Hello Amber Users,
I am following the Tutorial B1 on the amber website to run simulations in
vacuum, generalized born and explicit water for my protein molecule.
While running the simulations in explicit water the tutorial has calculated
the RMSD for the backbone of the DNA molecule.
I tried calculating the RMSD values in explicit water for the whole protein
molecule I am working on and I got RMSD values >50 which doesn't seem
right.
Does the tutorial work only for the backbone of a molecule? If so then how
do I determine the backbone atoms of my protein? and is there a way I can
calculate the RMSD value for the whole protein?
My input file reads:
trajin pdb_wat_md1.mdcrd
trajin pdb_wat_md2.mdcrd
rms first out pdb_wat.rms time 0.2
-
Thank You and Regards,
Aishani Chittoor Prem
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Received on Tue Sep 22 2015 - 14:00:04 PDT
