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.
http://archive.ambermd.org/201909/0335.html
On Sun, Nov 28, 2021 at 10:47 AM Seibold, Steve Allan <stevesei.ku.edu>
wrote:
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Nov 29 2021 - 08:30:02 PST
