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You've made it this far, with trajectories proudly in hand! Time to analyze the data.

Analysis

Below needs updating as of 6/2023

We use several different techniques in analyzing our trajectories. Some methods will be more relevant than others for certain projects, but generally you will want to begin with RMSD.

RMSD
Backup
Average Hydrogen Bonds
Stacking
VMD
Pymol

Useful Residue Numbering

Organism/Chain	Organism Identifier	Yeast Identifier	N1 Residue Number	N2 Residue Number
E. coli 16S	C1054	C1274	105	94
E. coli 16S	A1196	A1427	114	127
S. cerevisiae rps3	R146	R146	368	240
tRNA (A-site wobble, G)	nt 34	nt 34	167	408
tRNA (A-site nt2, G)	nt 35	nt 35	168	409
tRNA (A-site nt1, G)	nt 36	nt 36	169	410
mRNA (A-site nt1, C)	NA	NA	175	423
mRNA (A-site nt2, C)	NA	NA	176	424
mRNA (A-site wobble, U)	NA	NA	177	425
mRNA (+1 nt1, G)	NA	NA	178	426
mRNA (+1 nt2, C)	NA	NA	179	427
mRNA (+1 nt3, U)	NA	NA	180	428

To convert an .rst to a .pdb (example at /mindstore/home33ext/kscopino/BIN/make_pdb_to_rst.in):

   # path to prmtop
   parm /mindstore/home33ext/kscopino/HELMHOLTZ/5JUP_GC/179_WT/TLEAP/5JUP_GC_179C_wat.prmtop

   # rst file to convert
   trajin /mindstore/home33ext/kscopino/HELMHOLTZ/5JUP_GC/179_WT/TLEAP/5JUP_GC_179C_wat.rst

   # strip solvent and ions
   autoimage
   strip :WAT
   strip :Na+
   strip :Cl-

   # write output
   trajout /mindstore/home33ext/kscopino/mR146/5JUP/COD1_C2/TLEAP/5JUP_GC_179C_nowat.pdb pdb