Re: RMSD calculation

From: Bill Ross <>
Date: Tue 15 May 2001 14:49:39 -0700 (PDT)

        I have the AMBER6 trajectory file for 15 residues peptide in water
        after MD run. There is correspondent parm file for this system.
        I wanted to calculate the RMSD for all structures collected in the
        trajectory file with a fragment of the peptide structure (9 residues)
        with different parm file. How to do it in CARNAL or any other
        analysis program compatible to AMBER6?
I think the only way would be to map the structure with the 9
residues to an artificial coordinate file matching the 15-residue
prmtop. E.g. you could write a small program to pad the coordinates
with 0's for the other 6 residues (and maybe waters), or using a pdb
of the reference 9 residues, you could create the other 6 residues in
leap (matching the sequence in the trajectory version):

> x = sequence ( NALA ALA ALA ALA ALA ALA )
> savepdb x init.pdb

then join the 2 pdb files and

> x = loadpdb joined.pdb
> saveamberparm x ref.prm ref.crd

Then strip the waters from your trajectory and use ref.prm to
handle the trajectory using ref.crd as the coordinate ref for the
9 residues.

Bill Ross
Received on Tue May 15 2001 - 14:49:39 PDT
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