Hi Amber Users,
I performed the MD simulation of 50 ns for RNA-Protein complex with iwrap =
0. But after 47.5 ns simulation got stuck. The error was: it could not
identify the co-ordinates. To run whole simulation then I used iwrap = 1.
It run for 50 ns, but when I measured RMSD values for C-alpha pf protein it
went to 14-20 A.
I am confused that when I use iwrap why I get high values of RMSD, while
the same input file to calculate RMSD gives low values of RMSD without
using iwrap (i.e. iwrap = 0). But using iwrap = 0 simulation get stuck
after 47.5 ns.
Please suggest me how to get right values of RMSD. I used 'image' command
during RMSD calculation.
Input file to calculate the RMSD values and the graph plotted is attached
with this mail. Please have a look on it
Thanks
Richa
IIIT-A
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Received on Tue Jan 19 2016 - 22:00:03 PST
