Report chirality around alpha carbons in amino acids (L, D).
checkchirality [<name>] [<mask>] [out <filename>]
[<name>] Data set name.
[<mask>] Atoms to check.
[out <filename>] File to write results to.
[L] Number of frames ’L’ for each residue.
[D] Number of frames ’D’ for each resdiue.
Check the chirality around the alpha carbon in amino acid residues selected by <mask>. Note that cpptraj expects atom names to correspond to the PDB V3 standard: N, CA, C, CB. For each residue, the number of frames in which the amino acid is ’L’ or ’D’ will be recorded. For example, to check the chirality of all amino acids in a system and write to a file named chiral.dat with data set name DPDP:
checkchirality DPDP out chiral.dat Output will have format similar to: #Res DPDP[L] DPDP[D] 2.000 100 0
So in this example residue 2 was ’L’ for 100 frames and ’D’ for 0 frames.