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
