UBIQ 5 VAL C -163.00 -75.00 1.0
5 UBIQ 5 VAL C UBIQ 6 LYS N UBIQ 6 LYS CA UBIQ 6 LYS C -133.00 -85.00 1.0
6 UBIQ 6 LYS C UBIQ 7 THR N UBIQ 7 THR CA UBIQ 7 THR C -142.00 -58.00 1.0
7 UBIQ 7 THR C UBIQ 8 LEU N UBIQ 8 LEU CA UBIQ 8 LEU C -82.00 -42.00 1.0
Sixteen columns are needed to specify the segment name, residue number, residue name, and atom name of each of the four atoms that define the torsion angle. Finally, two columns give the lower and upper bounds on the angle (in degrees), followed by a force constant (in kcal/mol/rad2).
The J-couplings restraints table has a format similar to the torsion angle restraints, but in addition, each restraint includes karplus parameters:
VARS INDEX SEGNAME_I RESID_I RESNAME_I ATOMNAME_I \
SEGNAME_J RESID_J RESNAME_J ATOMNAME_J \
SEGNAME_K RESID_K RESNAME_K ATOMNAME_K \
SEGNAME_L RESID_L RESNAME_L ATOMNAME_L A B C PHASE OBSJ FC
FORMAT %3d %5d %4s %4s %4s %5d %4s %4s %4s %5d %4s %4s %4s %5d %4s %4s %4s %9.5f %9.5f %9.5f %9.5f %9.3f %.2f
1 UBIQ 1 MET C UBIQ 2 GLN N UBIQ 2 GLN CA UBIQ 2 GLN C 1.74000 -0.57000 0.25000 240.00000 2.30 1.0
2 UBIQ 3 ILE C UBIQ 4 PHE N UBIQ 4 PHE CA UBIQ 4 PHE C 1.74000 -0.57000 0.25000 240.00000 1.30 1.0
3 UBIQ 4 PHE C UBIQ 5 VAL N UBIQ 5 VAL CA UBIQ 5 VAL C 1.74000 -0.57000 0.25000 240.00000 0.80 1.0
4 UBIQ 5 VAL C UBIQ 6 LYS N UBIQ 6 LYS CA UBIQ 6 LYS C 1.74000 -0.57000 0.25000 240.00000 1.60 1.0
Once again, the first column defines an "index" number for each constraint. The next sixteen columns select the four atoms involved in the torsion angle. Three more columns define the Karplus parameters A, B, and C for that J-coupling (where Jcalc = A cos2 theta + B cos theta + C). The next column allows a phase correction (in degrees) to be applied to the Karplus calculation. This phase correction is necessary in cases where the atoms selected to define the torsion angle (in the above example, C..N..Ca..C atoms are used to define a backbone phi angle) are different from the atoms involved in creating the observed coupling (in this case, HN..Ha). Finally, the observed coupling constant (in Hz) is defined, together with a force constant (in kcal/mol/Hz2).
The format of the dipolar couplings restraints file is:
VARS SEGNAME_I RESID_I RESNAME_I ATOMNAME_I SEGNAME_J RESID_J RESNAME_J ATOMNAME_J D DD W FORMAT %5d %6s %6s %5d %6s %6s %9.3f %9.3f %.2f UBIQ 1 MET C UBIQ 2 GLN HN 3.993 0.333 3.00 UBIQ 2 GLN C UBIQ 3 ILE HN -5.646 0.333 3.00 UBIQ 3 ILE C UBIQ 4 PHE HN 1.041 0.333 3.00 UBIQ 4 PHE C UBIQ 5 VAL HN 0.835 0.333 3.00
The first eight columns select the two atoms involved in the dipolar coupling. The next column gives the observed value of the coupling (in Hz). The next column gives an indication of the possible range of values for this coupling, relative to the HN..N coupling. The final column defines a force constant (in kcal/mol/Hz2).
The NOE table format is somewhat more complex than the other experimental restraints tables:
VARS INDEX GROUP RESID_I RESNAME_I ATOMNAME_I SEGNAME_I RESID_J RESNAME_J ATOMNAME_J SEGNAME_J D_LO D_HI FC W S FORMAT %4d %3d %5d %6s %6s %4s %5d %6s %6s %4s %9.3f %9.3f %.2f %.2f %.2f 1 1 UBIQ MET 1 HA UBIQ MET 1 HG1 1.800 4.459 1.0 1.0 1.0 1 2 UBIQ MET 1 HA UBIQ MET 1 HG2 1.800 4.459 1.0 1.0 1.0 2 1 UBIQ MET 1 HA UBIQ MET 1 HG1 1.800 4.060 1.0 1.0 1.0 2 2 UBIQ MET 1 HA UBIQ MET 1 HG2 1.800 4.060 1.0 1.0 1.0 3 1 UBIQ MET 1 HB2 UBIQ MET 1 HE1 1.800 3.565 1.0 1.0 1.0 3 1 UBIQ MET 1 HB2 UBIQ MET 1 HE2 1.800 3.565 1.0 1.0 1.0 3 1 UBIQ MET 1 HB2 UBIQ MET 1 HE3 1.800 3.565 1.0 1.0 1.0 4 1 UBIQ MET 1 HE1 UBIQ MET 1 HG1 1.800 3.155 1.0 1.0 1.0 4 1 UBIQ MET 1 HE2 UBIQ MET 1 HG1 1.800 3.155 1.0 1.0 1.0 4 1 UBIQ MET 1 HE3 UBIQ MET 1 HG1 1.800 3.155 1.0 1.0 1.0 4 2 UBIQ MET 1 HE1 UBIQ MET 1 HG2 1.800 3.155 1.0 1.0 1.0 4 2 UBIQ MET 1 HE2 UBIQ MET 1 HG2 1.800 3.155 1.0 1.0 1.0 4 2 UBIQ MET 1 HE3 UBIQ MET 1 HG2 1.800 3.155 1.0 1.0 1.0
As in the J-coupling restraint file, the first column is an index number to identify a particular constraint. Columns 3-10 identify two atoms whose distance will be used in calculating the NOE energy. The next two columns define that restraint's lower and upper distance bounds (in Ångstroms), and the last column sets a force constant for that restraint (in kcal/mol/Å2).
But there are two differences in the NOE restraints file's format. The first is that more than one line of the file can be given the same index number. Having more than one line with the same index number tells dynamo that these lines are all part of a single NOE constraint. The second difference in the NOE restraints file format is the addition of the GROUP column. Like the INDEX column, the group column contains an integer. It is used in combination with the index column to define different possible assignments for a particular NOE restraint. Lines in the NOE restraints file which have the same index number and the same group number are treated as part of a single possible assignment for an NOE. The interatomic distances from each line's atoms are averaged together using an R-6 sum average. Lines (or groups of lines) with the same index number but different group numbers are treated as separate possible assignments for a given NOE.
The DYNAMO Annealing Stages
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 \
Simulated Annealing 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.
| 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
| Script Name | Purpose |
|---|---|
| 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 |
| scrollRama.tcl | Display Backbone Angle Trajectories |
| showTab.tcl | Show X/Y Table Graphs |
Creating New Residue Types
DYNAMO residue type parameters are located in a series of parameter directories defined by the environment variable DYNAMO_PARAMS. DYNAMO provides for three general classes of residues, with parameters in these default locations:
dynamo/params/protein Amino Acids dynamo/params/dna_rna Nucleic Acids dynamo/params/other Other Molecules
A given residue is defined by a TCL procedure in one of the above directories. The TCL procedure defines the atoms, bonds, angles, and torsions that describe the residue.
The master list of all the residues is stored in a table which defines the naming details of each residue, and the name of the TCL procedure which creates that residue:
dynamo/params/params.tab
So, in order to create a new DYNAMO residue, there are two basic steps:
TCL Residue Definition
As an example of how residues are defined in DYNAMO, consider the
TCL procedure "add_ala" which defines an alanine residue, in the
file "params/protein/ala":
proc add_ala { seg resID } \
{
add_Atom $seg ALA $resID C 12.0 0.0903 3.2072 0.48 -0.471 0.723 -1.504
add_Atom $seg ALA $resID CA 12.0 0.0903 3.2072 0.22 -0.376 0.324 -0.028
add_Atom $seg ALA $resID CB 12.0 0.0903 3.2072 -0.30 0.908 0.867 0.597
add_Atom $seg ALA $resID HA 1.0 0.0045 2.6157 0.10 -1.225 0.735 0.499
add_Atom $seg ALA $resID HB1 1.0 0.0045 2.6157 0.10 1.720 0.809 -0.116
add_Atom $seg ALA $resID HB2 1.0 0.0045 2.6157 0.10 1.157 0.278 1.467
add_Atom $seg ALA $resID HB3 1.0 0.0045 2.6157 0.10 0.763 1.895 0.893
add_Atom $seg ALA $resID HN 1.0 0.0498 1.4254 0.26 0.391 -0.265 1.965
add_Atom $seg ALA $resID N 14.0 0.1592 2.7618 -0.10 -0.397 -1.128 0.109
add_Atom $seg ALA $resID O 16.0 0.2342 2.6406 -0.48 -0.877 -0.080 -2.345
add_Bond_Intrares $seg ALA $resID C O 1.231 1000.000
add_Bond_Intrares $seg ALA $resID CA C 1.525 1000.000
add_Bond_Intrares $seg ALA $resID CA CB 1.521 1000.000
add_Bond_Intrares $seg ALA $resID CA HA 1.080 1000.000
add_Bond_Intrares $seg ALA $resID CB HB1 1.080 1000.000
add_Bond_Intrares $seg ALA $resID CB HB2 1.080 1000.000
add_Bond_Intrares $seg ALA $resID CB HB3 1.080 1000.000
add_Bond_Intrares $seg ALA $resID N CA 1.458 1000.000
add_Bond_Intrares $seg ALA $resID N HN 0.98 1000.000
add_Angle_Intrares $seg ALA $resID CA C O 120.800 500.000
add_Angle_Intrares $seg ALA $resID CA CB HB1 109.500 500.000
add_Angle_Intrares $seg ALA $resID CA CB HB2 109.500 500.000
add_Angle_Intrares $seg ALA $resID CA CB HB3 109.500 500.000
add_Angle_Intrares $seg ALA $resID CB CA C 110.500 500.000
add_Angle_Intrares $seg ALA $resID HA CA C 109.500 500.000
add_Angle_Intrares $seg ALA $resID HA CA CB 109.500 500.000
add_Angle_Intrares $seg ALA $resID HB1 CB HB2 109.500 500.000
add_Angle_Intrares $seg ALA $resID HB1 CB HB3 109.500 500.000
add_Angle_Intrares $seg ALA $resID HB2 CB HB3 109.500 500.000
add_Angle_Intrares $seg ALA $resID HN N CA 120.000 500.000
add_Angle_Intrares $seg ALA $resID N CA C 111.200 500.000
add_Angle_Intrares $seg ALA $resID N CA CB 110.400 500.000
add_Angle_Intrares $seg ALA $resID N CA HA 109.500 500.000
add_Improper_Intrares $seg ALA $resID HA N C CB 65.977 500.000
add_Improper_Intrares $seg ALA $resID HB1 HB2 CA HB3 -66.514 500.000
}
The first section is a series of calls to add_Atom, which defines each atom in turn, supplying its segment name, residue name, residue number, atom name, standard mass, Lennard-Jones epsilon and sigma parameters, electric charge, and optional initial coordinates. (Note: the electric charge is not currently used by the DYNAMO energy function).
The second section defines all the covalent bonds. Each one is defined by the segment name, residue name, residue number, and the two atom names that are to be connected, together with the equilibrium distance (in Angstroms) and the bond's force constant (in kcal/mol-A^2).
The third section defines all the bond angle constraints. It works just like the bond length section, but three atom names are given, the equilibrium value is in degrees, and the force constant is in kcal/mol-radian^2.
The fourth section defines the improper torsion angle constraints. Impropers are torsion angles used to maintain chirality or planarity. They are defined just like the bond angles, except that four atom names are given.
Commonly, the TCL procedure will be created by copying a related existing one, and adjusting it manually. Alternatively, there is a crude script "pdb2dyn.tcl" which attempts to generate an initial TCL procedure based on a residue in an existing PDB file, and this can also be manually adjusted.
Adding the New Residue to the Master Table
In order for DYNAMO to be able to use the TCL procedure for a new residue, it must be listed in the master parameter table:
dynamo/params/params.tab
The parameter table contains a header and comments to assist in adding new residue entries. In the case of alanine, the table contains this line with five items:
ala protein add_ala ALA ala
The information about each residue is:
Once the TCL residue procedure is created, and a suitable entry for the residue is inserted into the parameter table, DYNAMO will be able to create instances of that residue via "gmcEdit".
DYNAMO Torsion Angle Names and Definitions
Some DYNAMO facilities associate particular names with molecular torsion angles, for example, the commonly-used protein backbone angles phi and psi. A list of torsion angle names and definitions used by DYNAMO follows.
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