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

From: Seibold, Steve Allan <>
Date: Mon, 29 Nov 2021 16:15:03 +0000

Hi Carlos
Ok..thanks again for your help...I will look into it..


-----Original Message-----
From: Carlos Simmerling <>
Sent: Monday, November 29, 2021 10:07 AM
To: AMBER Mailing List <>
Subject: Re: [AMBER] Problems with RMSD of different proteins.

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 system.
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.;;sdata=Ml5cgypvCw2XhnV3dxEffCAH0MmLBqE%2BG6pqBoHvH10%3D&amp;reserved=0

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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