Dear Amber user,
After finishing the MD simulation, first I reimaged all the snapshot
in the trajectory:
trajin md1.mdcrd.gz
trajin md2.mdcrd.gz
trajout reimagined.mdcrd.gz
center :1-393
image familiar
go
Then, I calculated the rmsf of the whole protein with the following
ptraj file:
trajin reimagined.mdcrd.gz 1 2000 1
reference initial_solvated.inpcrd
rms reference :1-393
atomicfluct out RMSF_sidechain.dat
:1-393.CB,CG,CG1,CG2,CD1,CD2,CD,CE1,CE2,CE3,CE,CZ,CZ2,CZ3,OD1,OD2,OE1,OE2,OG,OG1,SG,SD,ND1,ND2,NE1,NE2,NE,NZ
byres
go
Then, I calculated the rmsd of a residue, that I'm interested in, for
example: residue 50, with the following ptraj file:
trajin reimagined.mdcrd.gz 1 2000 1
reference initial_solvated.inpcrd
rms reference out RMSD_50_sidechain.dat
:50.CB,CG,CG1,CG2,CD1,CD2,CD,CE1,CE2,CE3,CE,CZ,CZ2,CZ3,OD1,OD2,OE1,OE2,OG,OG1,SG,SD,ND1,ND2,NE1,NE2,NE,NZ
The rmsd of residue 50 is around 0.1, while the rmsf of residue 50
(calculated above) is 1.
It makes no sense to me. I mean, the average rmsd should be in the
same range with rmsf. Right?
Would you please tell me, which part I did is incorrect?
Thanks in advance,
Regards,
Binh
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Received on Tue May 21 2013 - 03:00:02 PDT
