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
