HI 6327 Session 5

1. Lecture: MD Practice II (PDF file)
2. Homework Assignment 2
3. Reading Assignment

Resources and Assignments:

1. Lecture: MD Practice II

You can download the example files used in class from the following links:

• CHARMM19 and CHARMM22 force fields
• Solvate.inp script
• Energy minimization example
• Output files of minimization example

Due at beginning of session 7.

1. Using X-PLOR, generate a PSF file for ALA dipeptide with cis petide bond (using the ALA definition and patch CISP in topallhdg.pro and the peptide linker toph19.pep in the above forcefield files). Submit both the X-PLOR script and the PSF file. Note: you don't need a PDB file for this.
2. Generate a PSF file with a monomeric protein of your choice from the Protein Data Bank, using the chain... coor... statement of X-PLOR. Using a suitable standard topology and parameter file, read in the generated PSF file and the unedited coordinates from the PDB file. Document the error messages (make a list of non-redundant messages and comment what went wrong and what steps might alleviate the errors).
3. Using X-PLOR scripting and the above scripts, delete everything (with the delete statement) except residue numbers 1-30 of segment ID "CHA" from the file "minimized.pdb" generated in the minimization example. Save the new structure (PDB and PSF files). Then embed the structure in a 6 A solvent shell using "solvate.inp" of this session. Energy minimize and then heat to 300K in steps of 30K within 10 picoseconds using a protocol of your choice (Berendsen, velocity rescaling, or Langevin dynamics), using a 1 femtosecond time step and constant dielectric constant, epsilon = 1. Continue with a 20 picosecond "production run" of free Newtonian dynamics (again 1 fs time step) and monitor the temperature (plot temperature as a function of simulation time; for this you need to use UNIX tools like "grep" and "awk" and apply them to the log file. Note: This assignment requires 1-2 days compute time. CHARMM19 and CHARMM22 forcefield files for proteins and TIP3 water can be downloaded above with the other scripts.

On the internet:
X-PLOR site: http://xplor.csb.yale.edu
Online Manual: http://alpha2.bmc.uu.se/local_html/xplor_mirror.html