Thanks Jason Swails and Carlos Simmerling for your reply. I got new
rmsd values, which looked reasonable.
Regards,
Binh
Quoting Jason Swails <jason.swails.gmail.com>:
> 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 - 05:30:02 PDT
