Dear Amber users,
I’m still not quite familiar with using CPPTRAJ. So I tried to calculate the
overall SASA of a protein that I’ve simulated in a solvent-mixture of
acetonitrile and water with the ‘surf’ command. Strangely, at the beginning
of the trajectory, the output gave very low areas, that increased to the end
from 1125 to 14488 (in VMD, the protein doesn’t seem to unfold or change its
conformation notably). Could this be because the acetonitrile molecules
aren’t recognized as solvent (when I did the same in pure water as solvent,
the values remained quite similar)?
In my fileshare link you can get the first frame of my trajectory, its
parameter file as well as the ‘surf’ output file for the simulation in the
solvent mixture (surfACE.dat) and in pure water (surf.dat):
[1]
http://jmp.sh/b/qmIfZACyYNMwuTqsT6wJ
Thank you very much for your help!
References
1.
http://jmp.sh/b/qmIfZACyYNMwuTqsT6wJ
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Received on Thu Apr 27 2017 - 01:30:03 PDT
