[AMBER] cpptraj rms with different pdb

From: Lenka <Vellryba.seznam.cz>
Date: Fri, 20 Sep 2019 21:24:59 +0200 (CEST)


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

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Received on Fri Sep 20 2019 - 12:30:02 PDT
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