In the rmsf you fit the entire protein. In the rmsd you fit only the
residue 50. To compare, you should use the same fitting mask.
On May 21, 2013 5:36 AM, <nguyentb.bii.a-star.edu.sg> wrote:
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 21 2013 - 04:30:02 PDT
