On Tue, May 21, 2013 at 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
>
An orthogonal comment to Carlos's (which is the appropriate explanation for
why you're seeing what you're seeing):
I'm guessing that the goal is to select all heavy atoms in residues 1-393.
May I suggest the following alternative:
:1-393&!.H=,h=
This will select all atoms that satisfy the condition [atoms in residues 1
to 393 and not any atom whose name starts with H or h]. It seems a bit
more succinct (and generalizable) than the one you've chosen. You can
use "ambmask" to check that the two masks pick identical atoms.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue May 21 2013 - 05:00:03 PDT
