Re: [AMBER] Problems with RMSD of different proteins.

From: Daniel Roe <>
Date: Wed, 1 Dec 2021 08:26:17 -0500


On Sun, Nov 28, 2021 at 10:47 AM Seibold, Steve Allan <> wrote:
> > trajin HADHR_amber.pdb
> Reading 'HADHR_amber.pdb' as PDB
> Error: PDB HADHR_amber.pdb: No frames read. atom=5265 expected 10544.
> Error: Could not set up 'HADHR_amber.pdb' for reading.
> Error: Could not set up input trajectory 'HADHR_amber.pdb'.

When you load a trajectory into cpptraj, if you don't specify a
topology it will by default try to use the first topology. In this
case your topology (HADHR.prmtop) has more atoms (10544) than the
structure you are loading (HADHR_amber.pdb); I'm guessing this is
because the topology has solvent and the structure does not. You could
just try using the PDBs themselves as topology files:

parm HADHR_amber.pdb
trajin HADHR_amber.pdb
parm HADHN_amber.pdb
reference HADHN_amber.pdb parm HADHN_amber.pdb

You may find the following tutorials useful for understanding how
cpptraj uses topology/trajectory info: and See also
here for useful cpptraj info:

Hope this helps,


> I must be doing something incorrect.
> Thanks for your help...
> Steve
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Wed Dec 01 2021 - 05:30:02 PST
Custom Search