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