Foundations of Computational Chemistry and Cheminformatics Homework #2

[Sulstice]

Hi All,

Today our objective is to look at the RMSD of the carbon alpha atoms of this trajectory of this kinase - 5tC0. Trajectory. I suggest using a jupyter notebook to analyze and plot your results.

Theory

The alpha carbons are the carbons that bound to the residue. We can gather information about the fluctuation of a residue based on the carbon it is connected too.

Implementation

We will be using pytraj to analyze our data.

import pytraj as pt
import plotly.graph_objects as go
import plotly.offline as pyo

# Load the Trajectory 

traj = pt.iterload('production_2.nc', 'topology.parm7')
print (traj)

# Load the Alpha Carbon Atoms and take the RMSD

data_ca_ref = pt.rmsd(traj, mask=['GLY']) # CA atoms

# Fix the the time scale. We are running on 2 femtoseconds so we need to cut our frames in half.

time = [float(i/20) for i in range(1, len(data_ca_ref) + 1)]

# Plot the RMSD

colors = ["#A800FF"]

pyo.init_notebook_mode()

fig = go.Figure()

fig.update_layout(legend=dict(itemsizing='constant'))
fig.update_layout(legend=dict(
        orientation="h",
        yanchor="bottom",
        y=1.02,
        xanchor="right",
        x=1,  
        font = dict(family = "Arial", size = 15),
        bordercolor="LightSteelBlue",
        borderwidth=2,
    ),
    legend_title = dict(font = dict(family = "Arial", size = 60))
)
fig.update_traces(line=dict(width=15))

fig.add_trace(
        go.Scattergl(
        x=time,
        y=data_ca_ref,
        name="CA Reference",
        mode='lines',
        line=dict(color=colors[0], width=3),
        showlegend=True
    ),
)

fig.update_xaxes(
                 ticks="outside",
                 tickwidth=3,
                 tickcolor='black',
                 tickfont=dict(family='Arial', color='black', size=40),
                 title_font=dict(size=46, family='Arial'),
                 title_text='Time (ns)',
                 ticklen=15,
)

fig.update_yaxes(
                 ticks="outside", 
                 tickwidth=3,
                 tickcolor='black', 
                 title_text='RMSD (Å)',
                 tickfont=dict(family='Arial', color='black', size=40),
                 title_font=dict(size=46, family='Arial'),
                 ticklen=15,
)    

fig.update_layout(
    title_text="RMSD CA",
    title_font=dict(size=44, family='Arial'),
    template='simple_white',
    xaxis_tickformat = 'i',
    bargap=0.2, # gap between bars of adjacent location coordinates,
    height=600,
    width=1500,
)

fig.show()

Example Figure:

Molecular Dynamics Data:

https://github.com/Global-Chem/Molecular-Dynamics-Learning-Material/tree/main/module_one

Post your RMSD plot here and any other interesting things you might find.