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
>
>
>
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 09 2018 - 12:00:02 PST
