Hi,
Thank you for your help.
I have sent you a dropbox link with the files.
Thanks again for helping.
L.
---------- Původní e-mail ----------
Od: Elvis Martis <elvis_bcp.elvismartis.in>
Komu: AMBER Mailing List <amber.ambermd.org>
Datum: 22. 9. 2019 5:37:24
Předmět: Re: [AMBER] cpptraj rms with different pdb
"Hi,
Is it possible to send the files off the list? I would like to reproduce
what you tried so I can know what must be happening?
Best Regards
On Sat, 21 Sep 2019 at 18:35, Lenka <Vellryba.seznam.cz> wrote:
> Hi, yes they are. I am not using trajectory in Chimera, just the reference
> structure and few frames extracted from the trajectory.
> ---------- Původní e-mail ----------
> Od: Elvis Martis <elvis_bcp.elvismartis.in>
> Komu: AMBER Mailing List <amber.ambermd.org>
> Datum: 21. 9. 2019 6:34:44
> Předmět: Re: [AMBER] cpptraj rms with different pdb
> "Hello
> Are the reference structures to compute rmsd same for cpptraj and chimera?
> To the best of my knowledge, chimera takes the first frame as a reference.
>
> Best Regards
>
>
>
> On Sat, 21 Sep 2019 at 00:57, Lenka <Vellryba.seznam.cz> wrote:
>
> >
> > Hi,
> >
> >
> >
> >
> >
> > I am trying to calculate rmsd between my trajectory and a pdb file.
> >
> >
> > Here is what I have done:
> >
> >
> >
> >
> >
> > parm parm1.prmtop
> > trajin all.nc
> > parm parm2.prmtop [ref2parm]
> > reference ref.pdb parm [ref2parm] [ref2]
> > rms ref [ref2] out test.dat
> >
> >
> >
> >
> > 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.
> >
> >
> > Any idea as to what am I doing wrong?
> >
> >
> >
> >
> >
> > Thank you very much
> >
> >
> >
> >
> >
> > L.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Sun Sep 22 2019 - 05:30:04 PDT
