[gmx-users] MD analysis

[Anu Chandran]

Dear all,

I have carried out simulations of two homologous proteins (~38kDA) using
Gromacs v4.5.3 using OPLS force field. The protein consists of three
domains. Structural studies using cystallography reported earlier showed
that the two proteins differ in the extent of orientations one domain can
take with respect to other. However the reason for  this difference is not
clear from the structure as the size of the domain and region connecting
them is almost the same in both. The only difference between the two are 32
residues spread over the sequence. Can anybody please suggest me as to how
to go about with the MD analysis to find out the reason for this difference
in the two structures ?

Visualization of the structures extracted from the trajectory showed the
domain to be flexible in two proteins but to different extents.


Thanking You,

 regards

Anu