Simulation report
Technical information
General information
Name: Smoothened in complex with cholesterol (apoform)
PDB id: 6D35
Activation state: Inactive
Description: Classical unbiased (NVT ensemble) complex flexibility assay.
Submitted by: GPCRmd community
System setup
Solvent type: TIP3P
Membrane type: Homogeneous
Membrane composition: POPC (99.7%), CLR (0.3%)
Ionic composition: Sodium ion (156 mM), Chloride (160 mM)
Number of molecules:
Water: 42994
POPC: 365
Chloride: 124
Sodium ion: 121
Cholesterol: 1
Uncharacterized protein: 1
Total number of atoms: 186024
Simulation details
Software and version: ACEMD3, GPUGRID
Forcefield and version: CHARMM, c36 Jul 2020
Time step : 4.0 fs
Delta : 0.2 ns
Replicates: 3
Accumulated simulation time: 1.5 µs
Additonal parameters: Available at "Simulation protocol & starting files"
Simulation components
Receptor
Mutations
Table of simulated mutations
(Mutations shown in blue at the viewer)
| Residue ID | Residue seq. position | Generic num. | From | To |
|---|---|---|---|---|
| 50 | 50 | - | V | I |
| 59 | 59 | - | S | A |
| 60 | 60 | - | W | L |
| 63 | 63 | - | S | T |
| 71 | 71 | - | T | S |
| 73 | 73 | - | E | D |
| 77 | 77 | - | N | D |
| 80 | 80 | - | L | S |
| 128 | 128 | - | G | A |
| 146 | 146 | - | R | Y |
| 197 | 197 | - | K | N |
| 205 | 205 | - | V | I |
Other molecules
