You need to load the average in as a reference, then use the "rms" command.
However, you need to use the "rms" command before you generate the average
structure, also.
trajin trajectory.mdcrd
rms first mass
average avg.pdb pdb
Then use that pdb as a reference:
trajin trajectory.mdcrd
reference avg.pdb
rms reference mass
atomicfluct _________ (I forget the exact usage).
Good luck!
Jason
On Mon, Jun 28, 2010 at 2:50 AM, REENU KHATTRI <ibi2008024.iiita.ac.in>wrote:
> hello sir i am calculating rmsd residue wise but result is not good i want
> to first align or superimpose the protein with average pdb and use this
> trajout file to perresidue wise calculation is any command to align a
> protein.
> RINU KHATTRI
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Jun 28 2010 - 05:00:04 PDT
