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IRed Analysis of MD Simulations

2021-05-14T16:52:11Z

Tessa17:

Calculating order parameters from MD Simulations

The analysis utilizes iRed software provided by the Dr. Rafael Bruschweiler Group.
All iRed calculations were completed on the HCC cluster.
#Create a pdb file of the trajectory in the same manner as the .xtc file.
#After the pdb file is created (will be very large), use the following scripts to extract the N and H coordinates for each atom at each time point in the trajectory
##awk ‘{if (($3 == “N”) && ($4 != “PRO”)) {print $6, $7, $8, $9:}} xxx.pdb > N-HCoor.dat
## awk ‘{if (($3 == “H”) && ($4 != “H1”)) {print $6, $7, $8, $9:}} xxx.pdb > H-NCoor.dat
#Once .dat files are created, use the python script below to run the iRed calculation
##In command line, run “ired_1vec_block.py --coor1 N-HCoor.dat --coor2 H-NCoor.dat --block 100

! /usr/bin/env python
from __future__ import division
import numpy as np
from optparse import OptionParser
import sys
def setupParserOptions():
parser=OptionParser()
parser.add_option('--coor1', dest='coor1',default='H-NCoor.dat',help = "Input coordinate file 1")
parser.add_option('--coor2', dest='coor2',default='N-HCoor.dat',help = "Input coordinate file 2")
parser.add_option('--block', dest='block', default = 1, help = 'Number of blocks')
return parser
def ired(hCoor_file, nCoor_file, block):
try:
h_all = np.loadtxt(hCoor_file)
except IOError:
print 'cannot open ', hCoor_file
try:
n_all = np.loadtxt(nCoor_file)
except IOError:
print 'cannot open ', nCoor_file
numLines = len(h_all)
numRes = len(set(h_all[:,0]))
numSnapshot = numLines // numRes
blockNum = int(block)
blockSize = numSnapshot // blockNum
if numLines != len(n_all):
print 'Error: The two coordinate files do not have same length.'
return
if np.mod(numLines, numRes) != 0:
print 'Error: Coordinate files do not formatted correctly.'
return
# initialize s2
s2_sum = np.zeros([1, numRes])
for i in range(blockNum):
hC = h_all[i*numRes*blockSize:(i+1)*numRes*blockSize, :]
nC = n_all[i*numRes*blockSize:(i+1)*numRes*blockSize, :]
# Calculate the bond vector orientations over the trajectory
hnC = hC[:,1:] - nC[:,1:]
# residue index
resNum = hC[0:numRes, 0]
# Construct matrix m
mMat = np.zeros([numRes, numRes])
#print numRes, numSnapshot, blockNum, blockSize
for a in range(0, numRes*blockSize, numRes):
# N-H vectors for the current snapshot
hnTemp = hnC[a:a+numRes, :]
# normalize the vectors
for b in range(numRes):
hnTemp[b,:] = hnTemp[b,:] / np.linalg.norm(hnTemp[b,:])
# Construct Rank 2 Legendre polynomial
c = np.dot(hnTemp, hnTemp.T)
mMat = mMat + (3*np.multiply(c, c)-1)/2
# Ensemble averaging
mMat = mMat / blockSize
#print np.shape(hnTemp), np.shape(hnTemp.T), np.shape(c), np.shape(mMat)
# Diagonalize matrix
dVals, v = np.linalg.eig(mMat)
Ind = dVals.argsort()[::-1] # sort eigenvalues in descending order
dSort = dVals[Ind]
eigVal = np.diag(dSort)
eigVec = v[:, Ind]
# Calculate the squared order parameters
s2_block = np.zeros(numRes)
for b in range(numRes):
sumOverModes = 0;
for a in range(5,numRes):
sumOverModes += eigVal[a,a] * (eigVec[b,a])**2
s2_block[b] = 1 - sumOverModes
s2_sum += s2_block
s2 = s2_sum / blockNum
# output
out = np.concatenate(([resNum], s2), axis = 0)
with open('ired_s2_1vec_%dblock.out' %(block), 'wb') as f:
np.savetxt(f, np.transpose(out), fmt='%i %.3f')
if __name__ == '__main__':
parser = setupParserOptions()
if len(sys.argv) <2:
parser.print_help()
sys.exit()
options, args=parser.parse_args()
print "**************************************************\nMD Block-averaged iRED S2 Calculation"
print "Input coordinate file: %s"%(options.coor1)
print "Input coordinate file: %s"%(options.coor2)
print "Number of MD block(s): %s"%(options.block)
f1 = options.coor1
f2 = options.coor2
try:
bn = int(options.block)
except ValueError:
print "Error: Number of block should be an integer."
ired(f1, f2, bn)

#Python script will output a .out file that contains the order parameter values for each amino acid residue.

IRed Analysis of MD Simulations

2021-05-14T16:51:56Z

Tessa17:

Calculating order parameters from MD Simulations

The analysis utilizes iRed software provided by the Dr. Rafael Bruschweiler Group.
All iRed calculations were completed on the HCC cluster.
#Create a pdb file of the trajectory in the same manner as the .xtc file.
#After the pdb file is created (will be very large), use the following scripts to extract the N and H coordinates for each atom at each time point in the trajectory
##awk ‘{if (($3 == “N”) && ($4 != “PRO”)) {print $6, $7, $8, $9:}} xxx.pdb > N-HCoor.dat
## awk ‘{if (($3 == “H”) && ($4 != “H1”)) {print $6, $7, $8, $9:}} xxx.pdb > H-NCoor.dat
#Once .dat files are created, use the python script below to run the iRed calculation
##In command line, run “ired_1vec_block.py --coor1 N-HCoor.dat --coor2 H-NCoor.dat --block 100

! /usr/bin/env python
from __future__ import division
import numpy as np
from optparse import OptionParser
import sys
def setupParserOptions():
parser=OptionParser()
parser.add_option('--coor1', dest='coor1',default='H-NCoor.dat',help = "Input coordinate file 1")
parser.add_option('--coor2', dest='coor2',default='N-HCoor.dat',help = "Input coordinate file 2")
parser.add_option('--block', dest='block', default = 1, help = 'Number of blocks')
return parser
def ired(hCoor_file, nCoor_file, block):
try:
h_all = np.loadtxt(hCoor_file)
except IOError:
print 'cannot open ', hCoor_file
try:
n_all = np.loadtxt(nCoor_file)
except IOError:
print 'cannot open ', nCoor_file
numLines = len(h_all)
numRes = len(set(h_all[:,0]))
numSnapshot = numLines // numRes
blockNum = int(block)
blockSize = numSnapshot // blockNum
if numLines != len(n_all):
print 'Error: The two coordinate files do not have same length.'
return
if np.mod(numLines, numRes) != 0:
print 'Error: Coordinate files do not formatted correctly.'
return
# initialize s2
s2_sum = np.zeros([1, numRes])
for i in range(blockNum):
hC = h_all[i*numRes*blockSize:(i+1)*numRes*blockSize, :]
nC = n_all[i*numRes*blockSize:(i+1)*numRes*blockSize, :]
# Calculate the bond vector orientations over the trajectory
hnC = hC[:,1:] - nC[:,1:]
# residue index
resNum = hC[0:numRes, 0]
# Construct matrix m
mMat = np.zeros([numRes, numRes])
#print numRes, numSnapshot, blockNum, blockSize
for a in range(0, numRes*blockSize, numRes):
# N-H vectors for the current snapshot
hnTemp = hnC[a:a+numRes, :]
# normalize the vectors
for b in range(numRes):
hnTemp[b,:] = hnTemp[b,:] / np.linalg.norm(hnTemp[b,:])
# Construct Rank 2 Legendre polynomial
c = np.dot(hnTemp, hnTemp.T)
mMat = mMat + (3*np.multiply(c, c)-1)/2
# Ensemble averaging
mMat = mMat / blockSize
#print np.shape(hnTemp), np.shape(hnTemp.T), np.shape(c), np.shape(mMat)
# Diagonalize matrix
dVals, v = np.linalg.eig(mMat)
Ind = dVals.argsort()[::-1] # sort eigenvalues in descending order
dSort = dVals[Ind]
eigVal = np.diag(dSort)
eigVec = v[:, Ind]

# Calculate the squared order parameters
s2_block = np.zeros(numRes)
for b in range(numRes):
sumOverModes = 0;
for a in range(5,numRes):
sumOverModes += eigVal[a,a] * (eigVec[b,a])**2
s2_block[b] = 1 - sumOverModes
s2_sum += s2_block
s2 = s2_sum / blockNum
# output
out = np.concatenate(([resNum], s2), axis = 0)
with open('ired_s2_1vec_%dblock.out' %(block), 'wb') as f:
np.savetxt(f, np.transpose(out), fmt='%i %.3f')
if __name__ == '__main__':
parser = setupParserOptions()
if len(sys.argv) <2:
parser.print_help()
sys.exit()
options, args=parser.parse_args()
print "**************************************************\nMD Block-averaged iRED S2 Calculation"
print "Input coordinate file: %s"%(options.coor1)
print "Input coordinate file: %s"%(options.coor2)
print "Number of MD block(s): %s"%(options.block)
f1 = options.coor1
f2 = options.coor2
try:
bn = int(options.block)
except ValueError:
print "Error: Number of block should be an integer."
ired(f1, f2, bn)

#Python script will output a .out file that contains the order parameter values for each amino acid residue.

IRed Analysis of MD Simulations

2021-05-14T16:50:18Z

Tessa17:

Calculating order parameters from MD Simulations

The analysis utilizes iRed software provided by the Dr. Rafael Bruschweiler Group.
All iRed calculations were completed on the HCC cluster.
#Create a pdb file of the trajectory in the same manner as the .xtc file.
#After the pdb file is created (will be very large), use the following scripts to extract the N and H coordinates for each atom at each time point in the trajectory
##awk ‘{if (($3 == “N”) && ($4 != “PRO”)) {print $6, $7, $8, $9:}} xxx.pdb > N-HCoor.dat
## awk ‘{if (($3 == “H”) && ($4 != “H1”)) {print $6, $7, $8, $9:}} xxx.pdb > H-NCoor.dat
#Once .dat files are created, use the python script below to run the iRed calculation
##In command line, run “ired_1vec_block.py --coor1 N-HCoor.dat --coor2 H-NCoor.dat --block 100

! /usr/bin/env python
from __future__ import division
import numpy as np
from optparse import OptionParser
import sys
def setupParserOptions():
parser=OptionParser()
parser.add_option('--coor1', dest='coor1',default='H-NCoor.dat',help = "Input coordinate file 1")
parser.add_option('--coor2', dest='coor2',default='N-HCoor.dat',help = "Input coordinate file 2")
parser.add_option('--block', dest='block', default = 1, help = 'Number of blocks')
return parser
def ired(hCoor_file, nCoor_file, block):
try:
h_all = np.loadtxt(hCoor_file)
except IOError:
print 'cannot open ', hCoor_file
try:
n_all = np.loadtxt(nCoor_file)
except IOError:
print 'cannot open ', nCoor_file
numLines = len(h_all)
numRes = len(set(h_all[:,0]))
numSnapshot = numLines // numRes
blockNum = int(block)
blockSize = numSnapshot // blockNum
if numLines != len(n_all):
print 'Error: The two coordinate files do not have same length.'
return
if np.mod(numLines, numRes) != 0:
print 'Error: Coordinate files do not formatted correctly.'
return
# initialize s2
s2_sum = np.zeros([1, numRes])
for i in range(blockNum):
hC = h_all[i*numRes*blockSize:(i+1)*numRes*blockSize, :]
nC = n_all[i*numRes*blockSize:(i+1)*numRes*blockSize, :]
# Calculate the bond vector orientations over the trajectory
hnC = hC[:,1:] - nC[:,1:]
# residue index
resNum = hC[0:numRes, 0]
# Construct matrix m
mMat = np.zeros([numRes, numRes])
#print numRes, numSnapshot, blockNum, blockSize

for a in range(0, numRes*blockSize, numRes):
# N-H vectors for the current snapshot
hnTemp = hnC[a:a+numRes, :]
# normalize the vectors
for b in range(numRes):
hnTemp[b,:] = hnTemp[b,:] / np.linalg.norm(hnTemp[b,:])

# Construct Rank 2 Legendre polynomial
c = np.dot(hnTemp, hnTemp.T)
mMat = mMat + (3*np.multiply(c, c)-1)/2

# Ensemble averaging
mMat = mMat / blockSize
#print np.shape(hnTemp), np.shape(hnTemp.T), np.shape(c), np.shape(mMat)

# Diagonalize matrix
dVals, v = np.linalg.eig(mMat)
Ind = dVals.argsort()[::-1] # sort eigenvalues in descending order
dSort = dVals[Ind]
eigVal = np.diag(dSort)
eigVec = v[:, Ind]

# Calculate the squared order parameters
s2_block = np.zeros(numRes)
for b in range(numRes):
sumOverModes = 0;
for a in range(5,numRes):
sumOverModes += eigVal[a,a] * (eigVec[b,a])**2
s2_block[b] = 1 - sumOverModes
s2_sum += s2_block

s2 = s2_sum / blockNum

# output
out = np.concatenate(([resNum], s2), axis = 0)
with open('ired_s2_1vec_%dblock.out' %(block), 'wb') as f:
np.savetxt(f, np.transpose(out), fmt='%i %.3f')

if __name__ == '__main__':
parser = setupParserOptions()
if len(sys.argv) <2:
parser.print_help()
sys.exit()

options, args=parser.parse_args()
print "**************************************************\nMD Block-averaged iRED S2 Calculation"
print "Input coordinate file: %s"%(options.coor1)
print "Input coordinate file: %s"%(options.coor2)
print "Number of MD block(s): %s"%(options.block)

f1 = options.coor1
f2 = options.coor2
try:
bn = int(options.block)
except ValueError:
print "Error: Number of block should be an integer."

ired(f1, f2, bn)

#Python script will output a .out file that contains the order parameter values for each amino acid residue.

IRed Analysis of MD Simulations

2021-05-14T16:48:21Z

Tessa17:

Calculating order parameters from MD Simulations

The analysis utilizes iRed software provided by the Dr. Rafael Bruschweiler Group.
All iRed calculations were completed on the HCC cluster.
#Create a pdb file of the trajectory in the same manner as the .xtc file.
#After the pdb file is created (will be very large), use the following scripts to extract the N and H coordinates for each atom at each time point in the trajectory
##awk ‘{if (($3 == “N”) && ($4 != “PRO”)) {print $6, $7, $8, $9:}} xxx.pdb > N-HCoor.dat
## awk ‘{if (($3 == “H”) && ($4 != “H1”)) {print $6, $7, $8, $9:}} xxx.pdb > H-NCoor.dat
#Once .dat files are created, use the python script below to run the iRed calculation
##In command line, run “ired_1vec_block.py --coor1 N-HCoor.dat --coor2 H-NCoor.dat --block 100

! /usr/bin/env python

from __future__ import division
import numpy as np
from optparse import OptionParser
import sys

def setupParserOptions():
parser=OptionParser()
parser.add_option('--coor1', dest='coor1',default='H-NCoor.dat',help = "Input coordinate file 1")
parser.add_option('--coor2', dest='coor2',default='N-HCoor.dat',help = "Input coordinate file 2")
parser.add_option('--block', dest='block', default = 1, help = 'Number of blocks')
return parser

def ired(hCoor_file, nCoor_file, block):
try:
h_all = np.loadtxt(hCoor_file)
except IOError:
print 'cannot open ', hCoor_file
try:
n_all = np.loadtxt(nCoor_file)
except IOError:
print 'cannot open ', nCoor_file

numLines = len(h_all)
numRes = len(set(h_all[:,0]))
numSnapshot = numLines // numRes
blockNum = int(block)
blockSize = numSnapshot // blockNum

if numLines != len(n_all):
print 'Error: The two coordinate files do not have same length.'
return
if np.mod(numLines, numRes) != 0:
print 'Error: Coordinate files do not formatted correctly.'
return

# initialize s2
s2_sum = np.zeros([1, numRes])

for i in range(blockNum):
hC = h_all[i*numRes*blockSize:(i+1)*numRes*blockSize, :]
nC = n_all[i*numRes*blockSize:(i+1)*numRes*blockSize, :]

# Calculate the bond vector orientations over the trajectory
hnC = hC[:,1:] - nC[:,1:]

# residue index
resNum = hC[0:numRes, 0]

# Construct matrix m
mMat = np.zeros([numRes, numRes])

#print numRes, numSnapshot, blockNum, blockSize

for a in range(0, numRes*blockSize, numRes):
# N-H vectors for the current snapshot
hnTemp = hnC[a:a+numRes, :]
# normalize the vectors
for b in range(numRes):
hnTemp[b,:] = hnTemp[b,:] / np.linalg.norm(hnTemp[b,:])

# Construct Rank 2 Legendre polynomial
c = np.dot(hnTemp, hnTemp.T)
mMat = mMat + (3*np.multiply(c, c)-1)/2

# Ensemble averaging
mMat = mMat / blockSize
#print np.shape(hnTemp), np.shape(hnTemp.T), np.shape(c), np.shape(mMat)

# Diagonalize matrix
dVals, v = np.linalg.eig(mMat)
Ind = dVals.argsort()[::-1] # sort eigenvalues in descending order
dSort = dVals[Ind]
eigVal = np.diag(dSort)
eigVec = v[:, Ind]

# Calculate the squared order parameters
s2_block = np.zeros(numRes)
for b in range(numRes):
sumOverModes = 0;
for a in range(5,numRes):
sumOverModes += eigVal[a,a] * (eigVec[b,a])**2
s2_block[b] = 1 - sumOverModes
s2_sum += s2_block

s2 = s2_sum / blockNum

# output
out = np.concatenate(([resNum], s2), axis = 0)
with open('ired_s2_1vec_%dblock.out' %(block), 'wb') as f:
np.savetxt(f, np.transpose(out), fmt='%i %.3f')

if __name__ == '__main__':
parser = setupParserOptions()
if len(sys.argv) <2:
parser.print_help()
sys.exit()

options, args=parser.parse_args()
print "**************************************************\nMD Block-averaged iRED S2 Calculation"
print "Input coordinate file: %s"%(options.coor1)
print "Input coordinate file: %s"%(options.coor2)
print "Number of MD block(s): %s"%(options.block)

f1 = options.coor1
f2 = options.coor2
try:
bn = int(options.block)
except ValueError:
print "Error: Number of block should be an integer."

ired(f1, f2, bn)

#Python script will output a .out file that contains the order parameter values for each amino acid residue.

IRed Analysis of MD Simulations

2021-05-14T16:46:21Z

Tessa17: Created page with "Calculating order parameters from MD Simulations The analysis utilizes iRed software provided by the Dr. Rafael Bruschweiler Group. All iRed calculations were completed on th..."

Calculating order parameters from MD Simulations

The analysis utilizes iRed software provided by the Dr. Rafael Bruschweiler Group.
All iRed calculations were completed on the HCC cluster.
#Create a pdb file of the trajectory in the same manner as the .xtc file.
#After the pdb file is created (will be very large), use the following scripts to extract the N and H coordinates for each atom at each time point in the trajectory
##awk ‘{if (($3 == “N”) && ($4 != “PRO”)) {print $6, $7, $8, $9:}} xxx.pdb > N-HCoor.dat
## awk ‘{if (($3 == “H”) && ($4 != “H1”)) {print $6, $7, $8, $9:}} xxx.pdb > H-NCoor.dat
#Once .dat files are created, use the python script below to run the iRed calculation
##In command line, run “ired_1vec_block.py --coor1 N-HCoor.dat --coor2 H-NCoor.dat --block 100

! /usr/bin/env python

from __future__ import division
import numpy as np
from optparse import OptionParser
import sys

def setupParserOptions():
parser=OptionParser()
parser.add_option('--coor1', dest='coor1',default='H-NCoor.dat',help = "Input coordinate file 1")
parser.add_option('--coor2', dest='coor2',default='N-HCoor.dat',help = "Input coordinate file 2")
parser.add_option('--block', dest='block', default = 1, help = 'Number of blocks')
return parser

def ired(hCoor_file, nCoor_file, block):
try:
h_all = np.loadtxt(hCoor_file)
except IOError:
print 'cannot open ', hCoor_file
try:
n_all = np.loadtxt(nCoor_file)
except IOError:
print 'cannot open ', nCoor_file

numLines = len(h_all)
numRes = len(set(h_all[:,0]))
numSnapshot = numLines // numRes
blockNum = int(block)
blockSize = numSnapshot // blockNum

if numLines != len(n_all):
print 'Error: The two coordinate files do not have same length.'
return
if np.mod(numLines, numRes) != 0:
print 'Error: Coordinate files do not formatted correctly.'
return

# initialize s2
s2_sum = np.zeros([1, numRes])

for i in range(blockNum):
hC = h_all[i*numRes*blockSize:(i+1)*numRes*blockSize, :]
nC = n_all[i*numRes*blockSize:(i+1)*numRes*blockSize, :]

# Calculate the bond vector orientations over the trajectory
hnC = hC[:,1:] - nC[:,1:]

# residue index
resNum = hC[0:numRes, 0]

# Construct matrix m
mMat = np.zeros([numRes, numRes])

#print numRes, numSnapshot, blockNum, blockSize

for a in range(0, numRes*blockSize, numRes):
# N-H vectors for the current snapshot
hnTemp = hnC[a:a+numRes, :]
# normalize the vectors
for b in range(numRes):
hnTemp[b,:] = hnTemp[b,:] / np.linalg.norm(hnTemp[b,:])

# Construct Rank 2 Legendre polynomial
c = np.dot(hnTemp, hnTemp.T)
mMat = mMat + (3*np.multiply(c, c)-1)/2

# Ensemble averaging
mMat = mMat / blockSize
#print np.shape(hnTemp), np.shape(hnTemp.T), np.shape(c), np.shape(mMat)

# Diagonalize matrix
dVals, v = np.linalg.eig(mMat)
Ind = dVals.argsort()[::-1] # sort eigenvalues in descending order
dSort = dVals[Ind]
eigVal = np.diag(dSort)
eigVec = v[:, Ind]

# Calculate the squared order parameters
s2_block = np.zeros(numRes)
for b in range(numRes):
sumOverModes = 0;
for a in range(5,numRes):
sumOverModes += eigVal[a,a] * (eigVec[b,a])**2
s2_block[b] = 1 - sumOverModes
s2_sum += s2_block

s2 = s2_sum / blockNum

# output
out = np.concatenate(([resNum], s2), axis = 0)
with open('ired_s2_1vec_%dblock.out' %(block), 'wb') as f:
np.savetxt(f, np.transpose(out), fmt='%i %.3f')

if __name__ == '__main__':
parser = setupParserOptions()
if len(sys.argv) <2:
parser.print_help()
sys.exit()

options, args=parser.parse_args()
print "**************************************************\nMD Block-averaged iRED S2 Calculation"
print "Input coordinate file: %s"%(options.coor1)
print "Input coordinate file: %s"%(options.coor2)
print "Number of MD block(s): %s"%(options.block)

f1 = options.coor1
f2 = options.coor2
try:
bn = int(options.block)
except ValueError:
print "Error: Number of block should be an integer."

ired(f1, f2, bn)

#Python script will output a .out file that contains the order parameter values for each amino acid residue.

Category:Protocols

2021-05-14T16:31:53Z

Tessa17:

''General Maintenance''
*[[Changing the high pressure dewar]]
*[[Filling a Magnet with Nitrogen]]
*[[Autoclaving Laboratory Glassware and Media]]
*[[Chemical Disinfection of Glassware]]
*[[Requesting Balance Calibration]]
*[[Requesting Pipette Calibration]]
*[[Using the UV-Vis]]
*[[Using and Maintaining pH Meter]]
*[[-80 Freezer Storage and Maintenance]]
*[[Freeze Dryer Maintenance]]
*[[Lab Notebook Guidelines]]
*[[Sample Barcoding]]

''Protein Preparation''
*[[Buffer Exchange and Solution Concentration]]
*[[Finding a Protein Target on the NESG website]]
*[[Choosing a Plasmid]]
*[[Plasmid Purification and Transformation Protocol]]
*[[Creating Stock Cultures of Bacteria]]
*[[Luria-Bertani Media]]
*[[M9 Minimal Media]]
*[[Protein Overexpression and Extraction]]
*[[SDS-PAGE Protocol]]
*[[Running a Cobalt Affinity Column]]
*[[Dialysis]]
*[[Centrifugal Protein Concentration and Buffer Exchange]]
*[[Using the Stirred Cell Concentrator]]

''Data Collection''
*[[Gap Sampling]]
*[[Water Suppression with presaturation pulses (zgpr/zgcppr]]
*[[Non-uniform Sampling]]
*[[Collecting a 15N Edited HSQC]]
*[[Collecting CEST Data]]

''Data Processing and Analysis''
*[[Analysis of 1D Line-Broadening Screen]]
*[[FastModelFree]]
*[[2D NMR Analysis (CCPNMR)]]
*[[1H NMR Analysis (SIMCA)]]
*[[1H NMR Analysis (ACDLab)]]
*[[Processing CEST Data]]
*[[Titration Data Analysis in nmrPipe]]
*[[Non-Uniform Sampling]]
*[[Chara]]
*[[2D NMR Processing in Linux and Windows]]
*[[2D Metabolomics NMRPipe Processing]]
*[[1D NMR Processing in Linux and Windows Example Script]]
*[[NMR Batch Correction Example Script]]
*[[PCA Classify Example Script]]
*[[Sample Collection and Processing for Protein Backbone Assignments]]
*[[Example Scripts for NMRPipe Processing]]

''Miscellaneous''
*[[Agarose Gel]]
*[[700 MHz NMR checklist]]
*[[500 MHz NMR checklist]]
*[[1D Macro]]
*[[Setting Up a Virtual Screen with AutoDock]]
*[[Simple Protein Crosslinking]]
*[[1D NMR Titrations]]
*[[Setting Up & Running MD Simulations]]
*[[Analyzing MD Simulations]]
*[[iRed Analysis of MD Simulations]]

Cell Culturing
*[[Cell Culturing Dr. Franco Lab]]

''Metabolomics''
*[[Metabolite Extraction]]
*[[MetPa for metabolomics]]
*[[Making Heatmaps]]
*[[One way ANOVA in R]]
*[[P-Value adjustment for multiple comparisons]]
*[[PCA-Utils]]
*[[NMR Tube Deep Cleaning]]
*[[Noise Removal for PCA]]
*[[Weighted Linear Least Squares]]
*[[Serum Preparation for 1D NMR]]
*[[Whole Blood Preparation for 1D NMR]]
*[[Urine Preparation for 1D NMR]]
*[[Cell Culture Preparation for 1D NMR]]
*[[LC-MS metabolomics guide-CIBC collaborations]]

''Demos''
*[[Peroxide Clock]]
*[[Traffic Light Reaction]]
*[[Orange Juice Clock]]
*[[Gummy Bear Freeze]]
*[[Lava Lamps]]
*[[Women in Science: Checklist]]
*[[Maxey Day: Checklist]]

Analyzing MD Simulations

2021-05-14T16:30:36Z

Tessa17: Created page with "Adapted using tutorial from "http://www.mdtutorials.com/gmx/lysozyme/index.html" All simulation analysis is done using the HCC cluster. # Once the simulation is done runnin..."

Adapted using tutorial from "http://www.mdtutorials.com/gmx/lysozyme/index.html"

All simulation analysis is done using the HCC cluster.

# Once the simulation is done running, the first step is to convert the trajectory. Do this by running “gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -center”.
## The -pbc flag corrects for periodicity and may need to be changed based on specific protein simulations. Instructions for changing this flag can be found in the GROMACS manual (https://manual.gromacs.org/2020/manual-2020.pdf).
# Once the .xtc file is created, many different analyses can be completed using the same general commands. The GROMACS manual is the best place to find useful commands, as well as a list of analyses that can be completed.
# Several of the most common analyses are RMSD, radius of gyration and solvent accessible surface area (SASA). The commands for these analyses are below.

RMSD
# Run the command “gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns”, making sure that input files -s and -f match exactly the naming conventions you used previously. Input “4” and “4” when prompted.
## Outputs RMSD values in ns for the duration of the simulation.

Radius of Gyration
# Run the command “gmx gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg”. Input “1” when prompted.
## Outputs radius of gyration values in ps for the duration of the simulation.

SASA
# Run the command “gmx sasa -s md_0_1.tpr -f traj1.xtc -tu ns -o sasa.xvg”, inputing “1” when prompted.
## Outputs SASA values in ns for the duration of the simulation.

Setting Up & Running MD Simulations

2021-05-14T16:30:02Z

Tessa17: Created page with "Adapted using tutorial from "http://www.mdtutorials.com/gmx/lysozyme/index.html" All simulation parameterization is done using the HCC cluster. # Download required PDB file..."

Adapted using tutorial from "http://www.mdtutorials.com/gmx/lysozyme/index.html"

All simulation parameterization is done using the HCC cluster.

# Download required PDB file from "https://www.rcsb.org/"
# Upload PDB file to desired folder on HCC cluster.
# In a terminal or command line, navigate to the working folder you added the PDB file to.
# Use "grep -v HOH prot.pdb > prot_clean.pdb to remove water from crystal structures.
## If PDB structure has other atoms, such as SO4, ligands or PO4, run this command again, replacing HOH with other atom.
## This can also be accomplished by removing the HOH lines in the PDB file using vi
# Run the command "gmx pdb2gmx -f prot_clean.pdb -o prot_processed.gro -water spce"
## This step will prompt you to chose a force field. A commonly used field is AMBER99SB
## This will convert the pdb file into a file that GROMACS can use
# Solvate the system by running "gmx editconf -f prot_processed.gro -o prot_newbox.gro -c -d 1.0 -bt cubic" and "gmx solvate -cp prot_newbox.gro -cs spc216.gro -o prot_solv.gro -p topol.top"
## These commands define a 1nm box around the protein, and then fill that box with water molecules
# At this point, it is beneficial to create the mdp files that GROMACS will use to run the simulations. These can be found at "http://www.mdtutorials.com/gmx/lysozyme/Files/"
# Next, you want to add counter-ions to the solvent. Run the commands "gmx grompp -f ions.mdp -c prot_solv.gro -p topol.top -o ions.tpr" and "gmx genion -s ions.tpr -o prot_solv_ions.gro -p topol.top -pname NA -nname CL -neutral"
## To run at physiological salt conditions, add the "-conc 0.1" flag before -pname
# Once solvent and ions are added, the system is ready for minimization. Edit "minim.mdp" to the desired number of steps (50,000 is fairly standard for this step). Run "gmx grompp -f minim.mdp -c prot_solv_ions.gro -p topol.top -o em.tpr" and gmx mdrun -v -deffnm em".
## Once minimization is complete, run command "gmx energy -f em.edr -o potential.xvg", inputting "10 0" when prompted and open .xvg file to check plot. Plot should show steady convergence of Epot.
# The next step is to equilibrate the temperature of the system. Edit the nvt.mdp file to run for 100ps by changing nsteps to 50,000. The reference temperature you want to run the simulation at can also be edited here by changing ref_t.
## Run commands "gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr" and "gmx mdrun -deffnm nvt". THE EQUILIBRATOIN MAY TAKE A FEW HOURS
## Plot these results using "gmx energy -f nvt.edr -o temperature.xvg" inputting "16 0" when prompted
## If temperature doesn't remain stable at the target temperature, a longer equilibration is necessary.
# Next, equilibrate the density of the system. Edit the npt.mdp as you did the nvt.mdp.
## Run commands "gmx grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr" and "gmx mdrun -deffnm npt" THE EQUILIBRATOIN MAY TAKE A FEW HOURS
## Plot results using "gmx energy -f npt.edr -o pressure.xvg" inputting "18 0" when prompted.
# The system is now ready for the production simulation. Edit the md.mdp to run for the desired length (500,000 steps is a 1ns simulation). Don't forget to edit the reference temperature.
## Run commands "gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr" and "gmx mdrun -deffnm md_0_1"
## However, longer runs will need to run using GPU cores. To do this, you must submit a slurm job to HCC. An example script is shown below.
#!/bin/sh
#SBATCH --time=168:00:00 # walltime limit (HH:MM:SS)
#SBATCH --nodes=3 # number of nodes
#SBATCH --ntasks-per-node=32 # 16 processor core(s) per node
#SBATCH --mem=32G # maximm memory per node
#SBATCH --gres=gpu:1
#SBATCH --partition=gpu # gpu node(s
#SBATCH --error=/work/powers/tessajoy17/SO237_2Pro/md.err
cd /work/powers/tessajoy17/SO237_2Pro
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr
gmx mdrun -deffnm md_0_1 -g md.log -x traj_comp.xtc -e ener.edr -nb gpu -cpi md_0_1.cpt -v
hostname
sleep 60

Category:Protocols

2021-01-07T17:39:34Z

Tessa17:

''General Maintenance''
*[[Changing the high pressure dewar]]
*[[Filling a Magnet with Nitrogen]]
*[[Autoclaving Laboratory Glassware and Media]]
*[[Chemical Disinfection of Glassware]]
*[[Requesting Balance Calibration]]
*[[Requesting Pipette Calibration]]
*[[Using the UV-Vis]]
*[[Using and Maintaining pH Meter]]
*[[-80 Freezer Storage and Maintenance]]
*[[Freeze Dryer Maintenance]]
*[[Lab Notebook Guidelines]]
*[[Sample Barcoding]]

''Protein Preparation''
*[[Buffer Exchange and Solution Concentration]]
*[[Finding a Protein Target on the NESG website]]
*[[Choosing a Plasmid]]
*[[Plasmid Purification and Transformation Protocol]]
*[[Creating Stock Cultures of Bacteria]]
*[[Luria-Bertani Media]]
*[[M9 Minimal Media]]
*[[Protein Overexpression and Extraction]]
*[[SDS-PAGE Protocol]]
*[[Running a Cobalt Affinity Column]]
*[[Dialysis]]
*[[Centrifugal Protein Concentration and Buffer Exchange]]
*[[Using the Stirred Cell Concentrator]]

''Data Collection''
*[[Gap Sampling]]
*[[Water Suppression with presaturation pulses (zgpr/zgcppr]]
*[[Non-uniform Sampling]]
*[[Collecting a 15N Edited HSQC]]
*[[Collecting CEST Data]]

''Data Processing and Analysis''
*[[Analysis of 1D Line-Broadening Screen]]
*[[FastModelFree]]
*[[2D NMR Analysis (CCPNMR)]]
*[[1H NMR Analysis (SIMCA)]]
*[[1H NMR Analysis (ACDLab)]]
*[[Processing CEST Data]]
*[[Titration Data Analysis in nmrPipe]]
*[[Non-Uniform Sampling]]
*[[NMRFAM-SPARKY Guide]]
*[[NMRFAM-SPARKY: Automated Peak Assignment]]
*[[2D NMR Processing in Linux and Windows]]
*[[2D Metabolomics NMRPipe Processing]]
*[[1D NMR Processing in Linux and Windows Example Script]]
*[[NMR Batch Correction Example Script]]
*[[PCA Classify Example Script]]
*[[Sample Collection and Processing for Protein Backbone Assignments]]
*[[Example Scripts for NMRPipe Processing]]

''Miscellaneous''
*[[Agarose Gel]]
*[[700 MHz NMR checklist]]
*[[500 MHz NMR checklist]]
*[[1D Macro]]
*[[Setting Up a Virtual Screen with AutoDock]]
*[[Simple Protein Crosslinking]]
*[[1D NMR Titrations]]
*[[Setting Up & Running MD Simulations]]
*[[Analyzing MD Simulations]]

Cell Culturing
*[[Cell Culturing Dr. Franco Lab]]

''Metabolomics''
*[[Metabolite Extraction]]
*[[MetPa for metabolomics]]
*[[Making Heatmaps]]
*[[One way ANOVA in R]]
*[[P-Value adjustment for multiple comparisons]]
*[[PCA-Utils]]
*[[NMR Tube Deep Cleaning]]
*[[Noise Removal for PCA]]
*[[Weighted Linear Least Squares]]
*[[Serum Preparation for 1D NMR]]
*[[Whole Blood Preparation for 1D NMR]]
*[[Urine Preparation for 1D NMR]]
*[[Cell Culture Preparation for 1D NMR]]
*[[LC-MS metabolomics guide-CIBC collaborations]]

''Safety and Inspections''
*[[Lab Responsibilities]]
*[[Inspection Checklist]]
*[[Safety Contacts, Resources]]

''Demos''
*[[Peroxide Clock]]
*[[Traffic Light Reaction]]
*[[Orange Juice Clock]]
*[[Gummy Bear Freeze]]
*[[Lava Lamps]]
*[[Batteries]]
*[[Rocket Launcher]]
*[[Women in Science: Checklist]]
*[[Maxey Day: Checklist]]

Category:Protocols

2021-01-07T15:47:37Z

Tessa17:

''General Maintenance''
*[[Changing the high pressure dewar]]
*[[Filling a Magnet with Nitrogen]]
*[[Autoclaving Laboratory Glassware and Media]]
*[[Chemical Disinfection of Glassware]]
*[[Requesting Balance Calibration]]
*[[Requesting Pipette Calibration]]
*[[Using the UV-Vis]]
*[[Using and Maintaining pH Meter]]
*[[-80 Freezer Storage and Maintenance]]
*[[Freeze Dryer Maintenance]]
*[[Lab Notebook Guidelines]]
*[[Sample Barcoding]]

''Protein Preparation''
*[[Buffer Exchange and Solution Concentration]]
*[[Finding a Protein Target on the NESG website]]
*[[Choosing a Plasmid]]
*[[Plasmid Purification and Transformation Protocol]]
*[[Creating Stock Cultures of Bacteria]]
*[[Luria-Bertani Media]]
*[[M9 Minimal Media]]
*[[Protein Overexpression and Extraction]]
*[[SDS-PAGE Protocol]]
*[[Running a Cobalt Affinity Column]]
*[[Dialysis]]
*[[Centrifugal Protein Concentration and Buffer Exchange]]
*[[Using the Stirred Cell Concentrator]]

''Data Collection''
*[[Gap Sampling]]
*[[Water Suppression with presaturation pulses (zgpr/zgcppr]]
*[[Non-uniform Sampling]]
*[[Collecting a 15N Edited HSQC]]
*[[Collecting CEST Data]]

''Data Processing and Analysis''
*[[Analysis of 1D Line-Broadening Screen]]
*[[FastModelFree]]
*[[2D NMR Analysis (CCPNMR)]]
*[[1H NMR Analysis (SIMCA)]]
*[[1H NMR Analysis (ACDLab)]]
*[[Processing CEST Data]]
*[[Titration Data Analysis in nmrPipe]]
*[[Non-Uniform Sampling]]
*[[NMRFAM-SPARKY Guide]]
*[[NMRFAM-SPARKY: Automated Peak Assignment]]
*[[2D NMR Processing in Linux and Windows]]
*[[2D Metabolomics NMRPipe Processing]]
*[[1D NMR Processing in Linux and Windows Example Script]]
*[[Sample Collection and Processing for Protein Backbone Assignments]]
*[[Example Scripts for NMRPipe Processing]]

''Miscellaneous''
*[[Agarose Gel]]
*[[700 MHz NMR checklist]]
*[[500 MHz NMR checklist]]
*[[1D Macro]]
*[[Setting Up a Virtual Screen with AutoDock]]
*[[Simple Protein Crosslinking]]
*[[1D NMR Titrations]]
*[[Setting Up & Running MD Simulations]]

Cell Culturing
*[[Cell Culturing Dr. Franco Lab]]

''Metabolomics''
*[[Metabolite Extraction]]
*[[MetPa for metabolomics]]
*[[Making Heatmaps]]
*[[One way ANOVA in R]]
*[[P-Value adjustment for multiple comparisons]]
*[[PCA-Utils]]
*[[NMR Tube Deep Cleaning]]
*[[Noise Removal for PCA]]
*[[Weighted Linear Least Squares]]
*[[Serum Preparation for 1D NMR]]
*[[Whole Blood Preparation for 1D NMR]]
*[[Urine Preparation for 1D NMR]]
*[[Cell Culture Preparation for 1D NMR]]
*[[LC-MS metabolomics guide-CIBC collaborations]]

''Safety and Inspections''
*[[Lab Responsibilities]]
*[[Inspection Checklist]]
*[[Safety Contacts, Resources]]

''Demos''
*[[Peroxide Clock]]
*[[Traffic Light Reaction]]
*[[Orange Juice Clock]]
*[[Gummy Bear Freeze]]
*[[Lava Lamps]]
*[[Batteries]]
*[[Rocket Launcher]]
*[[Women in Science: Checklist]]
*[[Maxey Day: Checklist]]

Category:Protocols

2019-08-28T21:36:02Z

Tessa17:

''General Maintenance''
*[[Changing the high pressure dewar]]
*[[Filling a Magnet with Nitrogen]]
*[[Autoclaving Laboratory Glassware and Media]]
*[[Chemical Disinfection of Glassware]]
*[[Requesting Balance Calibration]]
*[[Requesting Pipette Calibration]]
*[[Using the UV-Vis]]
*[[Using and Maintaining pH Meter]]
*[[-80 Freezer Storage and Maintenance]]
*[[Freeze Dryer Maintenance]]

''Protein Preparation''
*[[Buffer Exchange and Solution Concentration]]
*[[Finding a Protein Target on the NESG website]]
*[[Choosing a Plasmid]]
*[[Plasmid Purification and Transformation Protocol]]
*[[Creating Stock Cultures of Bacteria]]
*[[Luria-Bertani Media]]
*[[M9 Minimal Media]]
*[[Protein Overexpression and Extraction]]
*[[SDS-PAGE Protocol]]
*[[Running a Cobalt Affinity Column]]
*[[Dialysis]]
*[[Centrifugal Protein Concentration and Buffer Exchange]]
*[[Using the Stirred Cell Concentrator]]

''Data Collection''
*[[Gap Sampling]]
*[[Water Suppression with presaturation pulses (zgpr/zgcppr]]
*[[Non-uniform Sampling]]
*[[Collecting a 15N Edited HSQC]]
*[[Collecting CEST Data]]

''Data Processing and Analysis''
*[[Analysis of 1D Line-Broadening Screen]]
*[[FastModelFree]]
*[[2D NMR Analysis (CCPNMR)]]
*[[1H NMR Analysis (SIMCA)]]
*[[1H NMR Analysis (ACDLab)]]
*[[Processing CEST Data]]
*[[Titration Data Analysis in nmrPipe]]
*[[Non-Uniform Sampling]]
*[[NMRFAM-SPARKY Guide]]
*[[NMRFAM-SPARKY: Automated Peak Assignment]]
*[[NMR Processing in Linux and Windows]]
*[[Sample Collection and Processing for Protein Backbone Assignments]]
*[[Example Scripts for NMRPipe Processing]]

''Miscellaneous''
*[[Agarose Gel]]
*[[700 MHz NMR checklist]]
*[[500 MHz NMR checklist]]
*[[1D Macro]]
*[[Setting Up a Virtual Screen with AutoDock]]
*[[Simple Protein Crosslinking]]
*[[1D NMR Titrations]]

Cell Culturing
*[[Cell Culturing Dr. Franco Lab]]

''Metabolomics''
*[[MetPa for metabolomics]]
*[[Making Heatmaps]]
*[[Metabolite Extraction]]
*[[One way ANOVA in R]]
*[[P-Value adjustment for multiple comparisons]]
*[[PCA-Utils]]
*[[NMR Tube Deep Cleaning]]
*[[Noise Removal for PCA]]
*[[Weighted Linear Least Squares]]
*[[Serum Preparation for 1D NMR]]
*[[Urine Preparation for 1D NMR]]

''Safety and Inspections''
*[[Lab Responsibilities]]
*[[Inspection Checklist]]
*[[Safety Contacts, Resources]]

''Demos''
*[[Peroxide Clock]]
*[[Traffic Light Reaction]]
*[[Orange Juice Clock]]
*[[Gummy Bear Freeze]]
*[[Batteries]]
*[[Rocket Launcher]]
*[[Women in Science: Checklist]]
*[[Maxey Day: Checklist]]

Protein Software

2017-03-14T15:15:31Z

Tessa17:

Scripts, installation help, and other useful information for using various protein software

[[Category:NMRFAM-Sparky]]

Protein Software

2017-03-14T15:13:50Z

Tessa17:

Scripts, installation help, and other useful information for using various protein software

Protein Software

2017-03-14T15:13:10Z

Tessa17: Created page with "NMRFAM-Sparky NMRPipe"

NMRFAM-Sparky
NMRPipe

Main Page

2017-03-14T15:10:39Z

Tessa17:

'''Welcome to the BioNMR Wiki Page.'''

This wiki exists to provide better access to lab protocols for the Powers lab. It is not a replacement for lab notebooks. Feel free to begin documenting new lab protocols or procedures here, or even moving old protocols onto this wiki.

== Getting started ==
For those who need a quick and dirty introduction to MediaWiki formatting, try this reference card:
* [http://bionmr.unl.edu/w/MediaWikiRefCard.pdf MediaWiki Reference Card]

Other general MediaWiki information pages:
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]

=== Wiki Categories ===

[[Special:Categories|View All Categories]]

Commonly used categories:

* [[:Category:Protocols|Protocols]]
* [[:Category:Bioscreen|Bioscreen]]
* [[:Category:FAST-NMR|FAST-NMR]]
* [[:Category:Molecular Docking|Molecular Docking]]
* [[:Category:Metabolomics|Metabolomics]]
* [[:Category:Maxey Demos|Maxey Demos]]
* [[:Category:Protein expression|Protein expression]]
* [[:Category:SMACMS|SMACMS]]
* [[:Category:Lab Safety | Lab Safety]]
* [[:Category:Cell culture | culture and passage cells]]
* [[:Protein Software]]

And, very likely, an unpopular category:
* [[:Category:Sysadmin | System Administration]]

Main Page

2015-08-11T20:36:24Z

Tessa17:

'''Welcome to the BioNMR Wiki Page.'''

This wiki exists to provide better access to lab protocols for the Powers lab. It is not a replacement for lab notebooks. Feel free to begin documenting new lab protocols or procedures here, or even moving old protocols onto this wiki.

== Getting started ==
For those who need a quick and dirty introduction to MediaWiki formatting, try this reference card:
* [http://bionmr.unl.edu/w/MediaWikiRefCard.pdf MediaWiki Reference Card]

Other general MediaWiki information pages:
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]

=== Wiki Categories ===

[[Special:Categories|View All Categories]]

Commonly used categories:

* [[:Category:Protocols|Protocols]]
* [[:Category:Bioscreen|Bioscreen]]
* [[:Category:FAST-NMR|FAST-NMR]]
* [[:Category:Molecular Docking|Molecular Docking]]
* [[:Category:Metabolomics|Metabolomics]]
* [[:Category:Maxey Demos|Maxey Demos]]
* [[:Category:Protein expression|Protein expression]]
* [[:Category:SMACMS|SMACMS]]
* [[:Category:Lab Safety | Lab Safety]]
* [[:Category:Cell culture | culture and passage cells]]

And, very likely, an unpopular category:
* [[:Category:Sysadmin | System Administration]]