In [37]:

    

import MDAnalysis as mda
import matplotlib.pyplot as plt
%matplotlib inline


    

In [6]:

    

from MDAnalysis import *
from MDAnalysis.analysis.align import *
from MDAnalysis.analysis.rms import rmsd


    

In [9]:

    

import MDAnalysis
u = MDAnalysis.Universe('41w_ff.psf','50_frame.dcd')
ref = MDAnalysis.Universe(PSF,DCD)     # reference closed AdK (1AKE) (with the default ref_frame=0)
#ref = MDAnalysis.Universe(PSF,CRD)    # reference open AdK (4AKE)

import MDAnalysis.analysis.rms

R = MDAnalysis.analysis.rms.RMSD(u, ref,
           select="backbone",             # superimpose on whole backbone of the whole protein
           groupselections=["backbone and (resid 1-29 or resid 60-121 or resid 160-214)",   # CORE
                            "backbone and resid 122-159",                                   # LID
                            "backbone and resid 30-59"],                                    # NMP
           filename="rmsd_all_CORE_LID_NMP.dat")
R.run()
R.save()

import matplotlib.pyplot as plt
rmsd = R.rmsd.T   # transpose makes it easier for plotting
time = rmsd[1]
fig = plt.figure(figsize=(4,4))
ax = fig.add_subplot(111)
ax.plot(time, rmsd[2], 'k-',  label="all")
ax.plot(time, rmsd[3], 'k--', label="CORE")
ax.plot(time, rmsd[4], 'r--', label="LID")
ax.plot(time, rmsd[5], 'b--', label="NMP")
ax.legend(loc="best")
ax.set_xlabel("time (ps)")
ax.set_ylabel(r"RMSD ($\AA$)")
fig.savefig("rmsd_all_CORE_LID_NMP_ref1AKE.pdf")


    

    




---------------------------------------------------------------------------
IOError                                   Traceback (most recent call last)
<ipython-input-9-ea579482f2ff> in <module>()
      1 import MDAnalysis
----> 2 u = MDAnalysis.Universe('41w_ff.psf','50_frame.dcd')
      3 ref = MDAnalysis.Universe(PSF,DCD)     # reference closed AdK (1AKE) (with the default ref_frame=0)
      4 #ref = MDAnalysis.Universe(PSF,CRD)    # reference open AdK (4AKE)
      5 

/projects/4a420c65-bab9-4479-a810-f7137c0dcd19/.local/lib/python2.7/site-packages/MDAnalysis/core/AtomGroup.pyc in __init__(self, *args, **kwargs)
   3778             raise IOError("Failed to load from the topology file {0}"
   3779                           " with parser {1}.\n"
-> 3780                           "Error: {2}".format(self.filename, parser, err))
   3781         except ValueError as err:
   3782             raise ValueError("Failed to construct topology from file {0}"

IOError: Failed to load from the topology file 41w_ff.psf with parser <class 'MDAnalysis.topology.PSFParser.PSFParser'>.
Error: [Errno 5] Cannot open file or stream in mode='r'.: "'41w_ff.psf'"

In [46]:

    

import MDAnalysis
u = MDAnalysis.Universe('41wl_ff.psf','50_frame.dcd')
pdb = "./41wl_ff.pdb"
#ref1 = u.trajectory.
ref = MDAnalysis.Universe('41wl_ff.psf','50_frame.dcd')      # reference closed AdK (1AKE) (with the default ref_frame=0)
#mobile = Universe(PSF,DCD)
rmsd(u.atoms.CA.positions, ref.atoms.CA.positions)


    

    
Out[46]:





3.92068124672431e-07

In [1]:

    

RMSD = []
backbone = u.select_atoms("protein and (name C or name N or name CA)")
refbb = ref.select_atoms("protein and (name C or name N or name CA)")
backbone.coordinates()
#for ts in u.trajectory:
#    A = backbone.coordinates()
#    B = refbb.coordinates()
#    print A()
#    C = rmsd(A,B)
#    RMSD.append((u.trajectory.frame, )
#RMSD = np.array(RMSD)

#print RMSD


    

    




---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-1-45e6ff8cef41> in <module>()
      1 RMSD = []
----> 2 backbone = u.select_atoms("protein and (name C or name N or name CA)")
      3 refbb = ref.select_atoms("protein and (name C or name N or name CA)")
      4 backbone.coordinates()
      5 #for ts in u.trajectory:

NameError: name 'u' is not defined

In [18]:

    

len(u.trajectory)


    

    
Out[18]:





50

In [47]:

    

Rgyr = []
protein = u.select_atoms("protein")
for ts in u.trajectory:
   Rgyr.append((u.trajectory.frame, protein.radius_of_gyration()))
Rgyr = np.array(Rgyr)

print Rgyr
import matplotlib.pyplot as plt
ax = plt.subplot(111)
ax.plot(Rgyr[:,0], Rgyr[:,1], 'r--', lw=2, label=r"$R_G$")
ax.set_xlabel("Frame")
ax.set_ylabel(r"radius of gyration $R_G$ ($\AA$)")
ax.figure.savefig("Rgyr.pdf")
plt.draw()


    

    




[[  0.          14.45947817]
 [  1.          14.56343943]
 [  2.          14.66004709]
 [  3.          14.5950319 ]
 [  4.          14.65924899]
 [  5.          14.52109577]
 [  6.          14.52496548]
 [  7.          14.74254526]
 [  8.          14.74876355]
 [  9.          14.52289098]
 [ 10.          14.52560928]
 [ 11.          14.4352187 ]
 [ 12.          14.53671809]
 [ 13.          14.43235824]
 [ 14.          14.46688002]
 [ 15.          14.4705191 ]
 [ 16.          14.41274683]
 [ 17.          14.43789711]
 [ 18.          14.38424011]
 [ 19.          14.41613229]
 [ 20.          14.56441881]
 [ 21.          14.5337207 ]
 [ 22.          14.41597997]
 [ 23.          14.40583184]
 [ 24.          14.45525257]
 [ 25.          14.46460474]
 [ 26.          14.46638457]
 [ 27.          14.40691409]
 [ 28.          14.52930841]
 [ 29.          14.54878399]
 [ 30.          14.48549566]
 [ 31.          14.49806385]
 [ 32.          14.50785088]
 [ 33.          14.50795497]
 [ 34.          14.54129607]
 [ 35.          14.38962131]
 [ 36.          14.51879453]
 [ 37.          14.51302802]
 [ 38.          14.59042283]
 [ 39.          14.50376336]
 [ 40.          14.45130122]
 [ 41.          14.5705463 ]
 [ 42.          14.66729859]
 [ 43.          14.51986238]
 [ 44.          14.54526494]
 [ 45.          14.4653264 ]
 [ 46.          14.46804386]
 [ 47.          14.5561452 ]
 [ 48.          14.39166516]
 [ 49.          14.48221981]]






    

In [ ]: