Table 2. Results of simulations starting from different intermediate state of Trp-cage.
| S. No | Starting RMSDCα (Å) | Final RMSDCα (Å) | Final state | |||
| ff03 | ff99SB | ff99SB_ILDN | ff99SB_NMR | |||
| Set1 | ||||||
| 1 | 2.8 | 0.9 | 1.0 | 0.8 | 0.9 | Folded |
| 2 | 3.1 | 0.8 | 1.0 | 0.9 | 0.8 | Folded |
| 3 | 1.8 | 0.8 | 0.9 | 1.0 | 0.85 | Folded |
| 4 | 3.2 | 1.0 | 1.1 | 1.2 | 1.1 | Folded |
| 5 | 2.9 | 0.9 | 0.9 | 1.0 | 0.9 | Folded |
| Set2 | ||||||
| 6 | 3.9 | 0.8 | 0.8 | 1.0 | 1.1 | Folded |
| 7 | 4.0 | 1.0 | 1.2 | 1.2 | 1.1 | Folded |
| 8 | 4.9 | 0.9 | 1.2 | 1.1 | 1.0 | Folded |
| 9 | 5.5 | 1.1 | 1.3 | 1.2 | 0.9 | Folded |
| 10 | 4.5 | 1.0 | 0.9 | 1.0 | 1.0 | Folded |
| 11 | 3.8 | 2.9 | 3.9 | 3.4 | 3.5 | Misfolded |
| 12 | 4.1 | 4.5 | 4.4 | 4.3 | 4.5 | Collapsed |
| 13 | 5.0 | 6.2(1.0) | 6.0(0.8) | 6.5(1.9) | 6(0.9) | Unfolded (folded) |
| 14 | 4.0 | 7.0 | 6.5 | 5.5 | 6(1.2) | Unfolded (folded) |
| 15 | 3.5 | 4.0 | 5.0 | 4.5 | 3.5(1.0) | Collapsed (folded) |
Values in brackets correspond to the results of simulation with restraints on the side chain dihedral angles of the Trp6 residue to keep it close to the conformation in the native folded structure (see Methods for details). Start conditions for unrestraint and restraint simulations were the same. The Trp6 residue was in its native rotameric state in all the Set1 intermediate start structures and in non-native rotameric state in all the Set2 intermediate start structures.