[AMBER] Problems with RMSD of different proteins.

From: Seibold, Steve Allan <stevesei.ku.edu>
Date: Sun, 28 Nov 2021 15:47:10 +0000

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

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...

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Received on Sun Nov 28 2021 - 08:00:02 PST
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