Hello All,
I have done one MD similation for 1 ns for my protein, having two ligands and
one metal ion with GROMOS96 43a1 force field and dodecahedron box as tge unit
cell.
After simulation when i checked RMSD, it is increasing till 1ns and observing
the .gro file in VMD, I have seen that, my protein structre is very much
distorted, intialy it had tim barell topolgy with 8 beeta sheets and 8 alpha
sheets,,now only 7 sheets are remaing,one became coiled strucutre. What could b
the possible reason ?
Thanks in advance.
--
Sonali Dhindwal
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