[AMBER] rms to pdb for a subset of atoms [cpptraj]

From: Eiros Zamora, Juan <j.eiros-zamora14.imperial.ac.uk>
Date: Thu, 19 May 2016 13:55:25 +0000

Dear Amberists,

I’d like to calculate the per-frame rms deviation of my trajectories to a pdb structure that only has a subset of the atoms present in the trajectories (the trajectories have some residues that were added on top of the pdb).

I generated a pair of .prmtop and .inpcrd files of the incomplete pdb structure to load them as a ‘reference’ in cpptraj.

Now I’d like to calculate the rms of the backbone atoms of the regions that are present both in the trajectories and in the pdb, but I’m failing to achieve that. Is there anyway to specify cpptraj to do so?

I’m using the following commands:
> parm trajs_top.prmtop [traj_top] # Topology matching the trajectories
> parm ../refpdb.prmtop [pdb_top] # Topology matching the reference
> reference ../refpdb.inpcrd parm [pdb_top] [pdb_ref] # The reference coordinates
> trajin traj1/05_*.nc parm [traj_top]
> rms .CA,C,O,N,H out rms.dat mass ref [pdb_ref]
> run

But I get the following error:
> ACTION SETUP FOR PARM 'trajs_top.prmtop' (1 actions):
> 0: [rms .CA,C,O,N,H out rms.dat mass ref [pdb_ref]]
> Target mask: [.CA,C,O,N,H](2083)
> Reference mask: [.CA,C,O,N,H](1729)
> Warning: Number of atoms in target mask (2083) does not equal
> Warning: number of atoms in reference mask (1729).
> Warning: Setup incomplete for [rms]: Skipping

Because it’s trying to match all the backbone atoms in the trajectories (2083 atoms) to the pdb file (1729 atoms).

Any idea on how to tell cpptraj to ignore the regions that are not present in the reference structure?

Thanks for any suggestions,

AMBER mailing list
Received on Thu May 19 2016 - 07:00:04 PDT
Custom Search