Trajectory Analysis

1.Pre-processing the Trajectory

1.1.Combine the the trajectory files

gmx trjcat -f step7_1.trr step7_2.trr step7_3.trr step7_4.trr step7_5.trr step7_6.trr step7_7.trr step7_8.trr step7_9.trr step7_10 -o step_prod_10.xtc

1.2 Compress the the trajectory and save 1 frame out of every 100 frames.

gmx trjconv -f step_prod_10.xtc -n index_full.ndx -skip 100 -o step10_skip.xtc

1.3 Least square fit by alpha carbon fit trans+rot

 gmx trjconv -f step10_skip.xtc -s step7_1.tpr -fit rot+trans -n index_full.ndx  -o step10_fit.xtc

1.4 Combine energy trajectory

gmx eneconv ­-f step7_1.edr step7_2.edr step7_3.edr step7_4.edr step7_5.edr step7_6.edr step7_7.edr step7_8.edr step7_9.edr  step7_10.edr -o step7_1_9.edr

2.Analyse the rmsd ligand and gpcr

2.1 Make index for ligand (resid 1-66) and gpcr (resid 67-362)

gmx make_ndx -f step7_1.gro -o index_aC.ndx
r 1-66
name ligand
r 67-362
name gpcr

2.2 Analyse the rmsd of ligand (resid 1-66) and gpcr (resid 67-362) in the trjcectory

 gmx rms -f step10_fit.xtc -s step7_1.tpr -n index_aC.ndx -o rms400ns_cxcr1.xvg 
 gmx rms -f step10_fit.xtc -s step7_1.tpr -n index_aC.ndx -o rms400ns_ligand.xvg 
 gmx rms -f step10_fit.xtc -s step7_1.tpr -n index_aC.ndx -o rms400ns_relative.xvg 

sed '1,17d'  rms400ns_cxcr1.xvg  > rms400ns_cxcr1.dat 
sed '1,17d'  rms400ns_ligand.xvg  > rms400ns_ligand.dat 
sed '1,17d'  rms400ns_relative.xvg  > rms400ns_relative.dat 
python rmsd.py

rmsd_400ns.png

2.3 The relative distance from ligand to GPCR

distance_400ns.png

2.4 the relative coordinate of ligand relative to the cxcr1

Traj 428

ligandpos.png

Traj 422

ligandpos.png

Traj414

ligandpos.png

Traj331

ligandpos.png

3 Stable salt bridge found from trajectories.

Traj	Saltbr	Intensity	Saltbr	Intensity	Saltbr	Intensity
Traj 428	ASP331-LYS3	0.604	GLU4-ARG323	0.816	GLU70-ARG47	0.684
Traj 422	ASP331-LYS3	0.303	GLU4-ARG323	0.604	GLU70-ARG47	0.184
Traj 414	ASP331-LYS3	0.006	GLU4-ARG323	0.000	GLU70-ARG47	0.716
Traj 331	ASP331-LYS3	0.401	GLU4-ARG323	0.170	GLU70-ARG47	0.000

Traj	Saltbr	Intensity	Saltbr	Intensity	Saltbr	Intensity
Traj 428	ASP331-LYS3	0.604	GLU4-ARG323	0.816	GLU70-ARG47	0.684
Traj 422	ASP331-LYS3	0.303	GLU4-ARG323	0.604	GLU70-ARG47	0.184
Traj 414	ASP331-LYS3	0.006	GLU4-ARG323	0.000	GLU70-ARG47	0.716
Traj 331	ASP331-LYS3	0.401	GLU4-ARG323	0.170	GLU70-ARG47	0.000

ASP331-LYS3.png

GLU4-ARG323.png

GLU70-ARG47.png