Hi,
I have two crystal structures of the same protein. The first structure 156 residues, the second 159 residues. Residue 4 in the second structure is residue 1 in the first structure. I do not need the extra 3 residues from the second structure.
I try to calculate rmsd values between the structures in cpptraj like this:
parm first.prmtop
trajin first.nc
rmsd :1-156.CA :4-159.CA out rmsd.dat reftraj second.inpcrd parm second.prmtop
go
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: first.prmtop, 54511 atoms, 17503 res, box: Trunc. Oct., 17348 mol, 17342 solvent
INPUT TRAJECTORIES (1 total):
0: 'first.nc' is a NetCDF AMBER trajectory, Parm first.prmtop (Trunc. Oct. box) (reading 20000 of 20000)
Coordinate processing will occur on 20000 frames.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'first.prmtop' (1 actions):
0: [rmsd :1-156.CA :4-159.CA out ref.dat reftraj second.inpcrd parm second.prmtop]
Target mask: [:1-156.CA](156)
Reference mask: [:4-159.CA](153)
Warning: Number of atoms in target mask (156) does not equal
Warning: number of atoms in reference mask (153).
Warning: Setup incomplete for [rmsd]: Skipping
----------
The reference does have 159 residues but somehow residues 157,158,159 are cut off before the mask is applied.
I got it working the other way around like this, but it is not what I want:
parm second.prmtop
trajin second.nc
strip :1-3
rmsd :1-159.CA :1-156.CA out ref.dat reftraj first.inpcrd parm first.prmtop
go
How can I tell cpptraj to map the residue numbers correctly?
cheers
Martin
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Received on Tue Nov 06 2018 - 07:30:01 PST
