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,
>
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>
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> I am trying to calculate rmsd between my trajectory and a pdb file.
>
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> Here is what I have done:
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> parm parm1.prmtop
> trajin all.nc
> parm parm2.prmtop [ref2parm]
> reference ref.pdb parm [ref2parm] [ref2]
> rms ref [ref2] out test.dat
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>
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> I have stripped all the atoms from trajectories and pdb (and associated
> prmtops) so that there is an equal number of atoms.
>
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> For a sanity check, I got a few frames from the trajectory and compared
> the
> rmsd using Chimera.
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> 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.
>
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> Any idea as to what am I doing wrong?
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> Thank you very much
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> L.
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Received on Fri Sep 20 2019 - 23:00:01 PDT
