FastModelFree

Optimizing PDB Coordinates before using Fast Model Free

PDB Inertia

This program calculates the principal moments of inertia for the atoms in a standard pdb file.. By default the program writes the moments of inertia to standard output. Optionally, the program can output a new pdb file in which the molecule is translated so that its center of mass is located at the origin and rotated so that the moments of inertia are aligned with the Cartesian axes. At present, the program only reads lines starting with the 'ATOM' keyword and only recognizes the atoms H, C, N, O, P, S.

• Type the following command in the directory containing your pdb file
  • pdbinertial -r infile.pdb outfile.pdb

• This will output a translated and rotated pdb file.

R2R1 Diffusion

The program (r2r1_diffusion) uses the apprach of Tjandra, et al. [J. Am. Chem. Soc. 117:12562-12566 (1995)] to determine the diffusion tensors for spherical, and axially-symmetric motional models from experimental nitrogen-15 spin relaxation data.

Creating R2R1 file

• You will need to calculate the R2/R1 ratios and R2/R1 uncertainity ratios. This can be done with any program such as excel, kaleidograph, origin, etc. You simply divide the R2 values by the R1 values for each residue. The same goes for the uncertainty values. If there is an error such as dividing by 0, remove the errors and leave blank. Save the file as a tab deliminated text file.

Example File

Setting up input file

• Copy the ubq.in file into the directory containing your translated/rotated pdb file
  • The ubq.in file is located in /PROGRAMS/FMF_edited_21_02_06/r2r1_diffusion/linux

ubq.in File

• Editing the Ubq.in
  • Second Line
    • The 300 represents the number of spin systems in the R2/R1 data. You will need to change this to the correct number
    • The 500.13 represents the frequency of NMR you used. For example, if you use the 600 Mhz NMR, change to 600.13.
    • The 100 represents the # of simulations. 100 simulations in the minimum needed.
  • Third Line
    • The 4.0453e+7 is your initial estimate for D-isotropic tensor. This does not need to be changed unless you have an estimate
    • The 0.800 is the estimated Dpar/Dper tensor. If you do not know an estimate, set this to 1.00
    • The 0.872 and 0.628 are your Theta and Phi values. If you do not know an estimate, set these values to 0.000.
  • Fourth Line
    • The 0.8 and 1.2 represents the predicted the High and low ratio set limits on Dpar/Dper. These values do not need to be changed.
    • The 10 represents the number of steps of grid searching to be performed. This does not need to be changed. Increasing the number of steps may help accuracy, however may the calculation time
  • Fifth Line is your R2R1.txt file
  • Sixth Line is your input pdb file generated from pdbinertia
  • Seventh Line is your output pdb file

• Running the program
  • type the following command
    • r2r1_diffusion ubq.in > ubq.out
    • When the program is finished, you will need to check the Dpar/Dper value
      • Type vi ubq.out
      • Type :$
      • This will take you to the bottom of the file. Start scrolling up until you see the final parameters. Here is an example you will be seeing.

• If your Dpar/Dper value is the same as your minimum value or maximum value you set in the ubq.in file, you will need to increase the range and rerun the calculation.
• Your predicted Theta and Phi angles will be calcuated. Save those numbers to implement them into FastModelFree.
• The output pdb is what will be used for FastModelFree
  

Fast ModelFree

Setting up files for FastModelFree

• • You will need to copy the FMF.config into your directory containing your R2.txt, R1.txt, NOE.txt, and pdb file
  • FMF.config is located in /PROGRAMS/FMF_edited_21_02_06
    

FMF.config

• Parameter to modify
  • The manual for all the parameters are located in /PROGRAMS/FMF_edited_21_02_06.fmfdox.pdf.
  • tensor- Set as Isotropic for spherical or Axial Symmetric for non-spherical
    • Make sure the A and S is capitalized for Axial Symmetric or else it will autorun as Isotropic
    • You do not need a pdb file for Isotropic calculations
  • cutoff set to 0.95
  • Fcutoff set to 0.80
  • optimize set to Yes
  • maxloop set to 10. This means the program will stop after 10 iterations. If your final values have did not converge you may want to set to higher numbers such as 25 or 50 iterations.
  • almost1 set to 20. You can set to higher values just like maxloop
  • S2cutoff set to 0.7
  • seed set to 1985
  • numsim This is the number of simulation. If you want a quick and dirty estimate, you can set it to about 10 simulations. Final calculations should have a minimum of 500 simulations
  • jobname set this as the name of your protein. This is the title for all your output files.
  • gamma set to -2.71
  • rNH set to 1.02
  • N15CSA set to -160
  • tm This is your predicted correlation time. If you are unsure of a correlation time, 10.0 is a good start. The farther away from the actual value the more iterations is needed and longer it takes for calculations
    • You can use HyroNMR to help predict correlation time [[1]]
  • tmMin Set to 0.0 if first time. You can set this min value near the actual value when you have a general idea what the tm is.
  • tmMax Set to 40.0 if first time. You can set the max value near the actual value when you have a general idea what the tm is.
    • tmMin and tmMax are ranges you set to believe where the actual value is.
  • tmGrid set to 50. Can set to higher value for more thorough calculation
  • tmConv set to 0.001 This is the convergence cutoff. You want this to be small. The accuracy decreases as you increase this value.
  • Dratio This is your Dpar/Dper ratio you calculated using R2R1_diffusion calculations. You will find it in ubq.out file
  • DratioMin Set the value to be smaller than your Dratio
  • DratioMax Set the value to be larger than your Dratio
    • DratioMin and DratioMax are your ranges you set. You want this range to be large when your first start out. After multiple attempts you can decrease the range.
  • DratioConv set to 0.001
  • Phi This is the Phi that you calculated using R2R1_diffusion calculations. You will find it in ubq.out file
  • PhiMin set to 0
  • PhiMax set to 360
  • PhiGrid set to 20. Increase this value increases the thoroughness of the calculation
  • PhiConv set to 0.001
  • modle1only set to No
  • mdpb Name of your pdb file generated from R2R1_diffusion calculations
  • file{0}{R1} Name of your R1 file
  • file{0}{R2} Name of your R2 file
  • file{0}{NOE} Name of your NOE file
    • file{0}{field} Set to 500 if using 500 MHz NMR, 600 if using 600Mhz NMR, etc.