Jim Caldwell has created a simple example of how ptraj is often used. You will need the following files (shift-click or right-click in your browser):
The command you would run is just this:
ptraj prmtop < ptraj.in > ptraj.out
Here is the input file, with comments describing what everything does. It only covers some of the capabilities of ptraj, but it should be enough to get you started.
# system: 7mer peptide in a box of # periodic water (1577 Waters) # Read in the trajectory file # starting at 1 # 100 total snapshots # consider each one # trajin trj.5 1 100 1 # first calculate some things that don't depend on # the position of the solute in the box # do dihedral angles dihedral phi_1 :1@C :2@N :2@CA :2@C out phi_1 dihedral psi_1 :1@N :1@CA :1@C :2@N out psi_1 dihedral omega_1 :1@CA :1@C :2@N :2@CA out omega_1 dihedral phi_2 :2@C :3@N :3@CA :3@C out phi_2 dihedral psi_2 :2@N :2@CA :2@C :3@N out psi_2 dihedral omega_2 :2@CA :2@C :3@N :3@CA out omega_2 dihedral phi_3 :3@C :4@N :4@CA :4@C out phi_3 dihedral psi_3 :3@N :3@CA :3@C :4@N out psi_3 dihedral omega_3 :3@CA :3@C :4@N :4@CA out omega_3 dihedral phi_4 :4@C :5@N :5@CA :5@C out phi_4 dihedral psi_4 :4@N :4@CA :4@C :5@N out psi_4 dihedral omega_4 :4@CA :4@C :5@N :5@CA out omega_4 dihedral phi_5 :5@C :6@N :6@CA :6@C out phi_5 dihedral psi_5 :5@N :5@CA :5@C :6@N out psi_5 dihedral omega_5 :5@CA :5@C :6@N :6@CA out omega_5 dihedral phi_6 :6@C :7@N :7@CA :7@C out phi_6 dihedral psi_6 :6@N :6@CA :6@C :7@N out psi_6 dihedral omega_6 :6@CA :6@C :7@N :7@CA out omega_6 # calculate the distance between two atoms # over the 10 snapshots # output to the file "dist.list" distance end_to_end :1@N :7@N out dist_end_to_end.list ##calculate an "average" structure for the 10 ## snapshots and output to file "avgb4.pdb" average avgb4.pdb pdb #get the rms values for the whole system #referenced to the first snapshot rms first :1-1584 #now deal with drift # the peptide (residues 1->7) has drifted around # the box during MD. We'd like to view the system # with a "constant" solute. # note that this changes the coordinates you have in memory # first center the solute by itself center origin :1-7 # now image the whole system about the centered origin image origin center # now calculate a pseudo occupancy for the Waters about # the solute # in this case 9*3.0 = boxx # 13*3.0 = boxy # 9*3.0 = boxz # where the integer is the number of bins and the real # is the size of the bin (in Angstroms). # # max is the "minimum" occupancy "time" the site # must be occupied to be output to grid.list # (which is pseudo PDB file in the "new" reference frame) grid grid.list 9 3.0 13 3.0 9 3.0 :WAT max 0.8 # get an average pdbfile from the "new" reference # frame to use to with grid.lis from the last step # to display average avg.pdb pdb # save the final "new" snapshot as a PDB file # for alternate veiwing trajout test.pdb PDB # now do some H-Bond analysis # specify the electron pair DONOR # donor mask :1-7@O # specify the ACCEPTOR(s) acceptor WAT O H1 acceptor WAT O H2 # do the Hbond search/output hbond solventacceptor O H1 solventacceptor O H2 solventneighbor 2 series hbond # calculate the waters in the first and second solvation shells # (0-3.5A and 3.5-5.0A) and output to watershell.list watershell :1-7 watershell.list # save only the peptide for easy graphics viewing strip :WAT trajout trj.peptide nobox |
You can compare your outputs to those in the list below. This should only be necessary if you think the program did not work. Otherwise, the outputs should mostly be self-explanatory.