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LOGBOOK_Folders
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LOGBOOK_Folders
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LOOGBOOK of simulations
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folder protein domains gromacs FF (water) Ca2+ comments
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0 test C2-DSL 2018_plumed Martini2.1 no DLL4, PDB 5mvx
see if addition of DSL prevents unphysical binding
1 test C2 2018_plumed Martini2.1 no DLL4, PDB 5mvx
test with constraining z-movement (only bind to top of bilayer)
2 test C2 2018_plumed Martini2.1 no DLL4, PDB 5mvx
angular and moving roof restraint (plumed wall),
PG lips
3 test C2-DSL 2018_plumed Martini3 no DLL4, PDB 5mvx;
no membrane
4 test C2 2018_plumed Martini2.1 no DLL1, PDBD 4xbm
descending roof hight in plumed restraint
missing residues generated
5 test C2 2018_plumed Martini2.1 no DLL1, PDBD 4xbm
testing of -dm command in insane
6 test C2 2018_plumed Martini2.1 no DLL4, PDB 5mvx
PS (x6)
PC:PS:PE (80:15:5) (x6)
PC:PS:PG (80:15:5) (x6)
angular restraint
7 test C2 2018_plumed Martini2.1 no DLL1, PDBD 4xbm
OBS: had wrong angular restraint (wrong beads in plumed file).
PS:PS:PE (80:15:5) (x5)
angular restraint
8 PI3K C2 2018_plumed Martini2.1 no PDB 6btz; type 1
membrane with PIP2
PC (x5)
PC:PS (80:20) (x4)
PC:PS:PIP2 (80:15:5) (x6)
PC:PS:PIP2:PIP3 (80:13:5:2) (x0)
PC:PIP2 (90:10) (x6)
9 FVa C2 2018_plumed Martini2.1 no PDB 1czv; type 3
PC (x4)
PC:PS (80:20) (x4)
no PIP binding reported
10 F-spondin C2 2018_plumed Martini2.1 no PDB 2zou;
membrane with PC, PS, PIP2, PIP3
!! OBS: thought it was KIBRA (PDB 2z0u), not F-spondin (PDB 2zou)
11 RIM2 C2 2018_plumed Martini2.1 no PDB 2bwq; type 1
PC (x7)
PC:PS (80:20) (x7)
PC:PS:PIP2 (75:20:5) (x7)
PC:PS:PIP2:PIP3 (73:20:5:2) (x4) (umbrella)
Strong N-term binding via F2 and L3: maybe truncate or mutate?
F acts as a lipid and penetrates into hydrophobic lipid tail environment?
PMF testing in folder PCPSPIP2PIP3_0:
umbrella1: umbrella sampling with 0.15 nm spacing, time 500 ns
umbrella2: umbrella sampling with 0.10 nm spacing, time 500 ns
umbrella3: umbrella sampling with 0.05 nm spacing, time 500 ns
umbrella3: umbrella sampling with 0.05 nm spacing, time 1000 ns
12 KIBRA/WWC1 C2 2018_plumed Martini2.1 no PDB 6fjd; type 1
mutant C771A
MRGSHHHHHHGS not included: it is a tag, not part of UNIPROT sequence;
no missing residues (except from tag);
PC (x9)
PC:PS (80:20) (x9)
PC:PS:PIP2 (75:20:5) (x9)
PC:PS:PIP2:PIP3 (73:20:5:2) (x4)
13 MFG-E8 C2 2018_plumed Martini2.1 no PDB 2l9l; type 3
no missing residues, only HIS tag;
truncate expression tags -5 to -2
PC (x3)
PC:PS (80:20) (x9)
no PIP binding reported
14 SHIP2 C2 2018_plumed Martini2.1 no PDB 5okm; type 2
Missing res: linker from Ptase to C2 (not added), C-term PTER (added)
OBS: calculated with wrong beads in plumed file - that part needs recalculation (if needed)
PC (x5)
PC:PS (80:20) (x7)
PC:PS:PIP2 (80:15:5) (x7)
PC:PS:PIP3 (80:15:5) (x5)
PC:PS:PIP2:PIP3 (80:13:5:2) (x0)
15 SMURF2 C2 2018_plumed Martini2.1 no PDB 2jqz: type 2
PC:PIP1 (90:10) (x4)
PC:PIP2 (90:10) (x4)
PC:PIP3 (90:10) (x4)
PC (x0)
PC:PS (80:20) (x5)
PC:PS:PIP2 (80:15:5) (x3)
PC:PS:PIP2:PIP3 (80:13:5:2) (x0)
16 PTEN C2 2018_plumed Martini2.1 no PDB 1d5r; type 2
PC (x4)
PC:PIP2 (90:10) (x4)
PC:PIP3 (90:10) (x4)
PC:PS (80:20) (x8)
PC:PS:PIP2 (80:15:5) (x8)
17 FVIII C2 2018_plumed Martini2.1 no PDB 3hny; type 3
PC (x5)
PC:PS (80:20) (x5)
no PIP binding reported
18 RIM2_trunc C2 2018_plumed Martini2.1 no PDB 2bwq_t (without residue 1-3); type 1
Strong N-term binding via F2 and L3: in this simulation they have been removed
PC (x?)
PC:PS (80:20) (x3)
PC:PS:PIP2 (80:15:5) (x4)
PC:PS:PIP2:PIP3 (80:13:5:2) (x0)
19 DLL1 C2 2018_plumed Martini2.1 no PDB 4xbm; type 2
PC (x5)
PC:PS (80:20) (x7)
PC:PS:PIP2 (80:15:5) (x7)
PC:PS:PIP2:PIP3 (80:13:5:2) (x0)
20 DLL4 C2 2018_plumed Martini2.1 no PDB 5mvx; type 2
PC (x0)
PC:PS (80:20) (x7)
PC:PS:PIP2 (80:15:5) (x7)
PC:PS:PIP2:PIP3 (80:13:5:2) (x0)
21 DLL4_trunc C2 2018_plumed Martini2.1 no PDB 5mvx_t; type 2
truncated protein: removed C-terminal I148
PC (x3)
PC:PS (80:20) (x4)
PC:PS:PIP2 (80:15:5) (x4)
PC:PS:PIP2:PIP3 (80:13:5:2) (x0)
22 KIBRA_trunc C2 2018_plumed Martini2.1 no PDB 6fjd_t; type 1
truncated protein: removed C-terminal L125 (binding) and S126 (not binding)
mutant C771A
PC (x4)
PC:PS (80:20) (x4)
PC:PS:PIP2 (80:15:5) (x4)
PC:PS:PIP2:PIP3 (80:13:5:2) (x0)
23 PTEN_trunc C2 2018_plumed Martini2.1 no PDB 1d5r_t; type 2
truncated protein: removed N-terminal P1 and V2
mutant C771A
PC (x3)
PC:PS (80:20) (x4)
PC:PS:PIP2 (80:15:5) (x4)
PC:PS:PIP2:PIP3 (80:13:5:2) (x0)
24 SHIP2_trunc C2 2018_plumed Martini2.1 no PDB 5okm_t; type 2
removed 4 C-term: P131 (bind), T132 (no bind), E (no bind), R (no bind)
removed 3 N-term: Q1 (no bind), A2 (no bind), Y3 (bind)
PC (x4)
PC:PS (80:20) (x5)
PC:PS:PIP2 (80:15:5) (x5)
PC:PS:PIP2:PIP3 (80:13:5:2) (x0)
25 SHIP2_trunc2 C2 2018_plumed Martini2.1 no PDB 5okm_tt; type 2
truncated further
removed N-term: I1 (bind)
PC (x0)
PC:PS (80:20) (x0)
PC:PS:PIP2 (80:15:5) (x0)
PC:PS:PIP2:PIP3 (80:13:5:2) (x0)
26 DLL1_trunc C2 2018_plumed Martini2.1 no PDB 4xbm_t; type 2
removed S1 (minor bind), S2 (minor bind), G1 (no bind), S1 (bind)
PC (x0)
PC:PS (80:20) (x0)
PC:PS:PIP2 (80:15:5) (x0)
PC:PS:PIP2:PIP3 (80:13:5:2) (x0)
27 PI3K C2 2018_plumed Martini2.1 no PDB 6bu0; type 1
one C2 from assymmetric unit
PC (x0)
PC:PS (80:20) (x0)
PC:PS:PIP2 (80:15:5) (x0)
PC:PS:PIP2:PIP3 (80:13:5:2) (x0)
28 SHIP2 FL 2018_plumed Martini2.1 no PDB 5okm, C2 and Ptase
29 PTEN FL 2018_plumed Martini2.1 no PDB 1d5r, C2 and Ptase
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