On 31/03/2010 5:48 PM, sonali dhindwal wrote:
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 ?
There are many possible reasons, chief among them an inappropriate model
physics. With no idea what your metal ion is, how you've built your
topology and what ensemble you've used, we can't have any better ideas
for you. :-)
Mark
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