Guide for evaluating metrics for a Molecular dynamics (MD) simulation with AMBER Software on ASU Sol cluster

Follow the MDGuide to run the MD simulation first

Follow the MDGuide guide here: MDGuide

Using VPN to connect to ASU network:

Follow the VPN guide here: VPNGuide

After logging in:

pwd shows me home directory /home/ikazan

change directory to scratch space

cd /scratch/ikazan

create a new directory here by using

mkdir -pv evaluationdir1

change directory to the new one

cd evaluationdir1/

ls

the directory is empty

pwd shows me the current working directory

copy the sol path: /scratch/ikazan/evaluationdir1

Two options to download required files (I recommend option 2)

Option 1

open a new ternminal tab (this will be connected to your own computer)

download the parameter file under mdtrajectory on github

and download the trajectory from the dropbox link:

1btl.nc

go to the directory where you have the files and copy the them to sol

scp ./*.parm7 ikazan@login.sol.rc.asu.edu:/scratch/ikazan/evaluationdir1/

scp ./*.nc ikazan@login.sol.rc.asu.edu:/scratch/ikazan/evaluationdir1/

we are going to switch the termnial window to the sol session one

Option 2

copy the parameter and trajectory file directly on sol

cp -rv /scratch/ikazan/shared/test ./

Start an interactive session

we are going to start an interactive session by running

interactive

Reading the trajectory

load the necessary modules on sol by running:

module load amber/22v3

then we are going to start the evaluation process by following either Option 1 or 2.

Option 1

run

cpptraj

this will start the cpptraj software

first we need to load the parameter (topology) file

parm 1btl.parm7

then we are going to load the trajectory

trajin 1btl.nc

After succesfully loading the parameter and trajectory files we need to do some cleaning first by removing water molecules and the ions

strip :WAT,Cl-,Na+

then superimpose (align) the trajectory

autoimage origin

rms first mass @CA,C,N

Option 2

An easier way would be preparing the commands initially and running it later

Prepare readtraj.in input file:

vim readtraj.in

press i to enter edit mode

copy and paste the text below

parm 1btl.parm7
trajin 1btl.nc
strip :WAT,Cl-,Na+
autoimage origin
rms first mass @CA,C,N

press esc button on keyboard and then type :wq

run:

cpptraj -i readtraj.in

Root Mean Square Fluctuation (RMSF)

We will evaluate RMSF

RMSF is a measurement of flexibility. It measures how much amino acid residues of a protein move around over time during a molecular dynamics simulation. We will use the alpha carbon (CA) locations of amino acids to calculate the RMSF.

if you are following option 1:

atomicfluct out rmsf.txt @CA

at this point all the commands should be entered. To run the commands simply type:

run

After processing is complete, type quit to exit the application.

if you are following option 2 add the line at the end of the file and run it.

copy rmsf.txt back to your computer by running the following command on the terminal connected to your local computer

scp ikazan@login.sol.rc.asu.edu:/scratch/ikazan/evaluationdir1/rmsf.txt ./

Compare the rmsf.txt file you generated to the one provide under outputs folder on github

Now use your favorite tool to generate a plot

The python (python 3) code used to generate the plot is below:

import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt

df = pd.read_csv('rmsf.txt', delim_whitespace=True, header=0)
df['Residue'] = [26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290]

sns.set(style='ticks')
plt.figure(figsize=(6, 3))
sns.lineplot(x='Residue', y='AtomicFlx', data=df)
plt.xlabel('Residue')
plt.ylabel('RMSF (Å)')
plt.show()

Get PDB files from the trajectory

if you are following option 1:

trajout struct pdb offset 100 multi

at this point all the commands should be entered. To run the commands simply type:

run

After processing is complete, type quit to exit the application.

if you are following option 2 add the line at the end of the file and run it.

This will generate many files named struct***.pdb, we are going to grab the one with the largest number indicating the last frame of the simulation and rename it last.pdb.