[gmx-users] 3-10 or Pi helices are changing to Alpha over the time: 100 ns MD

[prasun kumar]

Hi Group

I have been trying to run a simulation that contains both 3-10 and alpha
helical peptides.

I am using "AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et
al., Proteins 78, 1950-58, 2010)" forcefield.....

Over the course of simulation, the 3-10 helix is changing to alpha as
suggested by do_dssp (I am using the newer version of DSSP).

Thanx in advance for the help.

Regards
Prasun
PRASUN (ASHOKA)
Desire + stability = Resolution
Resolution + Hard work = Success