ptraj

# ptraj example

trajin eq_density.rst                       coordinates file to read
trajout reimaged.rst restart          output file in the same format as the input
center :1                                                    center the box to the geometric center of residue 1
image center                                                    force all the molecules into the primary unit cell

#Run ptraj according this syntax:
ptraj dna_solv.top < test.ptraj



trajin md2.mdcrd 1 19000 5 [start stop offset]
strip :WAT,Na+                      #take care with blank spaces
center :1-20 mass origin 
image origin center familiar 
trajout output.pdb pdb append 

If you use cpptraj you can omit the 'append' keyword from the
'trajout' command since MODEL/ENDMDL keywords are added automatically
for multiple frame PDB output files.

trajin eq_density.rst
trajout reimaged.rst restart
center :1-12
image center

trajin cie_solv_md3.mdcrd
trajin cie_solv_md4.mdcrd
center :1-25 mass origin 
image origin center familiar 
trajout output.cdf netcdf

9.1 ptraj coordinate input/output commands

trajin filename [ start stop offset] [remdtraj remdtrajtemp reptemp] 

reference filename

trajout filename [ format ] [ nobox ] [ nowrap ] [ append ] [ remdtraj ] [ lessplitjaverage ] [ little j big ] \

[ dumpqj parse ] [ title title ] [ application application ] [ program program ]

filename [ format ]: Specify the name of a file for output coordinates (filename) written

in a specific format (format). Currently supported formats are:

• trajectory – Amber ascii trajectory, the default

• restart – Amber restart

• binpos – Scripps binary format

• pdb – PDB, the traditional format (not the newer CIF files); if molecule information is present, TER cards will be written between molecules.

• cdf | netcdf – Amber NetCDF binary trajectory

• charmm – CHARMM DCD binary trajectory

Note that the allowable formats include both trajectory files (i.e., a series of frames) and

files that traditionally include only a single coordinate set. In this latter case, the filename

will be appended with .N where N is the frame number (unless the optional keyword

append is specified).