I have PDB files from MD simulation and would like to calculate hydrodynamic radius (RH). I tried using HYDROPRO. It provides translational diffusion coeff. and Radius of gyration. from which RH should be derived. buT if some can walk me through that will be great.
Hydrodynamic radius https://en.wikipedia.org/wiki/Hydrodynamic_radius
Note that in biophysics, hydrodynamic radius refers to the Stokes radius,[2] or commonly to the apparent Stokes radius obtained from size exclusion chromatography.[3]
The theoretical hydrodynamic radius Rhyd refers to the Stokes radius,
arises in the study of the dynamic properties of polymers moving in a solvent. It is often similar in magnitude to the radius of gyration
Radius of Gyration https://en.wikipedia.org/wiki/Radius_of_gyration
[quote]
The radius of gyration is not that tough. Here's a python script to do
it in pymol. Do note that the hydrodynamic radius is something
related, but different.
from pymol import cmd
import math
def rgyrate(selection):
# Get the atoms for the selection
model=cmd.get_model(selection).atom
# Extract the coordinates
x=[i.coord for i in model]
# Get the masses
mass=[i.get_mass() for i in model]
# Mass-weighted coordinates
xm=[(m*i,m*j,m*k) for (i,j,k),m in zip(x,mass)]
# Sum of masses
tmass=sum(mass)
# First part of the sum under the sqrt
rr=sum(mi*i+mj*j+mk*k for (i,j,k),(mi,mj,mk) in zip(x,xm))
# Second part of the sum under the sqrt
mm=sum((sum(i)/tmass)**2 for i in zip(*xm))
# Radius of gyration
rg=math.sqrt(rr/tmass-mm)
# Print it...
print "Radius of gyration:", rg
return rg
cmd.extend("rgyrate",rgyrate)
Hope it helps,
Tsjerk
[/quote]
In contrast to the formula for the hydrodynamic radius in Wikipedia, this script weights the atoms by their mass
Program HydroPro calculate hydrodynamic radius from pdb (windows/linux executable) http://leonardo.inf.um.es/macromol/programs/programs.htm
Update: I did use HYDROPRO to calculate the hydrodynamic radius. My recent paper on peptide fluorophore tag in "Scientific reports" has these calculations as figure. I will add the link to the paper when its online.
I changed the PyMol script to make it a stand alone script capable of running on python3 independent of PyMol. Here is a link to it in case someone wants to use it in the future :-)
https://github.com/sarisabban/Rg
Hello Senthilkumar Kailasam,
I read your paper published in Scientific Reports, but I still can't figure out how you obtained hydrodynamic radius (RH) of FlAsH-FCMybbR from its PDB file using HYDROPRO as described in Fig. 2c. I am also attaching the HYDROPRO results from a single lysozyme PDB file. If you can show me how to obtain RH from these values, I would greatly appreciate it.
Senthilkumar Kailasam , as Shih-Hsien Liu asked you, I also would like to learn how to obtain Rh from the HYDROPRO parameters.
Thanks in advance.
Hi Everton and Shih-Hsien,
Sorry for the late reply. I had to dig into my oldfiles.
I used stokes law to calculate Rh(hydrodynamics radius). Using HYDROPRO on a PDB givs you the "Translational diffusion coefficient:"
https://warwick.ac.uk/fac/cross_fac/sciencecity/programmes/internal/themes/am2/booking/particlesize/intro_to_dls.pdf
Sari Sabban thank you for your script, however, I have the following error messages when running the Rg.py:
Traceback (most recent call last):
File "Rg.py", line 39, in
print('Rg = {}'.format(Rg(sys.argv[1])))
File "Rg.py", line 35, in Rg
rg = math.sqrt(rr / tmass-mm)
ZeroDivisionError: integer division or modulo by zero
Can you explain what the possible issues are? Mine PDB file is a small ligand, I attache here.
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