[AMBER] Question about RMSD in AMBER

From: Yingjie Lin <linyj1984.gmail.com>
Date: Tue, 27 Apr 2010 20:42:55 -0400

Dear all,

I've run 30ns simulation of a protein-ligand complex.
The protein has 289 residues, and the 290th "residue" corresponds to the ligand.

I am interested in checking how the ligand move in the simulation.
To be more specific, I would like to calculate RMSD of the ligand with respect to the ligand in another file (named fileA.pdb).

My script looks like this:
trajin ../EQ/complex.1.trj.gz 1 1000 25
trajin ../EQ/complex.2.trj.gz 1 1000 25

center origin :1-290
image origin center

rms first mass out complex_rmsf_ca.dat .CA

strip :291-119999999

reference fileA.pdb :1-290
rms reference mass out ligand_rmsf.dat :290
I am not sure about the last two lines. Since I want to "align the protein and then calculate RMSD for the ligand",
which of the following should I use?
        'reference fileA.pdb :1-290'
   or 'reference fileA.pdb :1-289'
   or 'reference fileA.pdb :290'

Thanks a lot!

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Received on Tue Apr 27 2010 - 18:00:03 PDT
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