Dear Amber users !
Dealing with short md simulation of a very flexible water soluble
protein, I removes pbc using the following protocol:
# center on the alpha helix located in the middle of protein
center :125-145 mass origin"
"image origin center"
"autoimage"
and then calculate rmsf using
"rms protToFirst .CA,C,O,N,H&!(:WAT|:lig) first out rmsf.xvg mass time 0.05"
>From this graph I see that the protein in some parts tends to be very
flexible (up to 0.9 A) even during 10 ns of the modeling. May the
protocol responsible for the first part (pbc) affect the calculation
of the rmsf profile ?
Many thanks in advance
Cheers
Enrico
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Received on Thu Jul 06 2023 - 09:00:02 PDT
