Dear Dan,
I have sent you an email with Dropbox link with all the files and the
originals. I stripped all atoms but CA,C and N.
I only sent every 100th frame from the original trajectory due to its size
(so there will be mismatch in number of frames).
Thank you for your help.
L.
---------- Původní e-mail ----------
Od: Daniel Roe <daniel.r.roe.gmail.com>
Komu: AMBER Mailing List <amber.ambermd.org>
Datum: 23. 9. 2019 14:17:31
Předmět: Re: [AMBER] cpptraj rms with different pdb
"Hi,
On Fri, Sep 20, 2019 at 3:25 PM Lenka <Vellryba.seznam.cz> wrote:
> I have stripped all the atoms from trajectories and pdb (and associated
> prmtops) so that there is an equal number of atoms.
>
> For a sanity check, I got a few frames from the trajectory and compared
the
> rmsd using Chimera.
>
> My issues is, that amber calculates the rmsd to be around 7 and Chimera
> around 1. Since the structures are very similar, Chimera is right.
As mentioned previously, given the same input and reference
structures, cpptraj and chimera should return a best-fit RMSD within
numerical precision.
There are a few places your calculation could have gone awry - most
notably with exactly what atoms you stripped from each structure (you
don't say exactly what you did so no way to check if it's ok or not).
In order for the RMSD calculation to work properly, not only the
number of atoms needs to match but the atom ordering as well. Could
you send me those files as well? Preferably the originals too if you
have them. Also any other relevant information (like what atoms were
stripped). Thanks,
-Dan
>
>
> Any idea as to what am I doing wrong?
>
>
>
>
>
> Thank you very much
>
>
>
>
>
> L.
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Received on Mon Sep 23 2019 - 08:00:02 PDT
