Research:remd tutorial
Example system: (ala)5 peptide in water
- Get coordinate file and parameter/topology file in Amber format.
/home/yues/amoebapro/helix/ala5-prot/wt6 A quick guide can be seen in http://water.bme.utexas.edu/wiki/index.php/Software:amber#A_Quick_Guide
- Prepare REMD input
/users/jzhen/amoebapro/remd-wt6 Files needed: ala5.inpcrd; temperature.dat;ala5.mdin Run set_remd_input.x to get corresponding inpcrd and mdin at each temperature
- Run REMD
Cmd: /users/jzhen/amoebapro/remd-wt6/run.4.ala5
- Extract trajectories for 298K
Note: before running the script, please change all “********” to “ 1” in ala5.mdcrd1.XXX Script in /users/jzhen/amoebapro/remd-wt6/analyze/extrac298Ktraj Cmd: ptraj ../ala5.prmtop extrac298Ktraj
- J-coupling Calculation
/users/jzhen/amoebapro/remd-wt6/analyze/
1. Extract phi psi angles for each residue: ptraj ../ala5.prmtop trajin1-5
2. covert the format of phi-psi torsion files to j-coupling calculation format ./get_phi_psi.sh
3. Get J-coupling values by running jcalc_amber_v3.py
usage: /jcalc.py XXX outp_root karplus_key
the input files with torsion angles should be named XXX2,XXX3...XXX6; Corresponding to residues 1 to 5. The naming comes from using blocked peptides, which we started out with. Each line of these files contains only phi and psi (no time). For the terminal residues the undefined torsion can be set to zero. outp_root is a root for naming the output and karplus key is one of {orig,dft1,dft2} as defined in the paper
- Fraction of Helix Calculation
Example System: (AAQAA)5 peptide in water /home/yues/amoebapro/helix/15/aaqaa-wt5-newwat
1. Tremd.sh is used to extract trajectory for each temperature
2. dihedral.sh is used to calculated phi psi angles for each trajectory
3. fraction.pl is used to calculate the helix fraction
4. helix_anl_garcia.py is Robert Best’s helical fraction script.