Recent changes to Complex Formation Tutorial

Complex Formation Tutorial modified by Ramneek

Ramneek — Wed, 26 Mar 2014 15:47:08 -0000

--- v9
+++ v10
@@ -1,11 +1,8 @@
-Welcome to the 2nd tutorial of eSBMTools. In this tutorial we'll see how to
-merge 2 proteins and simulate the resulting complex formed. This example merges
-the proteins '1IXM' & '1PEY' to form the protein '1F51'.
+Welcome to the 2nd tutorial of eSBMTools. In this tutorial we'll see how to merge 2 proteins and simulate the resulting complex formed. This example merges the proteins '1IXM' & '1PEY' to form the protein '1F51'.

 ********************************************************************************

-→ To start the tutorial, first run the python script present in the folder using 
-  the following command:
+→ To start the tutorial, first run the python script present in the folder using the following command:

                $> python buildComplex.py

@@ -16,14 +13,11 @@
            -startComplex.gro       -startComplex.top
                -startComplexContacts.top

-→ The next step is to use a custom script to generate a .mdp file for the
-  simulation. To do this, create a new file and copy the following code (which
-  can also be found in workflow.py from the previous example) into the
-  file:
+→ The next step is to use a custom script to generate a .mdp file for the simulation. To do this, create
+  a new file and copy the following code (which can also be found in workflow.py from the previous
+  example) into the file:

-**NOTE** If you are copying the code from workflow.py, make sure you call the
-createDefaultMdp() without any arguments. The default argument for this function
-is the one required for this example.
+**NOTE** If you are copying the code from workflow.py, make sure you call the createDefaultMdp() without any arguments. The default argument for this function is the one required for this example.

 **Code Start**

@@ -33,8 +27,8 @@

      path = os.getcwd() + '/'

-     #we need a file that sets all the parameters of the simulation, this is the mdp
-     #file, in esbm tools we use a dictionary syntax for this
+     #we need a file that sets all the parameters of the simulation, this is the mdp file, in esbm tools
+     #we use a dictionary syntax for this
      mdpDict = MdpFile.createDefaultMdp()

      #change the dictionary entries
@@ -47,24 +41,19 @@

 **Code End**

-  You can name this file custom.py (or anything else you want) and run this
-  script using the following command in the terminal:
+  You can name this file custom.py (or anything else you want) and run this script using the following
+  command in the terminal:

                $> python custom.py

   This will then create the required .mdp file for this simulation.

-**NOTE** Do not copy the MDP file from workflow.py as it contains the graining
-type set to C-alpha instead of All-Atom.
+**NOTE** Do not copy the MDP file from workflow.py as it contains the graining type set to C-alpha instead of All-Atom.

-→ Now that we have the files ready, we can run the simulation as normal. The
-  steps to be followed are exactly the same as in the previous example:
+→ Now that we have the files ready, we can run the simulation as normal. The steps to be followed are
+  exactly the same as in the previous example:

-
-
-
-**NOTE** Replace startxx with the file of your choice. The
-startComplexContacts.top can be used with startComplex.gro
+**NOTE** Replace startxx with the file of your choice. The startComplexContacts.top can be used with startComplex.gro

 → Run the GROMACS preprocessor with the following command:

@@ -83,7 +72,7 @@
                -traj.trr
                -traj.xtc

-→ If all goes well, this is what your trajectory should look like (in PyMol):
+→ If all goes well, this is what your trajectory should look like (in PyMol after coloring, etc.):

 ![Unrotated Protein](https://sourceforge.net/p/esbmtools/wiki/Complex%20Formation%20Tutorial/attachment/sc1.png)

Complex Formation Tutorial modified by Ramneek

Ramneek — Wed, 26 Mar 2014 15:16:06 -0000

Complex Formation Tutorial modified by Ramneek

Ramneek — Fri, 21 Mar 2014 13:59:11 -0000

--- v7
+++ v8
@@ -85,11 +85,11 @@

 → If all goes well, this is what your trajectory should look like (in PyMol):

-![Unrotated Protein](https://sourceforge.net/p/esbmtools/wiki/Complex%20Formation%20Tutorial/attachment/sc1.png)
+![Unrotated Protein](https://sourceforge.net/p/esbmtools/wiki/Complex%20Formation%20Tutorial/attachment/sc1.png)

   And rotating it, we can see the whole structure:

-![Rotated Protein](https://sourceforge.net/p/esbmtools/wiki/Complex%20Formation%20Tutorial/attachment/rot.png)
+![Rotated Protein](https://sourceforge.net/p/esbmtools/wiki/Complex%20Formation%20Tutorial/attachment/rot.png)

 ********************************************************************************

Complex Formation Tutorial modified by Ramneek

Ramneek — Thu, 20 Mar 2014 15:12:07 -0000

Complex Formation Tutorial modified by Ramneek

Ramneek — Thu, 20 Mar 2014 13:53:26 -0000

--- v5
+++ v6
@@ -85,11 +85,11 @@

 → If all goes well, this is what your trajectory should look like (in PyMol):

-!(https://sourceforge.net/p/esbmtools/wiki/Complex%20Formation%20Tutorial/attachment/sc1.png)
+![Unrotated Protein](https://sourceforge.net/p/esbmtools/wiki/Complex%20Formation%20Tutorial/attachment/sc1.png)

   And rotating it, we can see the whole structure:

-!(https://sourceforge.net/p/esbmtools/wiki/Complex%20Formation%20Tutorial/attachment/rot.png)
+![Rotated Protein](https://sourceforge.net/p/esbmtools/wiki/Complex%20Formation%20Tutorial/attachment/rot.png)

 ********************************************************************************

Complex Formation Tutorial modified by Ramneek

Ramneek — Thu, 20 Mar 2014 13:52:35 -0000

--- v4
+++ v5
@@ -83,6 +83,14 @@
                -traj.trr
                -traj.xtc

+→ If all goes well, this is what your trajectory should look like (in PyMol):
+
+!(https://sourceforge.net/p/esbmtools/wiki/Complex%20Formation%20Tutorial/attachment/sc1.png)
+
+  And rotating it, we can see the whole structure:
+
+!(https://sourceforge.net/p/esbmtools/wiki/Complex%20Formation%20Tutorial/attachment/rot.png)
+
 ********************************************************************************

 To understand the functions used in these files, view the Functions wiki.

Complex Formation Tutorial modified by Ramneek

Ramneek — Thu, 20 Mar 2014 13:50:10 -0000

Complex Formation Tutorial modified by Ramneek

Ramneek — Thu, 20 Mar 2014 13:26:35 -0000

--- v2
+++ v3
@@ -85,7 +85,6 @@

 ********************************************************************************

-To understand the functions used in these files, view the Functions wiki
-file.
+To understand the functions used in these files, view the Functions wiki.

 Cheers!

Complex Formation Tutorial modified by Ramneek

Ramneek — Wed, 19 Mar 2014 15:26:21 -0000

--- v1
+++ v2
@@ -85,7 +85,7 @@

 ********************************************************************************

-To understand the functions used in these files, view the Functionality.txt
+To understand the functions used in these files, view the Functions wiki
 file.

 Cheers!

Complex Formation Tutorial modified by Ramneek

Ramneek — Wed, 19 Mar 2014 15:17:58 -0000

Welcome to the 2nd tutorial of eSBMTools. In this tutorial we'll see how to
merge 2 proteins and simulate the resulting complex formed. This example merges
the proteins '1IXM' & '1PEY' to form the protein '1F51'.

→ To start the tutorial, first run the python script present in the folder using
the following command:

            $> python buildComplex.py

This script generates a number of files:

        -start1.gro         -start1.top
        -start2.gro         -start2.top
        -startComplex.gro       -startComplex.top
            -startComplexContacts.top

→ The next step is to use a custom script to generate a .mdp file for the
simulation. To do this, create a new file and copy the following code (which
can also be found in workflow.py from the previous example) into the
file:

NOTE If you are copying the code from workflow.py, make sure you call the
createDefaultMdp() without any arguments. The default argument for this function
is the one required for this example.

Code Start

 import os
 import random
 from eSBMTools import MdpFile

 path = os.getcwd() + '/'

 #we need a file that sets all the parameters of the simulation, this is the mdp
 #file, in esbm tools we use a dictionary syntax for this
 mdpDict = MdpFile.createDefaultMdp()

 #change the dictionary entries
 mdpDict['nsteps'] = 500000
 mdpDict['gen_seed'] = random.random()
 mdpDict['gen_temp'] = 138.0
 mdpDict['ref_t'] = 138.0
 MdpFile.writeMdpFile(path, 'md.mdp', mdpDict)

Code End

You can name this file custom.py (or anything else you want) and run this
script using the following command in the terminal:

            $> python custom.py

This will then create the required .mdp file for this simulation.

NOTE Do not copy the MDP file from workflow.py as it contains the graining
type set to C-alpha instead of All-Atom.

→ Now that we have the files ready, we can run the simulation as normal. The
steps to be followed are exactly the same as in the previous example:

NOTE Replace startxx with the file of your choice. The
startComplexContacts.top can be used with startComplex.gro

→ Run the GROMACS preprocessor with the following command:

    $> grompp -f md.mdp -c startxx.gro -p startxx.top

This will generate the corresponding mdout.mdp and the topol.tpr files.

→ Finally we run the simulation with the mdrun command as follows:

    $> mdrun -c startxx.gro

This then outputs 4 files:

            -ener.edr
            -state.cpt
            -traj.trr
            -traj.xtc

To understand the functions used in these files, view the Functionality.txt
file.

Cheers!