[AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory

From: bharat lakhani <lakhbharat.gmail.com>
Date: Wed, 24 Jun 2015 13:56:18 -0400

I am trying to calculate residue wise backbone rmsd between two proteins
and their respective trajectory that shares 80% percent sequence identity
and about 3A overall rmsd. The scipts does not seems to work for residues
wise rmsd although I am able to get overall rmsd for the structures.

parm StructureA.prmtop
trajin StructureA.pdb parmindex 0

parm StructureB.prmtop
trajin StructureA.pdb parmindex 1

strip !.CA,C,O,N

reference StructureB.pdb parmindex 1

rms reference :1-99.N,CA,C,O :1-99.N,CA,O perresavg perresavg.dat

Also when i use this following line

rms reference :1-99.N,CA,C,O :1-99.N,CA,O out perresavg.dat

I get this error which does not make sense to me since both proteins
contains same number of residues but different residues since they are
homologous (80% sequence similarity 3A overall rmsd)

     Mask [:1-99.N,CA,C,O] corresponds to 396 atoms.
Warning: Number of atoms in target mask (396) does not
         equal number of atoms in Ref mask (297).
Warning: Setup failed for [rms reference :1-99.N,CA,C,O :1-99.N,CA,O out
perresavg.dat]: Skipping

Bharat Lakhani
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Received on Wed Jun 24 2015 - 11:00:02 PDT
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