AMBER Archive (2009)

Subject: Re: Re: [AMBER] the different RMSD?

From: Thomas Cheatham (
Date: Sat Nov 14 2009 - 10:25:43 CST

> trajin nptm501.dcd 1 1000 20
> trajout 10ns.dcd
> reference m_in.pdb
> rms reference out rms.dat ":1-104_at_C,CA,N" time 40

Is there a 1-1 mapping in the names between m_in.pdb and your prmtop/
generated PDB's, or in other words does atom 100 in m_in.pdb correspond to
atom 100 in the prmtop? Often the atom ordering in the input PDB
(presumably from experiment or another program) is not preserved when you
build the topology/coordinates. Try using your topology/coordinates to
build a corresponding PDB with the expected atom ordering.

Alternatively, try:

rms first out rms.dat ":1-104_at_C,CA,N" time 40


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