-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathCOMMANDS.rtf
executable file
·78 lines (55 loc) · 2.71 KB
/
COMMANDS.rtf
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
COMMANDS
gmx editconf -f 4bvn_edited_TM1.pdb -o TM1_parallel.pdb -princ -rotate 0 0 90
gmx editconf -f TM1_parallel.pdb -o TM1_1.gro -center 2 4 4
gmx editconf -f TM1_parallel.pdb -o TM1_2.gro -center 6 4 4
cat TM1_1.gro TM1_2.gro > TM1_aligned.gro
Opened TM1_aligned.gro
Removed the section between the two proteins and doubled the number of atoms at the top
gmx editconf -f TM1_aligned.gro -o TM1_aligned_rotated_1.gro -rotate 0 0 90
gmx editconf -f TM1_aligned_rotated_1.gro -o TM1_aligned_rotated_2.gro -rotate 0 90 0
martini and the elastic network:
python2.7 martinize.py -f TM1TM1_rotated_2.gro -o TM1TM1.top -x TM1TM1_CG.pdb -dssp /Applications/xssp-3.0.10/mkdssp -p backbone -ff martini22 -elastic -ef 500 -el 0.5 -eu 0.9 -ea 0 -ep 0
OR
no constraints:
python2.7 martinize.py -f TM1_aligned.gro -o TM1.top -x TM1_CG.pdb -dssp /Applications/xssp-3.0.10/mkdssp -p backbone -ff martini22
gmx grompp -f minim-vacuum.mdp -c TM1_CG.pdb -p TM1.top -o minim-vacuum.tpr
gmx mdrun -deffnm minim-vacuum -v
python2.7 insane.py -f TM1_CG.pdb -o TM1_CG_system.gro -p system.top -pbc square -box 8,8,8 -l DPPC -u DPPC -center -sol W
edit system.top =
#include "martini.itp"
#include "Protein_A.itp"
#include "martini_v2.0_DPPC_01.itp"
#include "martini_v2.0_ions.itp"
[ system ]
; name
Protein in INSANE! Membrane UpperLeaflet>DPPC=1 LowerLeaflet>DPPC=1
[ molecules ]
; name number
Protein_A 1
Protein_A 1
DPPC 71
DPPC 63
W 2141
gmx grompp -f ions.mdp -c TM1_CG_system.gro -p system.top -o TM1_CG_system_ions.tpr
gmx genion -s TM1_CG_system_ions.tpr -o TM1_CG_system_ions.gro -p system.top -pname NA -nname CL -neutral yes
gmx grompp -f minim.mdp -c TM1_CG_system_ions.gro -p system.top -o TM1_em.tpr
gmx mdrun -v -deffnm TM1_em
Steepest Descents converged to machine precision in 28770 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -1.0829706e+05
Maximum force = 1.5905204e+01 on atom 79
Norm of force = 1.0778955e+00
gmx make_ndx -f TM1_CG_system_ions.gro -o index.ndx
gmx grompp -f nvt.mdp -c TM1_em.gro -r TM1_em.gro -p system.top -n index.ndx -o TM1_nvt.tpr
gmx mdrun -v -deffnm TM1_nvt
Core t (s) Wall t (s) (%)
Time: 4819.203 1204.801 400.0
(ns/day) (hour/ns)
Performance: 7.171 3.347
gmx grompp -f npt.mdp -c TM1_nvt.gro -r TM1_nvt.gro -t TM1_nvt.cpt -p system.top -n index.ndx -o TM1_npt.tpr
gmx mdrun -deffnm TM1_npt
Core t (s) Wall t (s) (%)
Time: 5139.730 1284.932 400.0
(ns/day) (hour/ns)
Performance: 67.242 0.357
gmx grompp -f md.mdp -c TM1_npt.gro -t TM1_npt.cpt -p system.top -n index.ndx -o TM1_md.tpr