Laboratory 3 Molecular Dynamics Analysis and Small Peptides

Argon and TRP-Cage Analysis

Today we will analyze all those long trajectories that we set up to run last week. We will also simulate another water box and a small solvated peptide.

1. Transfer the data from the long Argon runs onto your local computer. Each group should have unique data at different temperatures.
2. Load the trajectories into VMD as we have done before.
3. Calculate the RDF. Make sure you set the max R setting to 20.0
4. Save the rdf to a file as ARGON___.dat replacing the underscores with the simulation temperature. The temperature is found in the namd.conf file.
5. Find some friends and compare the RDFs. What are your observations? Send the .dat files to Riley

We are also going to simulate a small protein called the TRP-Cage. The necessary files have been provided in the directory TRP-Cage

1. Run the job, transfer the data to your local computer, and load the trajectory into VMD. (You should be getting good at this now!)
2. To make things easier to visualize go to “Graphics → Representations”
3. For selected atoms type ions. Change this representation’s drawing method to VDW.
4. Click Create Rep and for selected atoms type Backbone. Change this representation’s drawing method to Ribbon.
5. Click Create Rep and for selected atoms type Water. Change this representation’s drawing method to Line.
6. A way to track if a simulation has equilibrated is to look at how much the structure of the protein has changed since the beginning of the simulation. This is done by aligning the center of mass for the protein and calculating the root mean squared displacement (RMSD) of each backbone atom. Usually the RMSD rise quickly at the start of the simulation as a protein relaxes and plateaus once the system is equilibrated.
7. Go to analysis in VMD and select the “RMSD trajectory” tool. Click align and calculate. Then save the data using the drop down in the top left. Plot this in excel.
8. Now calculate two RDFs: the first between ions and type OT, and the second between backbone and type OT. The first is the structure of water around the ions and the second around the protein.

Simulation of a protein

Your turn! So far we’ve given you most things that you need to run a simulation. Now that you are experts in submitting jobs and analyzing the output, let’s take some time to see what goes into making these input files. First off, choose a peptide that you worked with in your last module. Coordinate with your friends so that everyone does a different peptide. For the following steps, I'm going to proceed as if I am preparing a gly-gly-ala (gga). Modify it appropriately for your peptide.Here is the NAMD documentation on this.

1. Build your peptide in Avogadro, then save it as a PDB.
2. Go ahead and put it somewhere convenient on your local computer.
3. Open up the file in VMD to view it
4. Open the Tk Console under the Extensions menu
5. In TkConsole, change directory to wherever you put your .pdb file.
6. In TkConsole, set a variable gga to store only the first peptide conformation:
   
   

   set gga [atomselect top protein frame 0]

7. Write a new pdb file saving only the protein (no NH2 will be saved) of the first frame
   
   

   $gga writepdb gga.pdb

8. Load your saved gga.pdb structure into VMD using the File → New Molecule menu.
9. Right-click on gga.pdb to remove it from the list of loaded molecules

1. Recall that one of the files that NAMD requires is a protein structure file (psf). VMD will generate one of these for us.
2. Open the automatic psf builder under Extensions → Modeling → Automatic PSF Builder
   • Change the basename to anything you like. gga_autopsf might be a good choice
   • Leave the default topology files
   • Click Load input files
   • Click Guess and split
   • Click create chains. (A message may pop up... this is fine.)
   • Click OK
3. VMD should automatically load your new file. If not load them using File → New Molecule. Remember to load the psf file first, followed by the pdb.
4. When the psf was generated, VMD added hydrogen to all of the amino acids. Hydrogens are not present in x-ray crystal structures because they are smaller than x-ray wavelengths and the single electron does not interact with x-rays

1. We want to encapsulate our protein in a sphere of water. Do do this, we first need to download the file wat_sphere.tcl and put it into your working directory
2. In TkConsole type
   
   

   source wat_sphere.tcl
                               
   addsphere gga_autopsf

3. You should see output in the console with center of mass and radius values. Copy these down -- they'll be important later.
4. Load the psf then pdb files (gga_autopsf_ws). You should see your protein surrounded by a minimal water sphere

1. Log on to your computer and make a new directory, call it whatever you like.... "lab3" might be nice. Within this file, make another directory. Call it whatever you like.
2. Download the configuration file from blackboard. Put this file (gga.conf) as well as the psf and pdb files you created into this directory. Also download the topology zip. After downloading it onto your local machine, unzip it, and put the whole file into the lab3 directory (not the solvated directory)
3. There are a few parameters to modify in the configuration file:
   • structure: this should be whatever you called your psf file
   • coordinates: this should be whatever you called your pdb file
   • parameters: ../topology/par_all27_prot_lipid.inp
   • Set temperature: leave it at 280 for now.
   • Under the heading "EXTRA PARAMETERS" there are five commented lines. Uncomment these and change the values from:
     sphericalBCcenter 30.3081743413, 28.8049907121, 15.353994423
     to your center of sphere coordinates (from the numbers you took note of above)
     and
     sphericalBCr1 26.0
     to the correct radius (from the numbers you took note of above)
   • Minimization: 1000
   • run: 2500
4. Copy one of your old .pbs submission scripts from one of your old jobs into your working directory. This file will need a few modifications as well.
   • The line beginning "export WD=" is followed by the location of your working directory. Change this to match your new working directory
   • The line "export input=namd.conf" will need to be updated to your new .conf file name.
   • The line beginning "export output=" will need to be updated with a new output logfile name.
   • At the top, there is a line containing nodes=1:ppn=8... make sure it is ppn=8 and not ppn=1.
5. Submit the job just as you have done in the past! Take note of the time when you submit it.
6. Let the job go a little while then check in on the output. How long has it been running? How many steps has it taken? Estimate how long (wallclock time) it will take to finish the calculation. Can you adjust the calculation so that it run for about three hours before completion? Kill the job, and make this modification to the number of run steps in your configuration file.
7. At this point you may want to finish the next step. Then return and submit this one right before you leave for the day.

1. Repeat all of the above, except the solvation step to create a protein in vacuum.
   • For this simulation, leave the five "EXTRA PARAMETERS" lines in the configuration file commented. (i.e. Leave the # in front of those lines so that NAMD doesn't read them)
   • Adjust the number of run steps you used for your solvated protein to match the number of run steps in this protein in vacuo. (It won't take as long for this one to complete)