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

From: Carlos Simmerling <>
Date: Mon, 29 Nov 2021 11:07:03 -0500

it sounds like the atoms still don't match in these files. you can't set a
reference or read a trajectory using the prmtop file unless it's the same
I suggest looking at a better way to go about this in cpptraj, described a
little in this email from Dan Roe (with much more detail in the manual of
course). This should be enough to get you started.

On Sun, Nov 28, 2021 at 10:47 AM Seibold, Steve Allan <>

> Hello Amber
> Thanks Carlos for your response. I tried to address your reply by ensuring
> that the proteins are the same length. So, again, I have been attempting to
> get an RMSD of two different proteins now the same length. I have taken
> both of them and generated separate amber pdb files using "pdb4amber".
> This produced two proteins with the same numbering (i.e. 1-684) of amino
> acids. I used these to produce a prmtop and inpcrd files for each protein.
> I made sure that cpptraj could open up both pdb files using their
> respective prmtop files.
> I then attempted to generate a RMSD between the two amber generated pdb
> files using the cpptraj input:
> parm HADHR.prmtop
> trajin HADHR_amber.pdb
> reference HADHN_amber.pdb
> rmsd reference :1-684.CA,C,N,O perres perresout HR_HN_residue.dat
> perresmask :1-684.CA,C,N,O perresavg HR_HN_avg.dat
> run
> quit
> The cpptraj trajin could not read the HADHR_amber.pdb which was made using
> pdb4amber. I got the following error printout:
> Reading 'HADHR.prmtop' as Amber Topology
> Radius Set: modified Bondi radii (mbondi)
> > 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'.
> I must be doing something incorrect.
> Thanks for your help...
> Steve
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Received on Mon Nov 29 2021 - 08:30:02 PST
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