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.
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> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Sep 21 2019 - 06:30:02 PDT
