Thanks for the reply, Carlos. The heavy atoms do have the same order but the reference structure does not have hydrogens. The reference structure is also 2 residues shorter even though the missing residues are not included in the RMS calculation command. Could any of the two be the issue?
-----Original Message-----
From: Carlos Simmerling [mailto:carlos.simmerling.gmail.com]
Sent: Friday, February 09, 2018 2:41 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] RMSD with cpptraj
are the atoms in the same order in the pdb file as in the trajectory file?
On Fri, Feb 9, 2018 at 2:38 PM, Rui, Huan <hrui.amgen.com> wrote:
> Hi all,
>
>
>
> I'm trying to use cpptraj to compute the RMSD between my trajectory
> and a crystal structure. The script works fine, but the RMSD values
> seems incorrect. My reference is this clean_update.pdb. it has the
> same residues as the protein in my trajectory. The first rms command
> produced RMSD at around 6 Ang for all the snapshots, but when I look
> at the final structure overlay produced by my "trajout" command, the
> two structures do not look like they are 6 Ang apart. Also after the
> alignment from the first rms command, I wrote down the distance
> between two CA atoms from resid 100, the output rmsd_test2.plo show
> that they are 4 Ang apart, though in the superposed pdb files they are
> only 0.5 Ang away. Here's how my cpptraj script look like:
>
>
>
> trajin step4_1.nc 1 500 1
>
> parm clean_update.pdb
>
> reference clean_update.pdb parm clean_update.pdb
>
> autoimage :1-170
>
> rms reference :3-165.CA :3-165.CA out rmsd_test.plo
>
> rms reference :100.CA :100.CA nofit out rmsd_test2.plo
>
> trajout testrmsd.pdb onlyframes 500
>
> run
>
> quit
>
>
>
> Could anybody give me some insights on why this is?
>
>
>
> Thank you very much in advance.
>
>
>
> Thanks,
>
> Huan
>
>
>
>
>
>
>
>
>
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Received on Fri Feb 09 2018 - 12:00:03 PST
