CPPTRAJ one-liners – AMBER-hub

Detailed description for most of these examples is available in the Running CPPTRAJ page.

Create a PDB file from a topology and a coordinate file.	`cpptraj -p topology-file.prmtop -y coordinate-file.coords -x output-file.pdb`
Review how many frames are in a trajectory file	`cpptraj -p topology-file.prmtop -y coordinate-file.coords -tl`
To read a file that contains CPPTRAJ commands	`cpptraj -i INPUTFILE`
To inspect residue number one from a topology. This also works for atoms using @1 instead of :1	`cpptraj -p topology-file.prmtop --mask :1`
To extract the charge from a residue.	`cpptraj -p topology-file.prmtop --charge :1`
Do RMSD analysis of the first molecule (which presumably is chain A) use the `^` operator. Then do RMSD of chain B (molecule 2) but still using the previous fit (to molecule 1) you would add the `nofit` keyword	rms R0 first ^1&@C,CA,N out rms.R0.dat rms R1 first ^2&@C,CA,N nofit out rms.R1.dat
To view more information (#Res, Name, First atom, Last atom, number of atoms, #Orig and #Mol) for residues one through ten.	`cpptraj -p topology-file.prmtop --resmask :1-10`
To extract a single frame from a trajectory file, use the `-ya` keyword to send arguments to `trajin`	`cpptraj -p topology-file.prmtop -y trajectory-file.nc -ya 'lastframe' -x output-file.pdb`
Quickly print the residues that are in a topology file	`cpptraj -p topology-file.prmtop --resmask \*` This will print all the residues in the topology file `cpptraj -p topology-file.prmtop --resmask :100` This will print information about residue ID 100
Run a loop inside CPPTRAJ – Example 1	parm A.prmtop for FRAME in 1,78,100,101,170 trajin A.nc $FRAME $FRAME done
Run a loop inside CPPTRAJ – Example 2	parm structure.psf for i=1;i<2;i++ trajin prod$i/output.xtc 1 250 1 strip :SOD,CLA,TIP3,TIP,POPC autoimage rms first F$i @CA dataset F$i legend Rep$i distance A$i :1088@CA :1370@CA distance B$i :1116@CA :1157@CA distance C$i :1162@CA :1189@CA distance D$i :1268@CA :1306@CA distance E$i :1330@CA :1350@CA # Execute trajectory processing to actually calculate the distances go # Calculate a parameter from the distances A100.$i = -14.43 (A$i)-7.62(B$i)+9.11(C$i)-6.32* \(D$i)-5.22(E$i)+278.88 clear trajin done writedata test.dat A100.